Diff of the two buildlogs: -- --- b1/build.log 2021-07-19 19:28:52.481237502 +0000 +++ b2/build.log 2021-07-19 19:30:26.521685004 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 21 13:50:32 -12 2022 -I: pbuilder-time-stamp: 1661133032 +I: Current time: Tue Jul 20 09:28:54 +14 2021 +I: pbuilder-time-stamp: 1626722934 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Jan 1 23:07:29 2019 -12 +gpgv: Signature made Thu Jan 3 01:07:29 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rapmap_0.12.0+dfsg-3.dsc @@ -33,136 +33,170 @@ dpkg-source: info: applying no_gomp_needed I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/46875/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11267/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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/11267/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11267/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='17f08f8b46c943e0ac90d52c0664db6f' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - 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='46875' - PS1='# ' - PS2='> ' + INVOCATION_ID=a65d312614a24b338fd1d45e9daf8d10 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=11267 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.Gq46Z4FSiw/pbuilderrc_4RBQ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Gq46Z4FSiw/b1 --logfile b1/build.log rapmap_0.12.0+dfsg-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.Gq46Z4FSiw/pbuilderrc_v3Yn --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Gq46Z4FSiw/b2 --logfile b2/build.log rapmap_0.12.0+dfsg-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 ionos5-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 02:46 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/46875/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 20 09:29 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 7 22:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/11267/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -305,7 +339,7 @@ Get: 83 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 python-markdown all 3.0.1-3 [60.6 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 35.0 MB in 0s (75.6 MB/s) +Fetched 35.0 MB in 1s (45.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -671,7 +705,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/rapmap-0.12.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/rapmap-0.12.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.12.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -742,7 +776,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/rapmap-0.12.0+dfsg' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/rapmap-0.12.0+dfsg -B/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -755,30 +789,30 @@ make[4]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build make[4]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu' -[ 15%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -[ 15%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -[ 23%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -[ 30%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o -cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp -cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp -[ 38%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -[ 46%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o +[ 7%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMap.cpp -[ 53%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o -[ 61%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o -[ 69%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o -[ 76%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o +[ 15%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o +cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/rapmap-0.12.0+dfsg/src/FastxParser.cpp +[ 30%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o +[ 30%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o +[ 38%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o +[ 46%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o +[ 53%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o +cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp +[ 61%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o +[ 69%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapUtils.cpp cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp +[ 76%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapFileSystem.cpp -cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/rapmap.dir/xxhash.c.o -c /build/rapmap-0.12.0+dfsg/src/xxhash.c -[ 84%] Building C object src/CMakeFiles/rapmap.dir/bit_array.c.o +[ 84%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o +cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/HitManager.cpp.o -c /build/rapmap-0.12.0+dfsg/src/HitManager.cpp -cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/rapmap-0.12.0+dfsg/src/FastxParser.cpp +[ 92%] Building C object src/CMakeFiles/rapmap.dir/bit_array.c.o +cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /build/rapmap-0.12.0+dfsg/src/rank9b.cpp cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/stringpiece.cc.o -c /build/rapmap-0.12.0+dfsg/src/stringpiece.cc -[ 92%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o +cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/rapmap.dir/xxhash.c.o -c /build/rapmap-0.12.0+dfsg/src/xxhash.c cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/rapmap.dir/bit_array.c.o -c /build/rapmap-0.12.0+dfsg/src/bit_array.c -cd /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /build/rapmap-0.12.0+dfsg/src/rank9b.cpp In file included from /build/rapmap-0.12.0+dfsg/include/zstr/zstr.hpp:16, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:62: /build/rapmap-0.12.0+dfsg/include/zstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const string&, std::ios_base::openmode)': @@ -868,6 +902,102 @@ class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; spp::sparsetable::size_type = long unsigned int]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >; spp::sparse_hashtable::key_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >; spp::sparse_hash_map::key_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:603:33: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable > >, spp::libc_allocator > > > >::group_type' {aka 'class spp::sparsegroup > >, spp::libc_allocator > > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable > >, spp::libc_allocator > > > >::group_type' {aka 'class spp::sparsegroup > >, spp::libc_allocator > > > >'} declared here + class sparsegroup + ^~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::value_type = std::pair >; spp::sparse_hashtable::key_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hash_map::mapped_type = rapmap::utils::SAInterval; spp::sparse_hash_map::key_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:759:34: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here + class sparsegroup + ^~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::value_type = std::pair >; spp::sparse_hashtable::key_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hash_map::mapped_type = rapmap::utils::SAInterval; spp::sparse_hash_map::key_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:780:34: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here + class sparsegroup + ^~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' +/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:756:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here + class sparsegroup + ^~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' +/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here + class sparsegroup + ^~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': @@ -971,102 +1101,6 @@ ^~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; spp::sparsetable::size_type = long unsigned int]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >; spp::sparse_hashtable::key_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >; spp::sparse_hash_map::key_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:603:33: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable > >, spp::libc_allocator > > > >::group_type' {aka 'class spp::sparsegroup > >, spp::libc_allocator > > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable > >, spp::libc_allocator > > > >::group_type' {aka 'class spp::sparsegroup > >, spp::libc_allocator > > > >'} declared here - class sparsegroup - ^~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::value_type = std::pair >; spp::sparse_hashtable::key_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hash_map::mapped_type = rapmap::utils::SAInterval; spp::sparse_hash_map::key_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:759:34: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here - class sparsegroup - ^~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::value_type = std::pair >; spp::sparse_hashtable::key_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hash_map::mapped_type = rapmap::utils::SAInterval; spp::sparse_hash_map::key_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:780:34: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here - class sparsegroup - ^~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' -/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:756:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here - class sparsegroup - ^~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' -/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here - class sparsegroup - ^~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' @@ -1163,19 +1197,19 @@ markdown_py -f README.html README.md make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg' dh_auto_test - cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=-j16 + cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=-j15 make[1]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process -j16 +/usr/bin/ctest --force-new-ctest-process -j15 Test project /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu Start 1: quasi_map_test Start 2: quasi_map_test_ph -1/2 Test #1: quasi_map_test ................... Passed 0.23 sec +1/2 Test #1: quasi_map_test ................... Passed 0.24 sec 2/2 Test #2: quasi_map_test_ph ................ Passed 0.26 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 0.26 sec +Total Test time (real) = 0.27 sec make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -1183,7 +1217,7 @@ dh_testroot dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/rapmap-0.12.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/rapmap-0.12.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/rapmap-0.12.0+dfsg -B/build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/rapmap-0.12.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -1228,22 +1262,24 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'rapmap-dbgsym' in '../rapmap-dbgsym_0.12.0+dfsg-3_amd64.deb'. dpkg-deb: building package 'rapmap' in '../rapmap_0.12.0+dfsg-3_amd64.deb'. dpkg-deb: building package 'rapmap-example-data' in '../rapmap-example-data_0.12.0+dfsg-3_all.deb'. dpkg-deb: building package 'rapmap-dev' in '../rapmap-dev_0.12.0+dfsg-3_all.deb'. -dpkg-deb: building package 'rapmap-dbgsym' in '../rapmap-dbgsym_0.12.0+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rapmap_0.12.0+dfsg-3_amd64.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/11267/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11267/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/46875 and its subdirectories -I: Current time: Sun Aug 21 13:51:52 -12 2022 -I: pbuilder-time-stamp: 1661133112 +I: removing directory /srv/workspace/pbuilder/11267 and its subdirectories +I: Current time: Tue Jul 20 09:30:26 +14 2021 +I: pbuilder-time-stamp: 1626723026