Thu May 11 03:47:00 UTC 2023 I: starting to build ivar/bookworm/i386 on jenkins on '2023-05-11 03:44' Thu May 11 03:47:00 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/10270/console.log Thu May 11 03:47:00 UTC 2023 I: Downloading source for bookworm/ivar=1.3.1+dfsg-7 --2023-05-11 03:47:00-- http://cdn-fastly.deb.debian.org/debian/pool/main/i/ivar/ivar_1.3.1%2bdfsg-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2086 (2.0K) [text/prs.lines.tag] Saving to: ‘ivar_1.3.1+dfsg-7.dsc’ 0K .. 100% 167M=0s 2023-05-11 03:47:00 (167 MB/s) - ‘ivar_1.3.1+dfsg-7.dsc’ saved [2086/2086] Thu May 11 03:47:00 UTC 2023 I: ivar_1.3.1+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ivar Binary: ivar, ivar-doc Architecture: any all Version: 1.3.1+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/andersen-lab/ivar Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/ivar Vcs-Git: https://salsa.debian.org/med-team/ivar.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), libhts-dev Package-List: ivar deb science optional arch=any ivar-doc deb doc optional arch=all Checksums-Sha1: 0618c6cb558643a035fef9579d83f75d42504980 630344 ivar_1.3.1+dfsg.orig.tar.xz c4df6bccddd8cb119b6d264d825097b25fa7351d 45912 ivar_1.3.1+dfsg-7.debian.tar.xz Checksums-Sha256: 1c506993b93b2f6b2fec7328e726bfb91a99a9d36c4b9e0bb174383143a2b192 630344 ivar_1.3.1+dfsg.orig.tar.xz 1b0042caa2ea053c2c345a5da13586ecddb0a2e18c6b3d6403a68d866f631390 45912 ivar_1.3.1+dfsg-7.debian.tar.xz Files: 073c189f9294476b494704928099f71f 630344 ivar_1.3.1+dfsg.orig.tar.xz 76bb18a9d09a34e18cab0fc5ad734e38 45912 ivar_1.3.1+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM+nacRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH8Hw//Zyd1sU1DHFFzJnI+1KZtXh1rjkCNWdNd aqsU1ZQ4LW2Er8SzcHrX+rldAnZ/gMP2FwBePNTkMnznaz60MVaB2a4Vc/jWEZ6o 5vfk9gua31/yHhxPBRkq56vFAB41B2+/xebveD/g1VJA3v4YMXhA4IWc1ooCaGUR XcMpCmYZSb8fCyWfjmy0rAeYsx3RsAlcHhjIpxS2hzhjlOL7egjVaW7TLuJzyv/G 7W2r1uXvt5v3ZlOP9/ytx6cpD5/vSCCmxnZbmaErM1JXHk+XIe6JVd6AIuuGc+Sf AdKHOnZsw/VHvmWZ4+iMFUUjAGbwZODQXZmg8o0rBVr1cW7l4khISC5KEwQPivHv jZJSL1WAm1M8N7nqK8DB3URIa49n4kf2/8dsoFVrNit1X7NVTFBppm1wC6Y4dQBG EajHo8zUi8XuJIbU0V76/qdkZUALkENC3rYTPpKXs+xoTXg4FZj+0zyJ0F+9BgoP 8+MoFEooZ//Ij+Joqhyt9Cjka2f1Kznjwoqg1hvaZgpvTpR5e0i1fD4+h8Mxehfm idcdhh0OCB9RpiVFxw4a1yc2FnsqVTfSkgWiaTLtAmoxTm9rH4je7NyEzs7v+L+Z FGBVPCss0GaarvaC80b5A/rIqfJVk8lE5LH3ZAF10fS91zoK0isAR6rPXGESpI53 3nYoqD8aRvM= =s0x5 -----END PGP SIGNATURE----- Thu May 11 03:47:00 UTC 2023 I: Checking whether the package is not for us Thu May 11 03:47:00 UTC 2023 I: Starting 1st build on remote node ionos12-i386.debian.net. Thu May 11 03:47:00 UTC 2023 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Thu May 11 03:55:44 UTC 2023 I: Deleting $TMPDIR on ionos12-i386.debian.net. W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Wed May 10 15:51:02 -12 2023 I: pbuilder-time-stamp: 1683777062 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: using eatmydata during job 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 Wed Oct 5 21:19:35 2022 -12 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/1129/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1129' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/pbuilderrc_sXw5 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/b1 --logfile b1/build.log ivar_1.3.1+dfsg-7.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos12-i386 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1129/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: i386 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 ... 19604 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 24.3 MB of archives. After unpacking 86.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-9 [527 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB] Fetched 24.3 MB in 1s (48.0 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 ... 19604 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_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... 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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:i386 (7.88.1-9) ... Setting up libcurl4-gnutls-dev:i386 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:i386 (1.16+ds-3) ... Setting up libhts-dev:i386 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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 I: Building the package I: Running cd /build/ivar-1.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ivar_1.3.1+dfsg-7_source.changes 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 i386 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=i686-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/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for 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... i686-pc-linux-gnu checking host system type... i686-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 -j8 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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp Using built-in specs. Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix COLLECT_GCC=g++ Supported LTO compression algorithms: zlib zstd Target: i686-linux-gnu gcc version 12.2.0 (Debian 12.2.0-14) 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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cppCOLLECT_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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -g -g -O2 /usr/lib/gcc/i686-linux-gnu/12/cc1plus -Wdate-time -quiet -Wformat=1 -v -Werror=format-security -I -Wall . -Wextra -Werror -I -std=c++11 .. -version -imultiarch -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. i386-linux-gnu -fstack-protector-strong -D_GNU_SOURCE -ffloat-store -D -fasynchronous-unwind-tables HAVE_CONFIG_H -o -D /tmp/ccTnKjbx.s _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/ccXnUH0a.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/cczAODll.s g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp Compiler executable checksum: 25b8ee161683f775815167f9fcaacb88 Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cppGNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-linux-gnu) compiled by GNU C version 12.2.0, -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -g -g -O2 -Wdate-time -Wformat=1GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -ffloat-store -fasynchronous-unwind-tables -o /tmp/cciq2YCj.swarning: 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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp Compiler executable checksum: 25b8ee161683f775815167f9fcaacb88 Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/ccqMfnPl.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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/cctDnMyV.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/ccd37MsT.s Compiler executable checksum: 25b8ee161683f775815167f9fcaacb88 Compiler executable checksum: 25b8ee161683f775815167f9fcaacb88 Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/cc6DFgAY.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 Compiler executable checksum: 25b8ee161683f775815167f9fcaacb88 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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o alignment.o /tmp/cczAODll.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'alignment.' 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-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=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/cc2oJOEg.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o remove_reads_from_amplicon.o /tmp/cctDnMyV.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'remove_reads_from_amplicon.' 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-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=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/cc6QV0Ec.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o call_variants.o /tmp/ccd37MsT.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'call_variants.' 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/cc2RRTat.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o ivar.o /tmp/ccXnUH0a.s GNU assembler version 2.40 (i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o allele_functions.o /tmp/cc2oJOEg.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'ivar.' 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-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=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/ccF59qeu.s COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o suffix_tree.o /tmp/cciq2YCj.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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 assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 Compiler executable checksum: 25b8ee161683f775815167f9fcaacb88 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'allele_functions.' 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-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=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/ccgYZyz2.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o trim_primer_quality.o /tmp/ccqMfnPl.s GNU assembler version 2.40 (i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o get_masked_amplicons.o /tmp/cc6QV0Ec.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'suffix_tree.' 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 -ffloat-store -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Using built-in specs. COLLECT_GCC=g++ Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/12/cc1plus -quiet -v -I . -I .. -imultiarch i386-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=i686 -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 -ffloat-store -fasynchronous-unwind-tables -o /tmp/ccBOgZSi.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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/i386-linux-gnu/c++/12" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/12/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/12 /usr/include/i386-linux-gnu/c++/12 /usr/include/c++/12/backward /usr/lib/gcc/i686-linux-gnu/12/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (i686-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: 25b8ee161683f775815167f9fcaacb88 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'trim_primer_quality.' MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o call_consensus_pileup.o /tmp/ccTnKjbx.s GNU assembler version 2.40 (i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o primer_bed.o /tmp/cc6DFgAY.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'call_consensus_pileup.' MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o interval_tree.o /tmp/ccBOgZSi.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o get_common_variants.o /tmp/cc2RRTat.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'get_common_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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o ref_seq.o /tmp/ccgYZyz2.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'ref_seq.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --gdwarf-5 --32 -o parse_gff.o /tmp/ccF59qeu.s GNU assembler version 2.40 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'parse_gff.' g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -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/i686-linux-gnu/12/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'ivar.' /usr/lib/gcc/i686-linux-gnu/12/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccnpE4LV.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_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o ivar /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-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/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' '-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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -ffloat-store -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 -j8 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 -ffloat-store -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/i686-linux-gnu/12/lto-wrapper Target: i686-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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) MAKEFLAGS=w -j8 -- DESTDIR=/build/ivar-1.3.1+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/12/:/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/12/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'ivar.' /usr/lib/gcc/i686-linux-gnu/12/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccAZZ3t7.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_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o ivar /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-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/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-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' '-ffloat-store' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' '-dumpdir' 'ivar.' make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /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_i386.deb'. dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.3.1+dfsg-7_i386.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_i386.buildinfo dpkg-genchanges --build=binary -O../ivar_1.3.1+dfsg-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/1129 and its subdirectories I: Current time: Wed May 10 15:53:44 -12 2023 I: pbuilder-time-stamp: 1683777224 Thu May 11 03:57:45 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Thu May 11 03:57:45 UTC 2023 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Thu May 11 03:59:01 UTC 2023 I: Deleting $TMPDIR on ionos6-i386.debian.net. Thu May 11 03:59:01 UTC 2023 I: ivar_1.3.1+dfsg-7_i386.changes: Format: 1.8 Date: Thu, 06 Oct 2022 11:17:06 +0200 Source: ivar Binary: ivar ivar-dbgsym ivar-doc Architecture: i386 all Version: 1.3.1+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ivar - functions broadly useful for viral amplicon-based sequencing ivar-doc - functions broadly useful for viral amplicon-based sequencing (doc Changes: ivar (1.3.1+dfsg-7) unstable; urgency=medium . [ Étienne Mollier ] * Mark gcc-12.patch as forwarded. . [ Andreas Tille ] * Packaging update Checksums-Sha1: e73bbce197b6bccff3bd100a69393a0b41eade96 1658944 ivar-dbgsym_1.3.1+dfsg-7_i386.deb d20aa1e329a0c3746e36e7ecb78d7aa9f782a69c 245320 ivar-doc_1.3.1+dfsg-7_all.deb 830dbd7c262f0c8a2a78c703738b049ade9381a5 6046 ivar_1.3.1+dfsg-7_i386.buildinfo 6cf38e3b075624d69910495db66437783f1917d8 221840 ivar_1.3.1+dfsg-7_i386.deb Checksums-Sha256: fbc1141440e61622856926d4a87f778c6df3777feabc22d4177452bb12f14b74 1658944 ivar-dbgsym_1.3.1+dfsg-7_i386.deb 3518e7cde5570bdd36e5692ff1d14aaea832721dcda96928b6ea3a374deb5512 245320 ivar-doc_1.3.1+dfsg-7_all.deb 0709e919490cb1d04a11a5422b32804fbce85a2c0289b5ec09fe2befbae3cedb 6046 ivar_1.3.1+dfsg-7_i386.buildinfo 4bac7d4cb75d518a4775bb5c57b74250a3329fbf8f03c974b12feef87dfdd96e 221840 ivar_1.3.1+dfsg-7_i386.deb Files: 2bc9b0be39bd7ccc7dc988b05526dba5 1658944 debug optional ivar-dbgsym_1.3.1+dfsg-7_i386.deb 44d6d28401f6780f1bf8bc202fef8809 245320 doc optional ivar-doc_1.3.1+dfsg-7_all.deb 87f27422e0aead88c73fb6a56d3f4d4d 6046 science optional ivar_1.3.1+dfsg-7_i386.buildinfo 520a93e88beb41e78c8b9186d87fbb57 221840 science optional ivar_1.3.1+dfsg-7_i386.deb Thu May 11 03:59:02 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/ivar_1.3.1+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/ivar_1.3.1+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/ivar_1.3.1+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/b1/ivar_1.3.1+dfsg-7_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.n5zg7qt0/b2/ivar_1.3.1+dfsg-7_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.328s) 0.328s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.037s) 0.037s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu May 11 03:59:03 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Thu May 11 03:59:03 UTC 2023 I: ivar from bookworm built successfully and reproducibly on i386. Thu May 11 03:59:04 UTC 2023 I: Submitting .buildinfo files to external archives: Thu May 11 03:59:04 UTC 2023 I: Submitting 8.0K b1/ivar_1.3.1+dfsg-7_i386.buildinfo.asc Thu May 11 03:59:05 UTC 2023 I: Submitting 8.0K b2/ivar_1.3.1+dfsg-7_i386.buildinfo.asc Thu May 11 03:59:06 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 11 03:59:06 UTC 2023 I: Done submitting .buildinfo files. Thu May 11 03:59:06 UTC 2023 I: Removing signed ivar_1.3.1+dfsg-7_i386.buildinfo.asc files: removed './b1/ivar_1.3.1+dfsg-7_i386.buildinfo.asc' removed './b2/ivar_1.3.1+dfsg-7_i386.buildinfo.asc'