I: pbuilder: network access will be disabled during build 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 W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ivar_1.3.1+dfsg-7.dsc] 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 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 dpkg-source: warning: cannot verify inline signature for ./ivar_1.3.1+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting ivar in ivar-1.3.1+dfsg dpkg-source: info: unpacking ivar_1.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.3.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix-warning.patch dpkg-source: info: applying forward-build-options.patch dpkg-source: info: applying gcc-11.patch dpkg-source: info: applying gcc-11_2.patch dpkg-source: info: applying privacy-breach.patch 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/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 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=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 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 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 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 Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 23.9 MB of archives. After unpacking 87.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-8 [380 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-8 [481 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] 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 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.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... 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Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-8) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... 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: 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 dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ivar-1.3.1+dfsg' rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:12: installing './compile' configure.ac:58: installing './config.guess' configure.ac:58: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./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... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for main in -lhts... no checking for main in -lpthread... no checking for main in -lz... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... no checking for GNU libc compatible realloc... no checking for memmove... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build 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 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 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) 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 -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 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) 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=.' 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'-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' 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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' '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/ccZ8oQFc.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 Using built-in specs. 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_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/ccF3SX9A.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 interval_tree.o interval_tree.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' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/12/cc1plus -quiet -v -I . -I ..COLLECT_GCC=g++ -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -DOFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa HAVE_CONFIG_H -DOFFLOAD_TARGET_DEFAULT=1 _FORTIFY_SOURCE=2 get_common_variants.cpp -quietTarget: x86_64-linux-gnu -dumpbase get_common_variants.cppConfigured 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 -dumpbase-ext .cppThread model: posix -mtune=genericSupported LTO compression algorithms: zlib -march=x86-64 zstd -g -g -O2gcc version 12.2.0 (Debian 12.2.0-14) -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/ccqfO354.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' '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" 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 #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. 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, 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 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 /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 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 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 /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 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" 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 /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 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 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 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 /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 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 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 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, 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: . .. /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 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 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" 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. 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 /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, /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. 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 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" 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: . .. /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 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. 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: . .. /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 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 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 /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 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 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 /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 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 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 /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 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 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/ccwZf2CL.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' '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 -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/ccB5tDDT.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' '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/ccF3SX9A.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' '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/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' '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 -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/ccZ8oQFc.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' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ref_seq.' 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.' 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' '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/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/cck2NQT9.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' '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' '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 -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 -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 -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/ccalc7sv.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' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'parse_gff.' g++ -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 -Wl,-z,relro -Wl,-z,now -o ivar 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 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/12/lto-wrapper 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) 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/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 make[3]: Entering directory '/build/ivar-1.3.1+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make[3]: Entering directory '/build/ivar-1.3.1+dfsg' make[3]: Leaving directory '/build/ivar-1.3.1+dfsg' make[2]: Leaving directory '/build/ivar-1.3.1+dfsg' make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ivar-1.3.1+dfsg' dh_auto_test --no-parallel make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/ivar-1.3.1+dfsg' Making check in src make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/src' Making check in tests make[3]: Entering directory '/build/ivar-1.3.1+dfsg/tests' make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search make[4]: Entering directory '/build/ivar-1.3.1+dfsg/tests' 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_variants.o test_variants.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.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 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread 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 -g -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread make[4]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make check-TESTS make[4]: Entering directory '/build/ivar-1.3.1+dfsg/tests' make[5]: Entering directory '/build/ivar-1.3.1+dfsg/tests' PASS: check_primer_trim PASS: check_trim PASS: check_quality_trim PASS: check_consensus PASS: check_allele_depth PASS: check_consensus_threshold PASS: check_consensus_min_depth PASS: check_consensus_seq_id PASS: check_primer_bed PASS: check_getmasked PASS: check_removereads PASS: check_variants PASS: check_common_variants PASS: check_unpaired_trim PASS: check_primer_trim_edge_cases PASS: check_isize_trim PASS: check_interval_tree PASS: check_amplicon_search ============================================================================ Testsuite summary for ivar 1.3.1 ============================================================================ # TOTAL: 18 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make[4]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make[3]: Entering directory '/build/ivar-1.3.1+dfsg' make[3]: Leaving directory '/build/ivar-1.3.1+dfsg' make[2]: Leaving directory '/build/ivar-1.3.1+dfsg' make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install 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' g++ -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 -Wl,-z,relro -Wl,-z,now -o ivar 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 Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/12/lto-wrapper 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) 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/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' 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' Making install in tests make[2]: Entering directory '/build/ivar-1.3.1+dfsg/tests' make[3]: Entering directory '/build/ivar-1.3.1+dfsg/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make[2]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' make[2]: Entering directory '/build/ivar-1.3.1+dfsg' make[3]: Entering directory '/build/ivar-1.3.1+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/ivar-1.3.1+dfsg' make[2]: Leaving directory '/build/ivar-1.3.1+dfsg' make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb 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 dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . 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/3551548 and its subdirectories I: Current time: Mon May 20 08:02:39 +14 2024 I: pbuilder-time-stamp: 1716141759