Sun Jul 4 17:27:35 UTC 2021 I: starting to build ivar/bullseye/i386 on jenkins on '2021-07-04 17:27' Sun Jul 4 17:27:35 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/9948/console.log Sun Jul 4 17:27:35 UTC 2021 I: Downloading source for bullseye/ivar=1.3+dfsg-1 --2021-07-04 17:27:35-- http://cdn-fastly.deb.debian.org/debian/pool/main/i/ivar/ivar_1.3+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2036 (2.0K) Saving to: ‘ivar_1.3+dfsg-1.dsc’ 0K . 100% 120M=0s 2021-07-04 17:27:35 (120 MB/s) - ‘ivar_1.3+dfsg-1.dsc’ saved [2036/2036] Sun Jul 4 17:27:35 UTC 2021 I: ivar_1.3+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ivar Binary: ivar, ivar-doc Architecture: any all Version: 1.3+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/andersen-lab/ivar Standards-Version: 4.5.1 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: 743fcaeac5b42311cb0d7d180932c8caeb0fcb6d 630292 ivar_1.3+dfsg.orig.tar.xz 4ed491f61b0494756f4c9494f6e529a3c271449f 42988 ivar_1.3+dfsg-1.debian.tar.xz Checksums-Sha256: 2d206795c0c3b94e41ea3d9b94d8ac1b8f3d2bbc1fd62b2c8c510475bad81ecc 630292 ivar_1.3+dfsg.orig.tar.xz deff74cce3a60d44b99dc7d1e6d784c42b1c9c78a02496562cab29ef093b12f6 42988 ivar_1.3+dfsg-1.debian.tar.xz Files: c54b862be202ef61b52d8dd7a69908ce 630292 ivar_1.3+dfsg.orig.tar.xz 9a75e6c5f1a30d33bea62971f4e3d017 42988 ivar_1.3+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEE5Qr9Va3SequXFjqLIdIFiZdLPpYFAl/WmVUUHHRtYW5jaWxs QGRlYmlhbi5vcmcACgkQIdIFiZdLPpZ93xAApnVT5YH1slrGuJPlLRScIHq05uyb iyU5SExb3ykxPECG0iBoCX3mfG+HF4ZGTOjdYR0ZfTlroXQmxuyB80dZl3Kkmx1F S4mfL9vMa98EK35Uj80k7U3VUXXIxKugUHBGO4vmWLly0q7VIUEUhDOHi4oKPz2B yWBjjU+8jDLVutGmVxbBUBTX/uMf6A9d9+iXOLYL//GYL00PddDyKFeMYil43Zjg 4kpyMa/37+dfUrarrjLYASn+LPU5ZspnFsT+hCmv4CAr8IVOGa1LLaVCm/RpozDb qpEcrp6JqI+CoqjclQdE4xOF+Q1puqz+2hCrAOvcS6V7zof1OCj7a73wSguT45xY MXDqMMUAj7RIVB+ZAHcQ0v7Bpwirba0htz/UIlEyNvZl0PRwoUkS7j7c2UgJD/e9 rDQHsP9El9Odg7hofQpPEZn9ZVIutWQeGTMOGN3aQHc4jf3OsNFA/1Y86XTQQRNb IXp05no/rcqIZyJUcudZkj/N4VkO+KOg5zuoBJmMj+CD3V84Mnm97gM/805Gp04D bqK4kD9WUt6M1s6qQ3VnZteDI9YELinxbkL5foXLU8AdTa9df/lzlmccIfjHqM0t ExpalhaBLCtOBzNaPvHlVn0h+jdBcw/oW7OjT95rI3tYkD80oHPQs5le+J3tIKZk 3mYXIwXfXGeeu84= =7GaV -----END PGP SIGNATURE----- Sun Jul 4 17:27:35 UTC 2021 I: Checking whether the package is not for us Sun Jul 4 17:27:35 UTC 2021 I: Starting 1st build on remote node ionos12-i386.debian.net. Sun Jul 4 17:27:35 UTC 2021 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Sun Jul 4 17:33:38 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 4 05:27:38 -12 2021 I: pbuilder-time-stamp: 1625419658 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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+dfsg-1.dsc] I: copying [./ivar_1.3+dfsg.orig.tar.xz] I: copying [./ivar_1.3+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Jk5XnzEM/trustedkeys.kbx': General error gpgv: Signature made Sun Dec 13 10:44:37 2020 -12 gpgv: using RSA key E50AFD55ADD27AAB97163A8B21D20589974B3E96 gpgv: issuer "tmancill@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ivar_1.3+dfsg-1.dsc dpkg-source: info: extracting ivar in ivar-1.3+dfsg dpkg-source: info: unpacking ivar_1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.3+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8295/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='f7f8ad1f8d464036ae79eafc9e614917' 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='8295' 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/tmp.c2ggZUUGZE/pbuilderrc_HIQD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/b1 --logfile b1/build.log ivar_1.3+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos12-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-2 (2021-06-21) i686 GNU/Linux I: ls -l /bin total 5780 -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 3 21:29 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/8295/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 ... 19675 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} libicu67{a} libldap-2.4-2{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} libsigsegv2{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 25.2 MB of archives. After unpacking 80.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3 [368 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.3 [471 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Fetched 25.2 MB in 12s (2080 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../10-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... 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Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:i386 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:i386 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-12) ... 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+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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+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+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:12: installing './compile' 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 thread-safe 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... 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 for stdlib.h... (cached) yes checking for GNU libc compatible malloc... no checking for stdlib.h... (cached) yes 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 -j10 make[1]: Entering directory '/build/ivar-1.3+dfsg' make all-recursive make[2]: Entering directory '/build/ivar-1.3+dfsg' Making all in src make[3]: Entering directory '/build/ivar-1.3+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -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 -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Using built-in specs. Using built-in specs. Using built-in specs. Using built-in specs. Using built-in specs. Using built-in specs. Using built-in specs. Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 zstdTarget: i686-linux-gnu gcc version 10.2.1 20210110 (Debian 10.2.1-6) Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC=g++ Target: i686-linux-gnu COLLECT_GCC=g++ Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 Target: i686-linux-gnu Supported LTO compression algorithms: zlibCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' zstdConfigured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 gcc version 10.2.1 20210110 (Debian 10.2.1-6) Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' Using built-in specs. /usr/lib/gcc/i686-linux-gnu/10/cc1plus /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet /usr/lib/gcc/i686-linux-gnu/10/cc1plus -v /usr/lib/gcc/i686-linux-gnu/10/cc1plus -I -quiet -quiet /usr/lib/gcc/i686-linux-gnu/10/cc1plus -v -quiet -I -quiet -v . -I /usr/lib/gcc/i686-linux-gnu/10/cc1plus . /usr/lib/gcc/i686-linux-gnu/10/cc1plus -v /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet . -v -I -I -quiet .. -I -imultiarch -quietCOLLECT_GCC=g++ -I -v .. . -imultiarch -I -I -v .. i386-linux-gnu -v ..Target: i686-linux-gnu -I i386-linux-gnuConfigured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 . -IThread model: posix -I . -imultiarch -D_GNU_SOURCE -I -imultiarch . -D_GNU_SOURCESupported LTO compression algorithms: zlib .. -I -imultiarch .. i386-linux-gnu i386-linux-gnu -D . i386-linux-gnu -I -D zstd -imultiarch -D_GNU_SOURCE -D_GNU_SOURCE HAVE_CONFIG_H -I -D_GNU_SOURCE .. -D HAVE_CONFIG_H i386-linux-gnu -D -D HAVE_CONFIG_H -D HAVE_CONFIG_H .. -imultiarch -imultiarch HAVE_CONFIG_H -D -D_GNU_SOURCEgcc version 10.2.1 20210110 (Debian 10.2.1-6) -D -D HAVE_CONFIG_H _FORTIFY_SOURCE=2 -D i386-linux-gnu i386-linux-gnu -D -D_GNU_SOURCE _FORTIFY_SOURCE=2 _FORTIFY_SOURCE=2 trim_primer_quality.cpp -D -quiet -D suffix_tree.cpp _FORTIFY_SOURCE=2 -D_GNU_SOURCE _FORTIFY_SOURCE=2 get_masked_amplicons.cpp remove_reads_from_amplicon.cpp -dumpbase HAVE_CONFIG_H _FORTIFY_SOURCE=2 -D -quiet _FORTIFY_SOURCE=2 -D alignment.cpp -quiet -quiet -quiet trim_primer_quality.cpp ivar.cpp -mtune=generic -dumpbase HAVE_CONFIG_H suffix_tree.cpp -mtune=generic -march=i686 -auxbase-strip suffix_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccrmsHlC.s call_variants.cpp -dumpbase -dumpbase get_masked_amplicons.cpp -dumpbase -march=i686 -quiet -auxbase-strip -D trim_primer_quality.o _FORTIFY_SOURCE=2 -quiet alignment.cppCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' 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call_consensus_pileup.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc2hqAup.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring duplicate 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GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: Compiler executable checksum: Compiler executable checksum: 660aCompiler executable checksum: 6667660a0a66Compiler executable checksum: 3167670a8831b931676688880ab9b91467b6146d31b6146d311288b612884eb9Compiler executable checksum: 6d4e30b91412b6666d5f30145f4eeeCompiler executable checksum: b512eebe4e0a b630b56d6612304e5f675fbe0a 30675fee3131eeeeb5b5b5bebebe8888 b9b91414b6b66d6d12124e4e30305f5feeeeb5b5bebe Compiler executable checksum: 660a673188b914b66d124e305feeb5be Compiler executable checksum: 660a673188b914b66d124e305feeb5be Compiler executable checksum: 660a673188b914b66d124e305feeb5be COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o alignment.o /tmp/ccRgecDt.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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/10/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 -mtune=generic -march=i686 -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc9YV1GU.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/i386-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/i686-linux-gnu/10/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 660a673188b914b66d124e305feeb5be COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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 .. --32 -o remove_reads_from_amplicon.o /tmp/cc2j5C3J.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o suffix_tree.o /tmp/ccrmsHlC.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o get_masked_amplicons.o /tmp/ccrLw983.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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/10/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 -mtune=generic -march=i686 -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc2myn2y.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/i386-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/i686-linux-gnu/10/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 660a673188b914b66d124e305feeb5be MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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/10/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 -mtune=generic -march=i686 -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccIkoYiL.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/i386-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/i686-linux-gnu/10/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 660a673188b914b66d124e305feeb5be MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o trim_primer_quality.o /tmp/ccmUYpbH.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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/10/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 -mtune=generic -march=i686 -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccYrJCxU.s COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o primer_bed.o /tmp/ccMFibYR.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/../../../../i686-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/i386-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/i686-linux-gnu/10/include /usr/local/include /usr/include/i386-linux-gnu /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o allele_functions.o /tmp/ccovMBDY.s COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o call_variants.o /tmp/cc6erx2O.s Compiler executable checksum: 660a673188b914b66d124e305feeb5be GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o ivar.o /tmp/ccqzXMCn.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o call_consensus_pileup.o /tmp/cc2hqAup.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o get_common_variants.o /tmp/cc9YV1GU.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o interval_tree.o /tmp/ccYrJCxU.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o ref_seq.o /tmp/ccIkoYiL.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' as -v -I . -I .. --32 -o parse_gff.o /tmp/cc2myn2y.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' g++ -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/10/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) MAKEFLAGS=w -j10 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/10/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccxwOQin.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/10/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../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/10/../../.. -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/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' Making all in tests make[3]: Entering directory '/build/ivar-1.3+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/ivar-1.3+dfsg' make[3]: Leaving directory '/build/ivar-1.3+dfsg' make[2]: Leaving directory '/build/ivar-1.3+dfsg' make[1]: Leaving directory '/build/ivar-1.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ivar-1.3+dfsg' dh_auto_test --no-parallel make -j1 check VERBOSE=1 make[2]: Entering directory '/build/ivar-1.3+dfsg' Making check in src make[3]: Entering directory '/build/ivar-1.3+dfsg/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' Making check in tests make[3]: Entering directory '/build/ivar-1.3+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+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -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 -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp g++ -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -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 -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 -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -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+dfsg/tests' make check-TESTS make[4]: Entering directory '/build/ivar-1.3+dfsg/tests' make[5]: Entering directory '/build/ivar-1.3+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 ============================================================================ # TOTAL: 18 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/ivar-1.3+dfsg/tests' make[4]: Leaving directory '/build/ivar-1.3+dfsg/tests' make[3]: Leaving directory '/build/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/ivar-1.3+dfsg' make[3]: Leaving directory '/build/ivar-1.3+dfsg' make[2]: Leaving directory '/build/ivar-1.3+dfsg' make[1]: Leaving directory '/build/ivar-1.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j10 install DESTDIR=/build/ivar-1.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/ivar-1.3+dfsg' Making install in src make[2]: Entering directory '/build/ivar-1.3+dfsg/src' g++ -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/10/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 10.2.1 20210110 (Debian 10.2.1-6) MAKEFLAGS=w -j10 -- DESTDIR=/build/ivar-1.3+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' /usr/lib/gcc/i686-linux-gnu/10/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccmL4teZ.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/10/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../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/10/../../.. -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/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' make[3]: Entering directory '/build/ivar-1.3+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/ivar-1.3+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ivar '/build/ivar-1.3+dfsg/debian/tmp/usr/bin' make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' make[2]: Leaving directory '/build/ivar-1.3+dfsg/src' Making install in tests make[2]: Entering directory '/build/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/ivar-1.3+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+dfsg/tests' make[2]: Leaving directory '/build/ivar-1.3+dfsg/tests' make[2]: Entering directory '/build/ivar-1.3+dfsg' make[3]: Entering directory '/build/ivar-1.3+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+dfsg' make[2]: Leaving directory '/build/ivar-1.3+dfsg' make[1]: Leaving directory '/build/ivar-1.3+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-dbgsym' in '../ivar-dbgsym_1.3+dfsg-1_i386.deb'. dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.3+dfsg-1_all.deb'. dpkg-deb: building package 'ivar' in '../ivar_1.3+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ivar_1.3+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: 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/8295 and its subdirectories I: Current time: Sun Jul 4 05:33:37 -12 2021 I: pbuilder-time-stamp: 1625420017 Sun Jul 4 17:33:38 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net. Sun Jul 4 17:33:38 UTC 2021 I: Preparing to do remote build '2' on ionos16-i386.debian.net. Sun Jul 4 17:34:25 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. Sun Jul 4 17:34:25 UTC 2021 I: ivar_1.3+dfsg-1_i386.changes: Format: 1.8 Date: Sun, 13 Dec 2020 22:18:59 +0100 Source: ivar Binary: ivar ivar-dbgsym ivar-doc Architecture: i386 all Version: 1.3+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: ivar - functions broadly useful for viral amplicon-based sequencing ivar-doc - functions broadly useful for viral amplicon-based sequencing (doc Closes: 977312 Changes: ivar (1.3+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.5.1 (routine-update) * Run test suite in a single thread. (Closes: #977312) Checksums-Sha1: 2439467d4f73c69534ffc92af626576ba822c581 582952 ivar-dbgsym_1.3+dfsg-1_i386.deb 0e2dd25e3642af0d7314d7aaec33df190735e24a 244560 ivar-doc_1.3+dfsg-1_all.deb e5c3a2463f15907b2291873d1e332de1387621e1 5742 ivar_1.3+dfsg-1_i386.buildinfo b4337a8234202ad4780203901d0305883f7a61ab 223060 ivar_1.3+dfsg-1_i386.deb Checksums-Sha256: 0dcf3acd9c591c1f0365f92fd790c024fe3e21ef65b8db7f18cf395c25167be7 582952 ivar-dbgsym_1.3+dfsg-1_i386.deb 888722e8814c09d5b40097403b0649c3d42ba59416f9bcafadc10950e8b5800b 244560 ivar-doc_1.3+dfsg-1_all.deb 8e0048229491b460876774a789ba7cc3533abc8f343bc7850cc8a5e38f69374e 5742 ivar_1.3+dfsg-1_i386.buildinfo 73ca40bb4ea4e54b61364b93b69c2182bea4ba9095944719b26fdb3d766e4d44 223060 ivar_1.3+dfsg-1_i386.deb Files: 94a88331a16c79d56fcef4db6b95bb12 582952 debug optional ivar-dbgsym_1.3+dfsg-1_i386.deb 1d42c882059419ae345872bdfb5bae37 244560 doc optional ivar-doc_1.3+dfsg-1_all.deb dad5cadc7632d6210c3629d24dc2f555 5742 science optional ivar_1.3+dfsg-1_i386.buildinfo b9f44bcc6f25ff01b1f6d108a53c4eb9 223060 science optional ivar_1.3+dfsg-1_i386.deb Sun Jul 4 17:34:26 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/ivar_1.3+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/ivar_1.3+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/ivar_1.3+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/b1/ivar_1.3+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/b2/ivar_1.3+dfsg-1_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: 0.384s) 0.384s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jul 4 17:34:28 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 4 17:34:28 UTC 2021 I: ivar from bullseye built successfully and reproducibly on i386. Sun Jul 4 17:34:29 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jul 4 17:34:29 UTC 2021 I: Submitting 8.0K b1/ivar_1.3+dfsg-1_i386.buildinfo.asc Sun Jul 4 17:34:31 UTC 2021 I: Submitting 8.0K b2/ivar_1.3+dfsg-1_i386.buildinfo.asc Sun Jul 4 17:34:32 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 4 17:34:32 UTC 2021 I: Done submitting .buildinfo files. Sun Jul 4 17:34:32 UTC 2021 I: Removing signed ivar_1.3+dfsg-1_i386.buildinfo.asc files: removed './b1/ivar_1.3+dfsg-1_i386.buildinfo.asc' removed './b2/ivar_1.3+dfsg-1_i386.buildinfo.asc'