Diff of the two buildlogs: -- --- b1/build.log 2021-08-12 12:24:16.788743992 +0000 +++ b2/build.log 2021-08-12 12:40:59.550958351 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 14 06:44:22 -12 2022 -I: pbuilder-time-stamp: 1663181062 +I: Current time: Fri Aug 13 02:24:24 +14 2021 +I: pbuilder-time-stamp: 1628771064 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 [./hisat2_2.2.1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.DZfOJDzR/trustedkeys.kbx': General error -gpgv: Signature made Wed Jan 27 05:00:17 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.RvyNlAH6/trustedkeys.kbx': General error +gpgv: Signature made Thu Jan 28 07:00:17 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hisat2_2.2.1-2.dsc @@ -36,137 +36,171 @@ dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/36409/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25847/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-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/25847/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25847/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=16' - 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=7' + 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='1ad92aa93fe4457bbe217ca6b963dc00' - 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='36409' - PS1='# ' - PS2='> ' + INVOCATION_ID=fcd54b2e2b384f8abe51f86cb2c41a1f + 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=25847 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.7qloWOFwcd/pbuilderrc_v9Jm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7qloWOFwcd/b1 --logfile b1/build.log hisat2_2.2.1-2.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://85.184.249.68:3128' + 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.7qloWOFwcd/pbuilderrc_dGuC --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7qloWOFwcd/b2 --logfile b2/build.log --extrapackages usrmerge hisat2_2.2.1-2.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://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-686-pae #1 SMP Debian 4.19.194-3 (2021-07-18) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Aug 4 2021 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 2020 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 Jul 28 2021 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 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 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 Jul 28 2021 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 Jul 28 2021 more - -rwsr-xr-x 1 root root 50720 Jul 28 2021 mount - -rwxr-xr-x 1 root root 13856 Jul 28 2021 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 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 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 Sep 13 03:48 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 Jul 28 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 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 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Jul 28 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/36409/tmp/hooks/D02_print_environment finished + total 5804 + -rwxr-xr-x 1 root root 1367848 Aug 5 10:25 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 Jul 29 09:09 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 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 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 Jul 29 09:09 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 Jul 29 09:09 more + -rwsr-xr-x 1 root root 50720 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 13856 Jul 29 09:09 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 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 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 Aug 13 02:30 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 11 21:48 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 Jul 29 09:09 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 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 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/25847/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -259,7 +293,7 @@ Get: 48 http://deb.debian.org/debian bullseye/main i386 libsimde-dev all 0.7.2-4 [259 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 pandoc-data all 2.9.2.1-1 [376 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 pandoc i386 2.9.2.1-1+b1 [19.1 MB] -Fetched 44.1 MB in 0s (92.5 MB/s) +Fetched 44.1 MB in 9s (4841 kB/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 ... 19675 files and directories currently installed.) @@ -476,8 +510,44 @@ 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 (1002 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 ... 22859 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/hisat2-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/hisat2-2.2.1/ && 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 hisat2 dpkg-buildpackage: info: source version 2.2.1-2 dpkg-buildpackage: info: source distribution unstable @@ -487,8 +557,8 @@ debian/rules clean dh clean dh_auto_clean - make -j16 clean -make[1]: Entering directory '/build/hisat2-2.2.1' + make -j7 clean +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird betreten rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \ hisat2-src.zip hisat2-bin.zip @@ -496,7 +566,7 @@ rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so -make[1]: Leaving directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird verlassen dh_clean debian/rules binary dh binary @@ -504,10 +574,10 @@ dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build -make[1]: Entering directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird betreten dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="27 January 2021" all doc - make -j16 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=27 January 2021" all doc -make[2]: Entering directory '/build/hisat2-2.2.1' + make -j7 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=27 January 2021" all doc +make[2]: Verzeichnis „/build/hisat2-2.2.1“ wird betreten /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"27 January 2021\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/build/hisat2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ @@ -552,9 +622,9 @@ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now -make[2]: Nothing to be done for 'doc'. +make[2]: Für das Ziel „doc“ ist nichts zu tun. In file included from gfm.h:43, - from hisat2_build.cpp:35: + from hisat2_repeat.cpp:36: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); @@ -562,7 +632,7 @@ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from gfm.h:43, - from hisat2_repeat.cpp:36: + from hisat2_build.cpp:35: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); @@ -578,7 +648,7 @@ | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from hisat2_build.cpp:35: +In file included from hisat2_repeat.cpp:36: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -587,11 +657,11 @@ from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from timer.h:26, - from hisat2_build.cpp:30: + from hisat2_repeat.cpp:31: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from hisat2_build.cpp:35: +In file included from hisat2_repeat.cpp:36: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -599,7 +669,7 @@ from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from timer.h:26, - from hisat2_build.cpp:30: + from hisat2_repeat.cpp:31: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -628,7 +698,7 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from hisat2_repeat.cpp:36: +In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -637,11 +707,11 @@ from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from timer.h:26, - from hisat2_repeat.cpp:31: + from hisat2_build.cpp:30: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from hisat2_repeat.cpp:36: +In file included from hisat2_build.cpp:35: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -649,7 +719,7 @@ from /usr/include/c++/10/locale:43, from /usr/include/c++/10/iomanip:43, from timer.h:26, - from hisat2_repeat.cpp:31: + from hisat2_build.cpp:30: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -703,9 +773,18 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from gfm.h:43, + from hgfm.h:24, + from hisat2_inspect.cpp:27: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 484 | this->verbose(), this->sanityCheck()); + | ^ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from ds.h:32, from sequence_io.h:28, - from hisat2_build.cpp:28: + from hisat2_repeat.cpp:29: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -717,7 +796,7 @@ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, - from hisat2_build.cpp:35: + from hisat2_repeat.cpp:36: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -727,9 +806,25 @@ multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from hisat2_inspect.cpp:25: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ +In file included from hisat2_inspect.cpp:25: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, - from hisat2_build.cpp:28: + from hisat2_repeat.cpp:29: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here @@ -745,15 +840,6 @@ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.h:43, - from hgfm.h:24, - from hisat2_inspect.cpp:27: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 484 | this->verbose(), this->sanityCheck()); - | ^ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -764,61 +850,9 @@ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ -In file included from hisat2_inspect.cpp:25: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:478:56: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ - 914 | off = OFF_MASK; - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ - 923 | OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ - 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -In file included from hisat2_build.cpp:35: -gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: -gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ -hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ -hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ -hisat2_build.cpp:801:56: required from here -gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] - 2167 | index_t template_len = 0; - | ^~~~~~~~~~~~ -In file included from hisat2_build.cpp:35: -gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: -gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ -hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ -hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ -hisat2_build.cpp:801:56: required from here -gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] - 2167 | index_t template_len = 0; - | ^~~~~~~~~~~~ -gfm.h:2342:106: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 2342 | std::numeric_limits::max(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from ds.h:32, from sequence_io.h:28, - from hisat2_repeat.cpp:29: + from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -830,7 +864,7 @@ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, - from hisat2_repeat.cpp:36: + from hisat2_build.cpp:35: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -840,17 +874,9 @@ multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from hisat2_inspect.cpp:25: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, - from hisat2_repeat.cpp:29: + from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here @@ -866,16 +892,6 @@ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:478:56: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ - 1071 | OFF_MASK, begin, end); - | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -1029,6 +1045,85 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:478:56: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ + 1071 | OFF_MASK, begin, end); + | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:478:56: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ + 914 | off = OFF_MASK; + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ + 923 | OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ + 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +In file included from hisat2_build.cpp:35: +gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: +gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ +hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ +hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ +hisat2_build.cpp:801:56: required from here +gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] + 2167 | index_t template_len = 0; + | ^~~~~~~~~~~~ +In file included from hisat2_build.cpp:35: +gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: +gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ +hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ +hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ +hisat2_build.cpp:801:56: required from here +gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] + 2167 | index_t template_len = 0; + | ^~~~~~~~~~~~ +gfm.h:2342:106: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 2342 | std::numeric_limits::max(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from hgfm.h:24, + from hisat2_inspect.cpp:27: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from hgfm.h:24, + from hisat2_inspect.cpp:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from hgfm.h:24, + from hisat2_inspect.cpp:27: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from hgfm.h:24, + from hisat2_inspect.cpp:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: @@ -1069,21 +1164,6 @@ 454 | this->verbose(), this->sanityCheck()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:453:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from blockwise_sa.h:29, - from gfm.h:43, - from hisat2_build.cpp:35: -diff_sample.h: In instantiation of ‘void DifferenceCoverSample::build(int) [with TStr = SString]’: -blockwise_sa.h:375:20: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ -blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ -blockwise_sa.h:206:29: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ -hgfm.h:1830:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hgfm.h:2211:30: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ -hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ -hisat2_build.cpp:801:56: required from here -diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 813 | sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); @@ -1095,31 +1175,52 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from hgfm.h:24, - from hisat2_inspect.cpp:27: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ +hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: +hisat2.cpp:3167:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from gfm.h:28, from hgfm.h:24, - from hisat2_inspect.cpp:27: + from hisat2.cpp:33: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from hgfm.h:24, - from hisat2_inspect.cpp:27: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ +hisat2.cpp:3168:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 3168 | auto_ptr ps(patsrcFact->create()); + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from gfm.h:28, from hgfm.h:24, - from hisat2_inspect.cpp:27: + from hisat2.cpp:33: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3189:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from hgfm.h:24, + from hisat2.cpp:33: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from blockwise_sa.h:29, + from gfm.h:43, + from hisat2_build.cpp:35: +diff_sample.h: In instantiation of ‘void DifferenceCoverSample::build(int) [with TStr = SString]’: +blockwise_sa.h:375:20: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ +blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ +blockwise_sa.h:206:29: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ +hgfm.h:1830:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hgfm.h:2211:30: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ +hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ +hisat2_build.cpp:801:56: required from here +diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 813 | sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from ds.h:32, from sequence_io.h:28, from hisat2_build.cpp:28: @@ -1166,6 +1267,17 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: +hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 4035 | auto_ptr refs( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from hgfm.h:24, + from hisat2.cpp:33: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = SString]’ blockwise_sa.h:375:20: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ @@ -1180,6 +1292,31 @@ | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29, + from gfm.h:43, + from hgfm.h:24, + from hisat2.cpp:33: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +blockwise_sa.h:478:56: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29, + from gfm.h:43, + from hgfm.h:24, + from hisat2.cpp:33: +multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from ds.h:32, + from sequence_io.h:28, from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -1196,6 +1333,11 @@ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:484:52: required from here +multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ @@ -1233,37 +1375,13 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: -hisat2.cpp:3167:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from hgfm.h:24, - from hisat2.cpp:33: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3168:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 3168 | auto_ptr ps(patsrcFact->create()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from hgfm.h:24, - from hisat2.cpp:33: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3189:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from hgfm.h:24, - from hisat2.cpp:33: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ +In file included from spliced_aligner.h:23, + from hisat2.cpp:46: +hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +hisat2.cpp:3556:58: required from here +hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -1280,94 +1398,6 @@ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ -hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: -hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 4035 | auto_ptr refs( - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from hgfm.h:24, - from hisat2.cpp:33: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: -hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 4035 | auto_ptr refs( - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from hgfm.h:24, - from hisat2.cpp:33: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ -blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ -blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ -hgfm.h:1843:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hgfm.h:2211:30: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ -hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ -hisat2_build.cpp:801:56: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ - 914 | off = OFF_MASK; - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ - 923 | OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ - 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29, - from gfm.h:43, - from hgfm.h:24, - from hisat2.cpp:33: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -blockwise_sa.h:478:56: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29, - from gfm.h:43, - from hgfm.h:24, - from hisat2.cpp:33: -multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:484:52: required from here -multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from spliced_aligner.h:23, - from hisat2.cpp:46: -hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -hisat2.cpp:3556:58: required from here -hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefId’ {aka ‘long long int’} [-Wsign-compare] 4404 | if(positions[p].first.tid != res.refid()) continue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -1415,6 +1445,46 @@ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: +hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 4035 | auto_ptr refs( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from hgfm.h:24, + from hisat2.cpp:33: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ +blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ +blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ +hgfm.h:1843:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hgfm.h:2211:30: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ +hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ +hisat2_build.cpp:801:56: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ + 914 | off = OFF_MASK; + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ + 923 | OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ + 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:46: hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: @@ -1426,14 +1496,6 @@ hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] 5991 | _repeatConcordant[r].second == left2.off()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from hgfm.h:24, - from hisat2.cpp:33: -gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: -hisat2.cpp:3815:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ -hisat2.cpp:4351:51: required from here -gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] - 6935 | int lastorig = -1; - | ^~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3556:58: required from here @@ -1519,6 +1581,14 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from hgfm.h:24, + from hisat2.cpp:33: +gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: +hisat2.cpp:3815:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ +hisat2.cpp:4351:51: required from here +gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] + 6935 | int lastorig = -1; + | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, @@ -1549,84 +1619,6 @@ multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29, - from gfm.h:43, - from hgfm.h:24, - from hisat2_inspect.cpp:27: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:478:56: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ - 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ - 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -In file included from aligner_seed2.h:109, - from aligner_driver.h:78, - from hi_aligner.h:41, - from spliced_aligner.h:23, - from hisat2.cpp:46: -group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ -hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hisat2.cpp:3556:58: required from here -group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1147 | if(new_node_bot - new_node_top < gws.map.size()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { - | ~~~~~~^~~~~~~~~~~~~~~~ -group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from spliced_aligner.h:23, - from hisat2.cpp:46: -hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hisat2.cpp:3556:58: required from here -hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2801 | if(rfoff >= contig_len) return 0; - | ~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2879 | if(alt_range.first >= alts.size()) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 3044 | for(int i = 0; i < alt.len; i++) { - | ~~^~~~~~~~~ -hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { - | ~~~~~^~~~~~~~ -hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 3161 | if(alignedLen == next_rdlen) return rdlen; - | ~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 3454 | if(best_rdoff < rdoff + rd_i) { - | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, @@ -1682,64 +1674,29 @@ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +In file included from ds.h:32, + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29, + from gfm.h:43, + from hgfm.h:24, + from hisat2_inspect.cpp:27: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ - 1071 | OFF_MASK, begin, end); - | ^~~~~~~~ -In file included from aligner_seed2.h:109, - from aligner_driver.h:78, - from hi_aligner.h:41, - from spliced_aligner.h:23, - from hisat2.cpp:46: -group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ -group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ -hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hisat2.cpp:3556:58: required from here -group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 789 | if(new_top - top == tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 795 | if(i + 1 < tmp_zOffs.size()) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from spliced_aligner.h:23, - from hisat2.cpp:46: -hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: -hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hisat2.cpp:3556:58: required from here -hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2660 | if(ht_range.first >= haplotypes.size()) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2675 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2713 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2744 | if(ht_list[h].first == ht_range.second) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ + 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ + 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, @@ -1788,6 +1745,71 @@ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:478:56: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ + 1071 | OFF_MASK, begin, end); + | ^~~~~~~~ +In file included from aligner_seed2.h:109, + from aligner_driver.h:78, + from hi_aligner.h:41, + from spliced_aligner.h:23, + from hisat2.cpp:46: +group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ +hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hisat2.cpp:3556:58: required from here +group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1147 | if(new_node_bot - new_node_top < gws.map.size()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { + | ~~~~~~^~~~~~~~~~~~~~~~ +group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from spliced_aligner.h:23, + from hisat2.cpp:46: +hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hisat2.cpp:3556:58: required from here +hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2801 | if(rfoff >= contig_len) return 0; + | ~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2879 | if(alt_range.first >= alts.size()) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 3044 | for(int i = 0; i < alt.len; i++) { + | ~~^~~~~~~~~ +hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { + | ~~~~~^~~~~~~~ +hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 3161 | if(alignedLen == next_rdlen) return rdlen; + | ~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 3454 | if(best_rdoff < rdoff + rd_i) { + | ~~~~~~~~~~~^~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -1812,20 +1834,6 @@ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from hisat2.cpp:46: -spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: -spliced_aligner.h:331:9: required from here -spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] - 408 | bool another_spliced = false; - | ^~~~~~~~~~~~~~~ -In file included from spliced_aligner.h:23, - from hisat2.cpp:46: -hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long long int]’: -spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ -spliced_aligner.h:331:9: required from here -hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] - 1926 | if(alt.seq == rdc) { - | ~~~~~~~~^~~~~~ -In file included from hisat2.cpp:46: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: spliced_aligner.h:331:9: required from here spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] @@ -1834,11 +1842,59 @@ spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from aligner_seed2.h:109, + from aligner_driver.h:78, + from hi_aligner.h:41, + from spliced_aligner.h:23, + from hisat2.cpp:46: +group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ +group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ +hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hisat2.cpp:3556:58: required from here +group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 789 | if(new_top - top == tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 795 | if(i + 1 < tmp_zOffs.size()) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:46: +hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: +hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hisat2.cpp:3556:58: required from here +hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2660 | if(ht_range.first >= haplotypes.size()) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 2675 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 2713 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 2744 | if(ht_list[h].first == ht_range.second) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +In file included from spliced_aligner.h:23, + from hisat2.cpp:46: hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long long unsigned int; TAlScore = long long int]’: spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ spliced_aligner.h:331:9: required from here @@ -1851,6 +1907,20 @@ hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from hisat2.cpp:46: +spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: +spliced_aligner.h:331:9: required from here +spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] + 408 | bool another_spliced = false; + | ^~~~~~~~~~~~~~~ +In file included from spliced_aligner.h:23, + from hisat2.cpp:46: +hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long long int]’: +spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ +spliced_aligner.h:331:9: required from here +hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] + 1926 | if(alt.seq == rdc) { + | ~~~~~~~~^~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -2238,15 +2308,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from edit.h:26, - from edit.cpp:21: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -2266,6 +2327,15 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ +In file included from edit.h:26, + from edit.cpp:21: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: @@ -2413,16 +2483,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from alphabet.h:27, - from gfm.h:40, - from gfm.cpp:21: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -2462,27 +2522,16 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from gfm.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from gfm.cpp:21: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, +In file included from alphabet.h:27, + from gfm.h:40, from gfm.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, @@ -2566,6 +2615,27 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from gfm.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from gfm.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from gfm.cpp:21: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from gfm.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -2690,6 +2760,26 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from gfm.h:59, + from hgfm.h:24, + from hisat2.cpp:33: +repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’: +repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized] + 41 | if(fw != o.fw) + | ~~^~ +repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized] + 43 | if(alleleID != o.alleleID) + | ~~^~~~~~~~ +In file included from gfm.h:59, + from hgfm.h:24, + from hisat2.cpp:33: +repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized] + 41 | if(fw != o.fw) + | ~~^~ +repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized] + 43 | if(alleleID != o.alleleID) + | ~~^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -2836,26 +2926,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.h:59, - from hgfm.h:24, - from hisat2.cpp:33: -repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’: -repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized] - 41 | if(fw != o.fw) - | ~~^~ -repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized] - 43 | if(alleleID != o.alleleID) - | ~~^~~~~~~~ -In file included from gfm.h:59, - from hgfm.h:24, - from hisat2.cpp:33: -repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized] - 41 | if(fw != o.fw) - | ~~^~ -repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized] - 43 | if(alleleID != o.alleleID) - | ~~^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -3186,22 +3256,37 @@ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from gfm.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from gfm.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from gfm.cpp:21: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from gfm.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3213,19 +3298,13 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.cpp:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.cpp:21: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -3236,29 +3315,13 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.cpp:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 484 | this->verbose(), this->sanityCheck()); - | ^ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.h:29, + from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3272,10 +3335,7 @@ from gfm.h:43, from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3286,11 +3346,8 @@ 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from edit.h:29, + from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here @@ -3306,41 +3363,6 @@ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from edit.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from edit.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -3374,9 +3396,79 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 484 | this->verbose(), this->sanityCheck()); + | ^ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from ds.h:32, - from edit.h:29, - from edit.cpp:21: + from read.h:25, + from aligner_result.h:27, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3390,7 +3482,10 @@ from gfm.h:43, from splice_site.h:34, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3401,8 +3496,11 @@ 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, - from edit.h:29, - from edit.cpp:21: + from read.h:25, + from aligner_result.h:27, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here @@ -3418,27 +3516,6 @@ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from gfm.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from gfm.cpp:21: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from gfm.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -3472,13 +3549,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -3598,25 +3668,82 @@ reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from edit.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from edit.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from gfm.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from gfm.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from gfm.cpp:21: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from gfm.h:28, + from gfm.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3628,19 +3755,13 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.cpp:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.cpp:21: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -3651,19 +3772,13 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.cpp:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.h:29, + from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3677,10 +3792,7 @@ from gfm.h:43, from splice_site.h:34, from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3691,11 +3803,8 @@ 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from edit.h:29, + from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here @@ -3744,45 +3853,13 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from edit.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from edit.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); @@ -3791,7 +3868,10 @@ blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3803,13 +3883,19 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -3820,13 +3906,19 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from edit.h:29, - from edit.cpp:21: + from read.h:25, + from aligner_result.h:27, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3840,7 +3932,10 @@ from gfm.h:43, from splice_site.h:34, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3851,8 +3946,11 @@ 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, - from edit.h:29, - from edit.cpp:21: + from read.h:25, + from aligner_result.h:27, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here @@ -3901,34 +3999,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from gfm.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from gfm.cpp:21: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from gfm.h:28, - from gfm.cpp:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -4368,6 +4438,45 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_seed.h:30, + from aligner_seed.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_seed.h:30, + from aligner_seed.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_seed.h:30, + from aligner_seed.cpp:21: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_seed.h:30, + from aligner_seed.cpp:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ repeat_builder.cpp: In function ‘std::string reverse_complement(const string&)’: repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; @@ -4557,8 +4666,9 @@ | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -4570,15 +4680,17 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -4589,8 +4701,9 @@ from reference.h:36, from splice_site.h:32, from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -4725,61 +4838,6 @@ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 484 | this->verbose(), this->sanityCheck()); - | ^ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: @@ -4824,6 +4882,18 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 484 | this->verbose(), this->sanityCheck()); + | ^ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -5301,6 +5371,49 @@ from edit.h:30, from aligner_result.h:30, from unique.h:38, + from unique.cpp:20: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, + from unique.cpp:20: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, + from unique.cpp:20: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, + from unique.cpp:20: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: @@ -5412,6 +5525,18 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, + from unique.cpp:20: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 484 | this->verbose(), this->sanityCheck()); + | ^ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -5455,23 +5580,12 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 484 | this->verbose(), this->sanityCheck()); - | ^ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5484,16 +5598,18 @@ from splice_site.h:32, from edit.h:30, from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ @@ -5505,8 +5621,9 @@ from splice_site.h:32, from edit.h:30, from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -5593,53 +5710,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -5845,6 +5915,53 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] @@ -5967,53 +6084,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -6786,45 +6856,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from splice_site.cpp:20: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from splice_site.cpp:20: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from splice_site.cpp:20: -gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from timer.h:26, - from reference.h:36, - from splice_site.h:32, - from edit.h:30, - from splice_site.cpp:20: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: -splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] - 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -6838,18 +6869,6 @@ | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from edit.h:29, - from splice_site.cpp:20: -ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’: -splice_site.cpp:722:59: required from here -ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 663 | std::memcpy(list_ + cur_, l, bytes); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from edit.h:30, - from splice_site.cpp:20: -splice_site.h:377:7: note: ‘class Exon’ declared here - 377 | class Exon { - | ^~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -6981,6 +7000,57 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from splice_site.cpp:20: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from splice_site.cpp:20: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from splice_site.cpp:20: +gfm.h:1189:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from timer.h:26, + from reference.h:36, + from splice_site.h:32, + from edit.h:30, + from splice_site.cpp:20: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: +splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] + 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from edit.h:29, + from splice_site.cpp:20: +ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’: +splice_site.cpp:722:59: required from here +ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 663 | std::memcpy(list_ + cur_, l, bytes); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from edit.h:30, + from splice_site.cpp:20: +splice_site.h:377:7: note: ‘class Exon’ declared here + 377 | class Exon { + | ^~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -7119,7 +7189,7 @@ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -make[2]: Leaving directory '/build/hisat2-2.2.1' +make[2]: Verzeichnis „/build/hisat2-2.2.1“ wird verlassen help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 @@ -7140,18 +7210,18 @@ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 -make[1]: Leaving directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird verlassen dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install -make[1]: Entering directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird betreten dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done -make[1]: Leaving directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird verlassen dh_installdocs dh_installchangelogs dh_installexamples @@ -7169,26 +7239,28 @@ dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol -make[1]: Entering directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird betreten dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " -make[1]: Leaving directory '/build/hisat2-2.2.1' +make[1]: Verzeichnis „/build/hisat2-2.2.1“ wird verlassen dh_md5sums dh_builddeb -dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-2_i386.deb'. -dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-2_i386.deb'. -dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-2_all.deb'. +dpkg-deb: Paket »hisat2-dbgsym« wird in »../hisat2-dbgsym_2.2.1-2_i386.deb« gebaut. +dpkg-deb: Paket »python3-hisat2« wird in »../python3-hisat2_2.2.1-2_all.deb« gebaut. +dpkg-deb: Paket »hisat2« wird in »../hisat2_2.2.1-2_i386.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hisat2_2.2.1-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/25847/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25847/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/36409 and its subdirectories -I: Current time: Wed Sep 14 06:47:15 -12 2022 -I: pbuilder-time-stamp: 1663181235 +I: removing directory /srv/workspace/pbuilder/25847 and its subdirectories +I: Current time: Fri Aug 13 02:40:58 +14 2021 +I: pbuilder-time-stamp: 1628772059