Diff of the two buildlogs: -- --- b1/build.log 2023-04-17 11:37:58.813596989 +0000 +++ b2/build.log 2023-04-17 11:39:38.037195191 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 16 23:33:14 -12 2023 -I: pbuilder-time-stamp: 1681731194 +I: Current time: Mon May 20 08:01:02 +14 2024 +I: pbuilder-time-stamp: 1716141662 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./ivar_1.3.1+dfsg.orig.tar.xz] I: copying [./ivar_1.3.1+dfsg-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Oct 5 21:19:35 2022 -12 +gpgv: Signature made Thu Oct 6 23:19:35 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,135 +33,167 @@ dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2727556/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3551548/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 20 08:01 /bin/sh -> /bin/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/3551548/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3551548/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=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(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=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9549563dcf5b4a3f98e35e6a98fd5835' - 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='2727556' - PS1='# ' - PS2='> ' + INVOCATION_ID=cb0ac2252583460997ba12c7ceb87a26 + 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=3551548 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/r-b-build.jESBk7uu/pbuilderrc_a7Qw --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jESBk7uu/b1 --logfile b1/build.log ivar_1.3.1+dfsg-7.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://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jESBk7uu/pbuilderrc_bUdG --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jESBk7uu/b2 --logfile b2/build.log --extrapackages usrmerge ivar_1.3.1+dfsg-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2727556/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 May 20 08:01 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3551548/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -246,7 +278,7 @@ Get: 45 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] -Fetched 23.9 MB in 1s (40.1 MB/s) +Fetched 23.9 MB in 0s (84.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19596 files and directories currently installed.) @@ -448,8 +480,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/ivar-1.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ivar_1.3.1+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/3551548/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/3551548/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/ivar-1.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ivar_1.3.1+dfsg-7_source.changes dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -478,7 +521,7 @@ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -537,15 +580,20 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j15 + make -j16 make[1]: Entering directory '/build/ivar-1.3.1+dfsg' make all-recursive make[2]: Entering directory '/build/ivar-1.3.1+dfsg' Making all in src make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o ivar.o ivar.cpp -Using built-in specs. g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp +Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp +Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 @@ -554,11 +602,23 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) +Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccTzQVH7.s -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -WextraCOLLECT_GCC=g++ + -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strongOFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa + -fasynchronous-unwind-tables -o /tmp/ccJ4OXNZ.sOFFLOAD_TARGET_DEFAULT=1 + +Target: x86_64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cck2NQT9.s Using built-in specs. COLLECT_GCC=g++ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu @@ -566,62 +626,166 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccnMbqHz.s +Using built-in specs. +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccPbIElG.s +COLLECT_GCC=g++ +OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa +OFFLOAD_TARGET_DEFAULT=1 +Target: x86_64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccPlLgag.s +Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp +COLLECT_GCC=g++ +OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa +OFFLOAD_TARGET_DEFAULT=1 +Target: x86_64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarchUsing built-in specs. + x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccs0bTu8.s +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp +COLLECT_GCC=g++ +OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa +OFFLOAD_TARGET_DEFAULT=1 +Target: x86_64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC=g++ +Using built-in specs. +OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa +OFFLOAD_TARGET_DEFAULT=1 +Target: x86_64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plusg++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp + -quiet -v -I . -I ..COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' 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'-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccalc7sv.s +COLLECT_GCC=g++ +OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa +OFFLOAD_TARGET_DEFAULT=1 +Target: x86_64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccEpRArD.s +Using built-in specs. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" +ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" -GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - +ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" +ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" +ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. +#include "..." search starts here: /usr/include/c++/12 /usr/include/x86_64-linux-gnu/c++/12 - /usr/include/c++/12/backward - /usr/lib/gcc/x86_64-linux-gnu/12/include - /usr/local/include - /usr/include/x86_64-linux-gnu - /usr/include -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -End of search list. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" -ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" -ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" -ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" -#include "..." search starts here: #include <...> search starts here: + /usr/include/c++/12/backward . + /usr/lib/gcc/x86_64-linux-gnu/12/include .. + /usr/local/include /usr/include/c++/12 + /usr/include/x86_64-linux-gnu /usr/include/x86_64-linux-gnu/c++/12 + /usr/include /usr/include/c++/12/backward /usr/lib/gcc/x86_64-linux-gnu/12/include +End of search list. /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp -Using built-in specs. COLLECT_GCC=g++ OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 @@ -630,24 +794,36 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccozKjck.s -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-securityGNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccwZf2CL.s +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. #include "..." search starts here: #include <...> search starts here: . .. +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 /usr/include/c++/12 /usr/include/x86_64-linux-gnu/c++/12 /usr/include/c++/12/backward @@ -661,47 +837,6 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc0ZLPNR.s -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccRdbbx3.s -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -Using built-in specs. -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccwKx3A2.s -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -749,20 +884,6 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccSeyC4h.s -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -782,23 +903,26 @@ /usr/lib/gcc/x86_64-linux-gnu/12/include /usr/local/include /usr/include/x86_64-linux-gnu - /usr/include -End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + compiled by GNU C version 12.2.0, /usr/include +End of search list. +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Using built-in specs. -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" +GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: @@ -817,32 +941,6 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccqg2pDX.s -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc9DOrMN.s -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -Using built-in specs. -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -850,41 +948,26 @@ GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" -ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" +GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. . .. /usr/include/c++/12 +ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" /usr/include/x86_64-linux-gnu/c++/12 /usr/include/c++/12/backward +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 /usr/lib/gcc/x86_64-linux-gnu/12/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc9K8vr6.s -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" @@ -894,20 +977,17 @@ .. /usr/include/c++/12 /usr/include/x86_64-linux-gnu/c++/12 - /usr/include/c++/12/backward +GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, /usr/include/c++/12/backward /usr/lib/gcc/x86_64-linux-gnu/12/include /usr/local/include /usr/include/x86_64-linux-gnu /usr/include End of search list. -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -916,7 +996,12 @@ ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" +GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 #include "..." search starts here: #include <...> search starts here: . @@ -929,32 +1014,14 @@ /usr/include/x86_64-linux-gnu /usr/include End of search list. +ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" +ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc9SsmX5.s -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp -Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/12" -ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/include-fixed" +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/12/../../../../x86_64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: @@ -973,42 +1040,6 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccpbN8Gr.s -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp -Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc3Rywky.s -Compiler executable checksum: Using built-in specs. -COLLECT_GCC=g++ -OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa -OFFLOAD_TARGET_DEFAULT=1 -Target: x86_64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-12-bTRWOB/gcc-12-12.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccuu1pfu.s -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) - compiled by GNU C version 12.2.0, 62b090dbbefa50644117a3c13d47369a GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -1035,7 +1066,8 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP +GNU C++11 (Debian 12.2.0-14) version 12.2.0 (x86_64-linux-gnu) + compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 @@ -1087,103 +1119,114 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: Compiler executable checksum: 6262b0b09090dbdbbebefafa5050646441411717a3a3c1c13d3d474736369a9a + +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: 62b090Compiler executable checksum: dbbefa50646241b017a390c1db3dbe47fa36509a6441 +17a3c13d47369a +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a +Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a Compiler executable checksum: 62b090dbbefa50644117a3c13d47369a COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o interval_tree.o /tmp/ccuu1pfu.s + as -v -I . -I .. --gdwarf-5 --64 -o interval_tree.o /tmp/ccwZf2CL.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccozKjck.s -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'interval_tree.' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccPbIElG.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'alignment.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/ccwKx3A2.s + as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/ccB5tDDT.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'remove_reads_from_amplicon.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o get_masked_amplicons.o /tmp/cc9K8vr6.s + as -v -I . -I .. --gdwarf-5 --64 -o get_masked_amplicons.o /tmp/ccF3SX9A.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_masked_amplicons.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o get_common_variants.o /tmp/cc9SsmX5.s + as -v -I . -I .. --gdwarf-5 --64 -o get_common_variants.o /tmp/ccqfO354.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o ref_seq.o /tmp/cc3Rywky.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/cckhfspx.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_common_variants.' +MAKEFLAGS=w -j16 +COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + as -v -I . -I .. --gdwarf-5 --64 -o ref_seq.o /tmp/ccEpRArD.s +GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o allele_functions.o /tmp/cc9DOrMN.s + as -v -I . -I .. --gdwarf-5 --64 -o allele_functions.o /tmp/ccZ8oQFc.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ref_seq.' -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/ccSeyC4h.s -GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'allele_functions.' -MAKEFLAGS=w -j15 +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/ccPlLgag.s +GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccTzQVH7.s + as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccJ4OXNZ.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/ccnMbqHz.s + as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/cck2NQT9.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccs0bTu8.s +GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccRdbbx3.s -GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/cc0ZLPNR.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/ccqzBpsK.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_consensus_pileup.' -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.' -MAKEFLAGS=w -j15 -COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.' -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/ccqg2pDX.s -GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'primer_bed.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' - as -v -I . -I .. --gdwarf-5 --64 -o parse_gff.o /tmp/ccpbN8Gr.s + as -v -I . -I .. --gdwarf-5 --64 -o parse_gff.o /tmp/ccalc7sv.s GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'parse_gff.' @@ -1198,11 +1241,11 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) -MAKEFLAGS=w -j15 +MAKEFLAGS=w -j16 COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' - /usr/lib/gcc/x86_64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccPVOag8.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o + /usr/lib/gcc/x86_64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccZJZ1NL.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/src' Making all in tests @@ -1316,7 +1359,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j15 install DESTDIR=/build/ivar-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j16 install DESTDIR=/build/ivar-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/ivar-1.3.1+dfsg' Making install in src make[2]: Entering directory '/build/ivar-1.3.1+dfsg/src' @@ -1331,15 +1374,15 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) -MAKEFLAGS=w -j15 -- DESTDIR=/build/ivar-1.3.1+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no +MAKEFLAGS=w -j16 -- DESTDIR=/build/ivar-1.3.1+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' - /usr/lib/gcc/x86_64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccqlNHPu.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o + /usr/lib/gcc/x86_64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/cckUhczj.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.' make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' - /bin/mkdir -p '/build/ivar-1.3.1+dfsg/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/ivar-1.3.1+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ivar '/build/ivar-1.3.1+dfsg/debian/tmp/usr/bin' make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/src' make[2]: Leaving directory '/build/ivar-1.3.1+dfsg/src' @@ -1376,8 +1419,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.3.1+dfsg-7_amd64.deb'. dpkg-deb: building package 'ivar' in '../ivar_1.3.1+dfsg-7_amd64.deb'. +dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.3.1+dfsg-7_amd64.deb'. dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.3.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../ivar_1.3.1+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../ivar_1.3.1+dfsg-7_amd64.changes @@ -1386,12 +1429,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3551548/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3551548/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/2727556 and its subdirectories -I: Current time: Sun Apr 16 23:37:58 -12 2023 -I: pbuilder-time-stamp: 1681731478 +I: removing directory /srv/workspace/pbuilder/3551548 and its subdirectories +I: Current time: Mon May 20 08:02:39 +14 2024 +I: pbuilder-time-stamp: 1716141759