Fri Jan 12 09:21:48 UTC 2024 I: starting to build consensuscore/bullseye/i386 on jenkins on '2024-01-12 09:21' Fri Jan 12 09:21:48 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_1/13391/console.log Fri Jan 12 09:21:48 UTC 2024 I: Downloading source for bullseye/consensuscore=1.1.1+dfsg-2 --2024-01-12 09:21:48-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/consensuscore/consensuscore_1.1.1%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2308 (2.3K) [text/prs.lines.tag] Saving to: ‘consensuscore_1.1.1+dfsg-2.dsc’ 0K .. 100% 365M=0s 2024-01-12 09:21:48 (365 MB/s) - ‘consensuscore_1.1.1+dfsg-2.dsc’ saved [2308/2308] Fri Jan 12 09:21:48 UTC 2024 I: consensuscore_1.1.1+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: consensuscore Binary: libconsensuscore-dev, python3-pbconsensuscore Architecture: any-amd64 any-i386 Version: 1.1.1+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/ConsensusCore Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/consensuscore Vcs-Git: https://salsa.debian.org/med-team/consensuscore.git Testsuite: autopkgtest-pkg-python Build-Depends: debhelper-compat (= 12), dh-python, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy Package-List: libconsensuscore-dev deb libdevel optional arch=any-amd64,any-i386 python3-pbconsensuscore deb python optional arch=any-amd64,any-i386 Checksums-Sha1: 06118ce273ef10180336ab071fd86dc60aea7168 363936 consensuscore_1.1.1+dfsg.orig.tar.xz e88b812229bbfcff404c9e930dce5a840d6ef610 8468 consensuscore_1.1.1+dfsg-2.debian.tar.xz Checksums-Sha256: 47865e3769e2d6647003f70ffce68f8a5b2f69a6ae04ff27d106b3ec84660d82 363936 consensuscore_1.1.1+dfsg.orig.tar.xz bc931dbda820f9e53569b0f2b241469cbde70383e2d0feb2d9b8a4efdd5c014f 8468 consensuscore_1.1.1+dfsg-2.debian.tar.xz Files: 17991299008d1c01e25ce3984b7fe7bd 363936 consensuscore_1.1.1+dfsg.orig.tar.xz 8c22a2d4cc3e6be1d328b850456fc88c 8468 consensuscore_1.1.1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl3uSJoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGEkw/7BYKVQBqDrFqBMppsS9QWF1c2yF8+UI5R rlegQEX+DmGGyf0nBUplq4vna78xd8viNsnuxZlVA10zt/DLbUwdW4makp0Zx0Kq lCttykxb8vtWpLr8TjIerYEVM0Y3pJ63tbRteczHjj7+4RLbzW16OBW2tMM1AwoB 0H5EhvtfY6WjclKgZtfnIERYxr/q9dF7SCu01sOO+rU0LxvtDSqji+AEgg2Pdx2C mC/pYi5kT1EeV0px/k/pf/k5ted0cxYpG3ydkwkWHFH/Pfuopn3Z08GBAf/Mu5Dp WSYgOYOsPpwLMsekTRfvdboWOlRZhiw70iCvAzaiUtssorKc1iMMIwNrboCJd12L n/L1RkiUhcFFovRlB3EgliKG8wk0Mm8azyJLB/7DDMK4+9nVeXMtCJF2dAtYTl9N 9vgQuJiV9O7VDj3rh7mh5/AqO9ptbbxtFVi5s3KPMpW0p4gy0l1kpT4yjiUZXOS9 euqz1/U9BCDSl2q7s7ESknXRWrboqXA3LYmfjqZAzDnvCuzirQCXgGCKLuDjYryO GtuiGqLfGyDaFdTxNo31/HKyfi05TSSZL/Uf77MlQTJ/R92/B3BKgBikPZM4tPqj B73UjZLETZ19xoH2cMM28SJlazgArlYeUj1V67aJKEHGWGIgGZdwV6eSqN5q7eey Ma1SBj/6XCo= =9tZA -----END PGP SIGNATURE----- Fri Jan 12 09:21:48 UTC 2024 I: Checking whether the package is not for us Fri Jan 12 09:21:48 UTC 2024 I: Starting 1st build on remote node ionos2-i386.debian.net. Fri Jan 12 09:21:48 UTC 2024 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Fri Jan 12 09:34:58 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 11 21:21:50 -12 2024 I: pbuilder-time-stamp: 1705051310 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [consensuscore_1.1.1+dfsg-2.dsc] I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz] I: copying [./consensuscore_1.1.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Gikd_hvx/trustedkeys.kbx': General error gpgv: Signature made Mon Dec 9 13:14:02 2019 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./consensuscore_1.1.1+dfsg-2.dsc dpkg-source: info: extracting consensuscore in consensuscore-1.1.1+dfsg dpkg-source: info: unpacking consensuscore_1.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking consensuscore_1.1.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying check_boost_version.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20719/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=8 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='82c6769fd435444e8082997bcb05187e' 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='20719' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/pbuilderrc_pUfA --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-2.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 ionos2-i386 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 5844 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 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 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 7 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 Jan 20 2022 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 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 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 Jan 7 09:24 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 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 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 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/20719/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 (= 12), dh-python, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17763 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy 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-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu67{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-setuptools{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} swig{a} swig4.0{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 49.9 MB of archives. After unpacking 302 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 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 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u5 [101 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 tzdata all 2021a-1+deb11u10 [286 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 dh-exec i386 0.23.2 [27.0 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3+deb11u1 [147 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 52 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2+deb11u5 [149 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3+deb11u1 [1960 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libpython3.9 i386 3.9.2-1 [1715 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libpython3.9-dev i386 3.9.2-1 [3822 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libpython3-dev i386 3.9.2-3 [21.7 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libpython3-all-dev i386 3.9.2-3 [1068 B] Get: 62 http://deb.debian.org/debian bullseye/main i386 python3-all i386 3.9.2-3 [1060 B] Get: 63 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 python3.9-dev i386 3.9.2-1 [515 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 python3-dev i386 3.9.2-3 [24.8 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 python3-all-dev i386 3.9.2-3 [1068 B] Get: 67 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-4 [366 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 swig4.0 i386 4.0.2-1 [1443 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 swig all 4.0.2-1 [330 kB] Fetched 49.9 MB in 4s (12.0 MB/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 ... 17763 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:i386 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 18630 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... 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Unpacking libpython3-all-dev:i386 (3.9.2-3) ... Selecting previously unselected package python3-all. Preparing to unpack .../44-python3-all_3.9.2-3_i386.deb ... Unpacking python3-all (3.9.2-3) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../45-zlib1g-dev_1%3a1.2.11.dfsg-2+deb11u2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Selecting previously unselected package python3.9-dev. Preparing to unpack .../46-python3.9-dev_3.9.2-1_i386.deb ... Unpacking python3.9-dev (3.9.2-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../47-python3-dev_3.9.2-3_i386.deb ... Unpacking python3-dev (3.9.2-3) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../48-python3-all-dev_3.9.2-3_i386.deb ... Unpacking python3-all-dev (3.9.2-3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../49-python3-pkg-resources_52.0.0-4_all.deb ... Unpacking python3-pkg-resources (52.0.0-4) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../50-python3-numpy_1%3a1.19.5-1_i386.deb ... Unpacking python3-numpy (1:1.19.5-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../51-python3-setuptools_52.0.0-4_all.deb ... Unpacking python3-setuptools (52.0.0-4) ... Selecting previously unselected package swig4.0. Preparing to unpack .../52-swig4.0_4.0.2-1_i386.deb ... Unpacking swig4.0 (4.0.2-1) ... Selecting previously unselected package swig. Preparing to unpack .../53-swig_4.0.2-1_all.deb ... Unpacking swig (4.0.2-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:i386 (1:5.39-3+deb11u1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3+deb11u1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 12 09:28:03 UTC 2024. Universal Time is now: Fri Jan 12 09:28:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.2.10-2+deb11u5) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up swig4.0 (4.0.2-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up liblapack3:i386 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.21-4) ... Setting up swig (4.0.2-1) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:i386 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... 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 po-debconf (1.0.21+nmu1) ... 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 libpython3.9:i386 (3.9.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:i386 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up dh-exec (0.23.2) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libpython3-dev:i386 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-all (3.9.2-3) ... Setting up libpython3-all-dev:i386 (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-all-dev (3.9.2-3) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-2_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig4.0 PYTHON_INCLUDE = /usr/include/python3.9 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:191:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:192:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:193:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:194:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:195:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:196:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d ar crs /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o touch /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.9 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make test make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' /usr/bin/make -f make/Cpp.mk -j8 make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp:5: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (2 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (2 ms total) [----------] 2 tests from SparseVectorTest [ RUN ] SparseVectorTest.BasicTest [ OK ] SparseVectorTest.BasicTest (0 ms) [ RUN ] SparseVectorTest.BasicTest2 [ OK ] SparseVectorTest.BasicTest2 (0 ms) [----------] 2 tests from SparseVectorTest (0 ms total) [----------] 1 test from SparseVector [ RUN ] SparseVector.CopyTest [ OK ] SparseVector.CopyTest (0 ms) [----------] 1 test from SparseVector (0 ms total) [----------] 7 tests from MutationTest [ RUN ] MutationTest.BasicTest [ OK ] MutationTest.BasicTest (0 ms) [ RUN ] MutationTest.DeleteTest [ OK ] MutationTest.DeleteTest (0 ms) [ RUN ] MutationTest.InsertTest [ OK ] MutationTest.InsertTest (0 ms) [ RUN ] MutationTest.ApplyMutationsTest [ OK ] MutationTest.ApplyMutationsTest (0 ms) [ RUN ] MutationTest.ApplyMutationsToSamePositionTest [ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) [----------] 7 tests from MutationTest (1 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (18 ms) [----------] 2 tests from AffineAlignmentTests (18 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest [ OK ] IupacAlignmentTests.BasicTest (0 ms) [----------] 1 test from IupacAlignmentTests (0 ms total) [----------] 1 test from LinearAlignmentTests [ RUN ] LinearAlignmentTests.BasicTest [ OK ] LinearAlignmentTests.BasicTest (0 ms) [----------] 1 test from LinearAlignmentTests (0 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (1 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest [ OK ] RecursorTest/0.MediumSizedTest (0 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (1 ms) [----------] 7 tests from RecursorTest/0 (2 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (3 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/1 (3 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMismatchTest [ OK ] RecursorTest/2.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest [ OK ] RecursorTest/2.MediumSizedTest (3 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (3 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (3 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (25 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (25 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (31 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (30 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (31 ms) [----------] 5 tests from RecursorFuzzTest/0 (142 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (64 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (66 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (65 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (30 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (31 ms) [----------] 5 tests from RecursorFuzzTest/1 (257 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (73 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (76 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (85 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (23 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (23 ms) [----------] 5 tests from RecursorFuzzTest/2 (280 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (61 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (62 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (63 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (22 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (23 ms) [----------] 5 tests from RecursorFuzzTest/3 (231 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (1 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (1 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest [ OK ] MutationScorerTest/0.BasicTest (0 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest [ OK ] MutationScorerTest/0.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (3 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (1 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (4 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (0 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (3 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (3 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic [ OK ] MatrixTest/0.Basic (0 ms) [ RUN ] MatrixTest/0.Nullability [ OK ] MatrixTest/0.Nullability (0 ms) [ RUN ] MatrixTest/0.Ranges [ OK ] MatrixTest/0.Ranges (0 ms) [ RUN ] MatrixTest/0.IsColumnEmpty [ OK ] MatrixTest/0.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/0.SSE [ OK ] MatrixTest/0.SSE (0 ms) [ RUN ] MatrixTest/0.ToHostArray [ OK ] MatrixTest/0.ToHostArray (0 ms) [ RUN ] MatrixTest/0.NonSequentialAccess [ OK ] MatrixTest/0.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/0.Holes [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 [ OK ] MatrixTest/0.BigBandedMatrix (4 ms) [ RUN ] MatrixTest/0.BigIrregularBandedMatrix [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) [----------] 11 tests from MatrixTest/0 (4 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (10 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) [----------] 11 tests from MatrixTest/1 (10 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (1 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (1 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (6 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (0 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (820 ms) [----------] 8 tests from PoaConsensus (827 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (1 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (0 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (5 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (56 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (61 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (62 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (44 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (5 ms) [----------] 5 tests from QvEvaluatorTest (229 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (2033 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig4.0 PYTHON_INCLUDE = /usr/include/python3.9 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.9 -I /usr/lib/python3/dist-packages/numpy/core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9 creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages/ConsensusCore.py to ConsensusCore.cpython-39.pyc running install_egg_info running egg_info creating build/Python/ConsensusCore.egg-info writing build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_python3 I: dh_python3 fs:343: renaming _ConsensusCore.so to _ConsensusCore.cpython-39-i386-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installinit -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-39-i386-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-2_i386.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2_i386.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../consensuscore_1.1.1+dfsg-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/20719 and its subdirectories I: Current time: Thu Jan 11 21:34:57 -12 2024 I: pbuilder-time-stamp: 1705052097 Fri Jan 12 09:34:58 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Fri Jan 12 09:34:58 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Fri Jan 12 09:38:59 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Fri Jan 12 09:38:59 UTC 2024 I: consensuscore_1.1.1+dfsg-2_i386.changes: Format: 1.8 Date: Mon, 09 Dec 2019 14:01:32 +0100 Source: consensuscore Binary: libconsensuscore-dev python3-pbconsensuscore python3-pbconsensuscore-dbgsym Architecture: i386 Version: 1.1.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libconsensuscore-dev - algorithms for PacBio multiple sequence consensus -- development python3-pbconsensuscore - algorithms for PacBio multiple sequence consensus -- Python 3 Closes: 936328 Changes: consensuscore (1.1.1+dfsg-2) unstable; urgency=medium . * Use 2to3 to convert from Python2 and Python3 Closes: #936328 * Add myself to Uploaders * debhelper-compat 12 * Standards-Version: 4.4.1 * Remove trailing whitespace in debian/copyright Checksums-Sha1: e102947eb2de262906778113159b5974ad0c7693 7021 consensuscore_1.1.1+dfsg-2_i386.buildinfo 15418d51e7871675c0af26d68960b855405b673b 466252 libconsensuscore-dev_1.1.1+dfsg-2_i386.deb 1693daac3a413d1405ac80615a7e26524cfa72e5 9484168 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2_i386.deb 95d2d8ef2599d5d4a8391f132e6fa073edcb7bd1 668180 python3-pbconsensuscore_1.1.1+dfsg-2_i386.deb Checksums-Sha256: 21d7ec036079561580c6d45cfbd9c9f7de44d451137416d58d644caebb221f55 7021 consensuscore_1.1.1+dfsg-2_i386.buildinfo 727d39dedcf8d8f877b629ed1f3a59b8a1e3d7c1853d3e1eb009150c5fd16f7e 466252 libconsensuscore-dev_1.1.1+dfsg-2_i386.deb eea5f43fec80547277ccc8d71e76b1a32c430843d83a8953e2fc15ff7af6da8a 9484168 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2_i386.deb 8ee29393bb160ccc60be62e0f0078a2c4f03a0878139d32ad3516ee00e3f4b05 668180 python3-pbconsensuscore_1.1.1+dfsg-2_i386.deb Files: 0297d99a57a1cae422814e987964bc17 7021 science optional consensuscore_1.1.1+dfsg-2_i386.buildinfo c7e9de982c0a19141e2489c5ef3f0dfb 466252 libdevel optional libconsensuscore-dev_1.1.1+dfsg-2_i386.deb 6100dc8cf1d0d7cc936d9c1b1845db45 9484168 debug optional python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2_i386.deb f901298e373b615c5de37a90490f7095 668180 python optional python3-pbconsensuscore_1.1.1+dfsg-2_i386.deb Fri Jan 12 09:39:00 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/consensuscore_1.1.1+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/consensuscore_1.1.1+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/consensuscore_1.1.1+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/b1/consensuscore_1.1.1+dfsg-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.1ZLsXZ8t/b2/consensuscore_1.1.1+dfsg-2_i386.changes ## close_archive (total time: 0.000s) 0.000s 26 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## command (total time: 616.971s) 287.624s 918 calls readelf 276.545s 113 calls diff 47.237s 132 calls objdump 2.490s 26 calls xz 2.075s 2 calls objcopy 0.637s 22 calls strings 0.311s 11 calls nm 0.025s 14 calls cmp 0.025s 14 calls cmp (external) 0.003s 58 calls cmp (internal) ## compare_files (cumulative) (total time: 1759.013s) 337.781s 1 call abc.DotChangesFile 337.760s 3 calls abc.DebFile 337.659s 6 calls abc.XzFile 336.177s 3 calls abc.DebDataTarFile 333.575s 2 calls abc.ElfFile 70.067s 10 calls diffoscope.comparators.elf.ElfCodeSection 2.964s 33 calls diffoscope.comparators.elf.ElfSection 1.639s 1 call abc.ArFile 1.257s 2 calls diffoscope.comparators.elf.ElfStringSection 0.091s 3 calls abc.TarFile 0.019s 2 calls abc.TextFile 0.014s 3 calls abc.Md5sumsFile 0.009s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 2.735s) 2.490s 26 calls diffoscope.comparators.xz.XzContainer 0.121s 128 calls diffoscope.comparators.deb.DebTarContainer 0.087s 32 calls diffoscope.comparators.deb.DebContainer 0.021s 66 calls diffoscope.comparators.ar.ArContainer 0.015s 28 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 5.065s) 5.065s 1622 calls linediff ## has_same_content_as (total time: 0.033s) 0.027s 35 calls abc.ElfFile 0.002s 3 calls abc.DebDataTarFile 0.001s 8 calls abc.TextFile 0.001s 6 calls abc.Md5sumsFile 0.000s 6 calls abc.XzFile 0.000s 3 calls abc.TarFile 0.000s 3 calls abc.DebFile 0.000s 33 calls diffoscope.comparators.elf.ElfSection 0.000s 1 call abc.ArFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 2 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 542.923s) 542.923s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 26 calls diffoscope.comparators.xz.XzContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## output (total time: 204.763s) 179.636s 1 call html 15.401s 1 call text 9.726s 1 call json ## recognizes (total time: 1.903s) 1.178s 1142 calls diffoscope.comparators.utils.archive.ArchiveMember 0.278s 4472 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.231s 726 calls diffoscope.comparators.elf.ElfSection 0.102s 12 calls diffoscope.comparators.binary.FilesystemFile 0.070s 220 calls diffoscope.comparators.elf.ElfCodeSection 0.024s 324 calls diffoscope.comparators.debian.DebControlMember 0.018s 44 calls diffoscope.comparators.elf.ElfStringSection 0.001s 22 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 48 calls abc.Md5sumsFile 0.000s 10 calls abc.DotChangesFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink ## specialize (total time: 0.527s) 0.527s 113 calls specialize Fri Jan 12 09:48:03 UTC 2024 E: consensuscore failed to build reproducibly in bullseye on i386. Fri Jan 12 09:48:03 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bullseye/i386/consensuscore_1.1.1+dfsg-2.diffoscope.html Fri Jan 12 09:52:49 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Jan 12 09:52:49 UTC 2024 I: Submitting 8.0K b1/consensuscore_1.1.1+dfsg-2_i386.buildinfo.asc Fri Jan 12 09:52:50 UTC 2024 I: Submitting 8.0K b2/consensuscore_1.1.1+dfsg-2_i386.buildinfo.asc Fri Jan 12 09:52:51 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jan 12 09:52:51 UTC 2024 I: Done submitting .buildinfo files. Fri Jan 12 09:52:51 UTC 2024 I: Removing signed consensuscore_1.1.1+dfsg-2_i386.buildinfo.asc files: removed './b1/consensuscore_1.1.1+dfsg-2_i386.buildinfo.asc' removed './b2/consensuscore_1.1.1+dfsg-2_i386.buildinfo.asc'