Mon May 20 19:43:56 UTC 2024 I: starting to build consensuscore/unstable/i386 on jenkins on '2024-05-20 19:43' Mon May 20 19:43:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/12936/console.log Mon May 20 19:43:56 UTC 2024 I: Downloading source for unstable/consensuscore=1.1.1+dfsg-7 --2024-05-20 19:43:56-- http://deb.debian.org/debian/pool/main/c/consensuscore/consensuscore_1.1.1%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2328 (2.3K) [text/prs.lines.tag] Saving to: ‘consensuscore_1.1.1+dfsg-7.dsc’ 0K .. 100% 300M=0s 2024-05-20 19:43:56 (300 MB/s) - ‘consensuscore_1.1.1+dfsg-7.dsc’ saved [2328/2328] Mon May 20 19:43:56 UTC 2024 I: consensuscore_1.1.1+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: consensuscore Binary: libconsensuscore-dev, python3-pbconsensuscore Architecture: any Version: 1.1.1+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/ConsensusCore Standards-Version: 4.6.2 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 (= 13), architecture-is-64-bit [!i386], architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev Package-List: libconsensuscore-dev deb libdevel optional arch=any python3-pbconsensuscore deb python optional arch=any Checksums-Sha1: 06118ce273ef10180336ab071fd86dc60aea7168 363936 consensuscore_1.1.1+dfsg.orig.tar.xz 411978f41eeb4990333b4d58ef5f0774e79e8a89 10136 consensuscore_1.1.1+dfsg-7.debian.tar.xz Checksums-Sha256: 47865e3769e2d6647003f70ffce68f8a5b2f69a6ae04ff27d106b3ec84660d82 363936 consensuscore_1.1.1+dfsg.orig.tar.xz a3a14e0f188d22d3e7d77cf5f7f0d1cf1575a3bc71c04336bc2392f1c5889057 10136 consensuscore_1.1.1+dfsg-7.debian.tar.xz Files: 17991299008d1c01e25ce3984b7fe7bd 363936 consensuscore_1.1.1+dfsg.orig.tar.xz f424059779de3d65f09a18cd2d9b316e 10136 consensuscore_1.1.1+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYAT9YACgkQPCZ2P2xn 5uLqtxAAv/8Q251QRDNHDdqMMcx8g8pSgdWkI3CtNY4XoZ1rSJEFBLxaSt0pZf60 l2bMZHGH7SohyqrWnXsrsUwByyQpvMC7rgstBjM7N8TFT3O8Q4G2GnugHixFvMet XUr5BlGb8XnNCKy8Bjh6JDJrlv1Ipnvo+u1GEhiW4Jb5QAteecxq1Zo9hFlacF0Y +XYvu4T4JzkAFIxTo1AqtCtj5yZU0kukc8pR4qQaX0gp00EvHwejZT2oa32w893S y4davnj8VSy6VSZZpjp1SWN4t/uG9LjsxU5Hw7vnSHmk+HYEMUSuugl5wCf/7g99 C9uFrV62DeMr5qp4XmRQqy0AmmvFidJeSh2NbEzBbHytSRIHJjjDckuZBcqn9JlL 5JFZQFjOpjCShSOTePMZ6unbHPYCq9cQAk715bmRpktr5ZzzBLAAiWZ7kFY7rpka fSfd52Uy71bYnNUSwGkjXA+lM7fL0cvTUdW2InUsYNU9/BBvhXuipc0VO1tzbyYO Zv6X3lVW5YjiS83od/DLKPdOxOtbBFVVYBN8LQywP2/v9495OnXJQvezpUALr1W5 WvHU8wRFU2JOBakTacVOGkcCDOvfQnWtT5owQzyEpvBTebgaRjYQpduhLyNFihi4 4j0DH0ds42WZEyKKEOMCBhwD0AVE1MiRzbIn636zrYGlqJ0ZyPI= =uv0b -----END PGP SIGNATURE----- Mon May 20 19:43:56 UTC 2024 I: Checking whether the package is not for us Mon May 20 19:43:56 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Mon May 20 19:43:56 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Mon May 20 19:50:38 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 22 14:06:55 -12 2025 I: pbuilder-time-stamp: 1750644415 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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-7.dsc] I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz] I: copying [./consensuscore_1.1.1+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 24 16:07:50 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-7.dsc: no acceptable signature found 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-7.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 dpkg-source: info: applying sequence_setuptools.patch dpkg-source: info: applying portable_simd.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/75291/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 parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5a2cfb23372b48af98aa94d2cc6c7d2f' 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='75291' 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.mygvBpB5/pbuilderrc_9XDn --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mygvBpB5/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-7.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 21 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/75291/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19703 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 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. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} 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} libboost1.83-dev{a} libdata-optlist-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libparams-util-perl{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libsimde-dev{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{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} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} swig{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, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 69.7 MB of archives. After unpacking 415 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.11-minimal i386 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.11-minimal i386 3.11.9-1 [1918 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpython3.11-stdlib i386 3.11.9-1 [1795 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 python3.11 i386 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 13 http://deb.debian.org/debian unstable/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.3-1 [2224 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.1-1 [98.5 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 architecture-properties i386 0.1.1+b1 [1900 B] Get: 27 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libparams-util-perl i386 1.102-3 [24.4 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libsub-install-perl all 0.929-1 [10.5 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libsub-prototype-perl i386 0.03-2+b2 [9756 B] Get: 41 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.11-1 [10.4 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 44 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 dh-exec i386 0.30 [26.2 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 python3-distutils all 3.12.3-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240422 [107 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-2.1+b1 [10.6 MB] Get: 60 http://deb.debian.org/debian unstable/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B] Get: 61 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.2-1 [165 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.1.0-1 [733 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libpython3.11t64 i386 3.11.9-1 [1982 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libpython3.11-dev i386 3.11.9-1 [4632 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.11.8-1 [9600 B] Get: 71 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.3-1 [1945 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.3-1 [2141 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.3-1 [5240 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.11.8-1 [1068 B] Get: 75 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.2-1 [465 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.3-1 [659 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.11.8-1 [1056 B] Get: 78 http://deb.debian.org/debian unstable/main i386 python3.11-dev i386 3.11.9-1 [501 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.11.8-1 [26.1 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.3-1 [499 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.11.8-1 [1072 B] Get: 82 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-10 [5468 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 swig i386 4.2.1-1 [1499 kB] Fetched 69.7 MB in 1s (67.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19703 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.9-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_i386.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:i386 (3.11.9-1) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20019 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_i386.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../5-libreadline8t64_8.2-4_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_i386.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21011 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_i386.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../01-libpython3.12-minimal_3.12.3-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../02-python3.12-minimal_3.12.3-1_i386.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-4_i386.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.1-1_i386.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../11-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.1-1_i386.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package architecture-properties:i386. Preparing to unpack .../13-architecture-properties_0.1.1+b1_i386.deb ... Unpacking architecture-properties:i386 (0.1.1+b1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../16-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../17-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../18-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../23-libparams-util-perl_1.102-3_i386.deb ... Unpacking libparams-util-perl (1.102-3) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../24-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../25-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../26-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libsub-prototype-perl. Preparing to unpack .../27-libsub-prototype-perl_0.03-2+b2_i386.deb ... Unpacking libsub-prototype-perl (0.03-2+b2) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../28-libsub-override-perl_0.11-1_all.deb ... Unpacking libsub-override-perl (0.11-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../29-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../30-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../31-libelf1t64_0.191-1+b1_i386.deb ... Unpacking libelf1t64:i386 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../32-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../33-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../34-libxml2_2.9.14+dfsg-1.3+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../35-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../36-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../37-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../38-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package dh-exec. Preparing to unpack .../39-dh-exec_0.30_i386.deb ... Unpacking dh-exec (0.30) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../40-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../41-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../42-python3-distutils_3.12.3-1_all.deb ... Unpacking python3-distutils (3.12.3-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../43-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../44-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../45-libblas3_3.12.0-3_i386.deb ... Unpacking libblas3:i386 (3.12.0-3) ... Selecting previously unselected package libboost1.83-dev:i386. Preparing to unpack .../46-libboost1.83-dev_1.83.0-2.1+b1_i386.deb ... Unpacking libboost1.83-dev:i386 (1.83.0-2.1+b1) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../47-libboost-dev_1.83.0.2+b2_i386.deb ... Unpacking libboost-dev:i386 (1.83.0.2+b2) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../48-libexpat1-dev_2.6.2-1_i386.deb ... Unpacking libexpat1-dev:i386 (2.6.2-1) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../49-libgfortran5_14.1.0-1_i386.deb ... Unpacking libgfortran5:i386 (14.1.0-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../50-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../51-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../52-libjs-sphinxdoc_7.2.6-7_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-7) ... Selecting previously unselected package liblapack3:i386. Preparing to unpack .../53-liblapack3_3.12.0-3_i386.deb ... Unpacking liblapack3:i386 (3.12.0-3) ... Selecting previously unselected package libpython3.11t64:i386. Preparing to unpack .../54-libpython3.11t64_3.11.9-1_i386.deb ... Unpacking libpython3.11t64:i386 (3.11.9-1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../55-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libpython3.11-dev:i386. Preparing to unpack .../56-libpython3.11-dev_3.11.9-1_i386.deb ... Unpacking libpython3.11-dev:i386 (3.11.9-1) ... Selecting previously unselected package libpython3-dev:i386. Preparing to unpack .../57-libpython3-dev_3.11.8-1_i386.deb ... Unpacking libpython3-dev:i386 (3.11.8-1) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../58-libpython3.12-stdlib_3.12.3-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.3-1) ... Selecting previously unselected package libpython3.12t64:i386. Preparing to unpack .../59-libpython3.12t64_3.12.3-1_i386.deb ... Unpacking libpython3.12t64:i386 (3.12.3-1) ... Selecting previously unselected package libpython3.12-dev:i386. Preparing to unpack .../60-libpython3.12-dev_3.12.3-1_i386.deb ... Unpacking libpython3.12-dev:i386 (3.12.3-1) ... Selecting previously unselected package libpython3-all-dev:i386. Preparing to unpack .../61-libpython3-all-dev_3.11.8-1_i386.deb ... Unpacking libpython3-all-dev:i386 (3.11.8-1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../62-libsimde-dev_0.8.2-1_all.deb ... Unpacking libsimde-dev (0.8.2-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../63-python3.12_3.12.3-1_i386.deb ... Unpacking python3.12 (3.12.3-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../64-python3-all_3.11.8-1_i386.deb ... Unpacking python3-all (3.11.8-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../65-python3.11-dev_3.11.9-1_i386.deb ... Unpacking python3.11-dev (3.11.9-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../66-python3-dev_3.11.8-1_i386.deb ... Unpacking python3-dev (3.11.8-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../67-python3.12-dev_3.12.3-1_i386.deb ... Unpacking python3.12-dev (3.12.3-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../68-python3-all-dev_3.11.8-1_i386.deb ... Unpacking python3-all-dev (3.11.8-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../69-python3-numpy_1%3a1.26.4+ds-10_i386.deb ... Unpacking python3-numpy (1:1.26.4+ds-10) ... Selecting previously unselected package swig. Preparing to unpack .../70-swig_4.2.1-1_i386.deb ... Unpacking swig (4.2.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-2) ... Setting up libsimde-dev (0.8.2-1) ... Setting up libboost1.83-dev:i386 (1.83.0-2.1+b1) ... Setting up swig (4.2.1-1) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:i386 (0.1.1+b1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up libpython3.12-minimal:i386 (3.12.3-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:i386 (0.191-1+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 23 02:07:19 UTC 2025. Universal Time is now: Mon Jun 23 02:07:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... 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 (2.6.2-1) ... Setting up autopoint (0.21-14) ... Setting up libparams-util-perl (1.102-3) ... Setting up libgfortran5:i386 (14.1.0-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libboost-dev:i386 (1.83.0.2+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.12-minimal (3.12.3-1) ... Setting up liblapack3:i386 (3.12.0-3) ... 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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libjs-sphinxdoc (7.2.6-7) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up groff-base (1.23.0-4) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libpython3.12-stdlib:i386 (3.12.3-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:i386 (3.11.9-1) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:i386 (3.12.3-1) ... Setting up libpython3.11-dev:i386 (3.11.9-1) ... Setting up libsub-override-perl (0.11-1) ... Setting up libpython3-stdlib:i386 (3.11.8-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:i386 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:i386 (3.12.3-1) ... Setting up libpython3-all-dev:i386 (3.11.8-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up python3-all (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up dh-exec (0.30) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-numpy (1:1.26.4+ds-10) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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-7_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 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_3.12_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 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_3.11_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config I: pybuild base:311: python3.11 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:311: /usr/bin/python3.12 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/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; 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; 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; 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; 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; 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; 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; 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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.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++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.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++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.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/swig/4.2.1 /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:28: 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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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/python3.12 -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' I: pybuild base:311: /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/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.11 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/swig/4.2.1 /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:28: 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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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/python3.11 -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, 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( | ^~~~~~~~~~~~~~~~~~~~ mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.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. [----------] 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 (7 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 (7 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (65 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (69 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (78 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (48 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (4 ms) [----------] 5 tests from QvEvaluatorTest (264 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (1 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (1 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (0 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 (0 ms) [----------] 7 tests from RecursorTest/0 (0 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 (2 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 (2 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 (2 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 (17 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (17 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (22 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (23 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (23 ms) [----------] 5 tests from RecursorFuzzTest/0 (102 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (57 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (56 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (59 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (24 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (23 ms) [----------] 5 tests from RecursorFuzzTest/1 (219 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (51 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (51 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (61 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (19 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (19 ms) [----------] 5 tests from RecursorFuzzTest/2 (202 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (55 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (57 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (59 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (19 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (19 ms) [----------] 5 tests from RecursorFuzzTest/3 (209 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (0 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (1 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (1 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (1 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 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 (4 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (632 ms) [----------] 8 tests from PoaConsensus (638 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 (0 ms) [----------] 8 tests from MutationScorerTest/0 (2 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 (0 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 (1 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (3 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 (0 ms) [----------] 8 tests from MutationScorerTest/2 (2 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (1 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 (0 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) [----------] 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 (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (1 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 (0 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 (4 ms total) [----------] 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) [----------] 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 (0 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) [----------] 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) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (1690 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 dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 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/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.12 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/swig/4.2.1 /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:28: 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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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/python3.12 -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 /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_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/python3.12 creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore.py to ConsensusCore.cpython-312.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' adding license file 'LICENSES' 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/python3.12/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:311: /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/swig/4.2.1 PYTHON_INCLUDE = /usr/include/python3.11 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/swig/4.2.1 /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:28: 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 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -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/python3.11 -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 /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11 creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages/ConsensusCore.py to ConsensusCore.cpython-311.pyc running install_egg_info running 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 reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' adding license file 'LICENSES' 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/python3.11/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' find debian -name meson.build -delete make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 fs:418: renaming _ConsensusCore.so to _ConsensusCore.cpython-311-i386-linux-gnu.so I: dh_python3 fs:418: renaming _ConsensusCore.so to _ConsensusCore.cpython-312-i386-linux-gnu.so debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' 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 -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild 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 dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_i386.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7_i386.deb'. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-7_i386.deb'. dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-7_i386.buildinfo dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/75291 and its subdirectories I: Current time: Sun Jun 22 14:13:34 -12 2025 I: pbuilder-time-stamp: 1750644814 Mon May 20 19:50:39 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Mon May 20 19:50:39 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Mon May 20 20:00:39 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Mon May 20 20:00:39 UTC 2024 I: consensuscore_1.1.1+dfsg-7_i386.changes: Format: 1.8 Date: Sun, 24 Mar 2024 17:07:25 +0100 Source: consensuscore Binary: libconsensuscore-dev python3-pbconsensuscore python3-pbconsensuscore-dbgsym Architecture: i386 Version: 1.1.1+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libconsensuscore-dev - algorithms for PacBio multiple sequence consensus -- development python3-pbconsensuscore - algorithms for PacBio multiple sequence consensus -- Python 3 Changes: consensuscore (1.1.1+dfsg-7) unstable; urgency=medium . * Team upload. * d/control: resume building on i386. * d/rules: add openmp-simd and -O3 flags. Checksums-Sha1: 104a7db58719a5fb68c0e5fe0986f514890c23cf 7141 consensuscore_1.1.1+dfsg-7_i386.buildinfo 77daf3f196bfe3c15c6ece1599edfa6a01ba330d 499132 libconsensuscore-dev_1.1.1+dfsg-7_i386.deb 4ca385d481e0fd3daf8576bc870c483f0cc0f987 16567028 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_i386.deb 9089a9dc09dfede914c91486aac4e01d17bc172f 927100 python3-pbconsensuscore_1.1.1+dfsg-7_i386.deb Checksums-Sha256: 2bcac9f2d92bd7e312f75fdf63f51286fb5b9858755a2b0634a4ed1dc31adf4f 7141 consensuscore_1.1.1+dfsg-7_i386.buildinfo 9135fb387d5fd3cbab75c41a182f8684d364b66332ac86cf87c5dd0b62000c20 499132 libconsensuscore-dev_1.1.1+dfsg-7_i386.deb 33b47f0dae6512ee5de5242649851dcbbd92b8f5a7664e6534b69bd04c0f0e43 16567028 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_i386.deb 63cdc50f6d814af8c80b1f4dbf67547394e8b1ef3320d66ff0b8a7dade85da1c 927100 python3-pbconsensuscore_1.1.1+dfsg-7_i386.deb Files: 1334bf6b5d749066f0baefeb8d9a1770 7141 science optional consensuscore_1.1.1+dfsg-7_i386.buildinfo 4d00ef7240e832271932292b82f65a23 499132 libdevel optional libconsensuscore-dev_1.1.1+dfsg-7_i386.deb 835afdd62cda29f30bad3a3835f8086d 16567028 debug optional python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7_i386.deb b3d9a6bcd0e29f8eaa2bbd094567a45a 927100 python optional python3-pbconsensuscore_1.1.1+dfsg-7_i386.deb Mon May 20 20:00:40 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_11-12936.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.mygvBpB5/consensuscore_1.1.1+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.mygvBpB5/consensuscore_1.1.1+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.mygvBpB5/consensuscore_1.1.1+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.mygvBpB5/b1/consensuscore_1.1.1+dfsg-7_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.mygvBpB5/b2/consensuscore_1.1.1+dfsg-7_i386.changes ## close_archive (total time: 0.001s) 0.000s 28 calls diffoscope.comparators.xz.XzContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 10 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## command (total time: 1541.591s) 710.615s 2162 calls readelf 703.076s 246 calls diff 114.293s 300 calls objdump 5.993s 88 calls xz 5.630s 4 calls objcopy 1.593s 55 calls strings 0.317s 11 calls nm 0.034s 14 calls cmp 0.034s 14 calls cmp (external) 0.005s 56 calls cmp (internal) ## compare_files (cumulative) (total time: 5501.952s) 1026.723s 1 call abc.DotChangesFile 1026.674s 3 calls abc.DebFile 1026.488s 6 calls abc.XzFile 1023.962s 3 calls abc.DebDataTarFile 1021.211s 5 calls abc.ElfFile 366.443s 20 calls diffoscope.comparators.elf.ElfCodeSection 7.803s 71 calls diffoscope.comparators.elf.ElfSection 1.513s 7 calls diffoscope.comparators.elf.ElfStringSection 0.936s 1 call abc.ArFile 0.126s 3 calls abc.TarFile 0.027s 2 calls abc.TextFile 0.024s 2 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.023s 3 calls abc.Md5sumsFile ## container_extract (total time: 6.564s) 5.987s 28 calls diffoscope.comparators.xz.XzContainer 0.341s 134 calls diffoscope.comparators.deb.DebTarContainer 0.181s 34 calls diffoscope.comparators.deb.DebContainer 0.035s 66 calls diffoscope.comparators.ar.ArContainer 0.019s 28 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 18.432s) 18.432s 3498 calls linediff ## has_same_content_as (total time: 0.047s) 0.039s 38 calls abc.ElfFile 0.003s 3 calls abc.DebDataTarFile 0.001s 8 calls abc.TextFile 0.001s 6 calls abc.Md5sumsFile 0.001s 71 calls diffoscope.comparators.elf.ElfSection 0.001s 6 calls abc.XzFile 0.000s 3 calls abc.TarFile 0.000s 3 calls abc.DebFile 0.000s 1 call abc.ArFile 0.000s 1 call abc.DotChangesFile 0.000s 20 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 7 calls diffoscope.comparators.elf.ElfStringSection 0.000s 2 calls diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 1373.425s) 1373.424s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 28 calls diffoscope.comparators.xz.XzContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 10 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## output (total time: 346.107s) 295.600s 1 call html 29.398s 1 call text 21.109s 1 call json ## recognizes (total time: 4.858s) 3.799s 1180 calls diffoscope.comparators.utils.archive.ArchiveMember 0.773s 4862 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.219s 12 calls diffoscope.comparators.binary.FilesystemFile 0.068s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.411s) 0.411s 170 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 22min 53.820s CPU time consumed: 26min 53.647s Mon May 20 20:24:03 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Mon May 20 20:24:03 UTC 2024 E: consensuscore failed to build reproducibly in unstable on i386. Mon May 20 20:36:44 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 20 20:36:44 UTC 2024 I: Submitting 8.0K b1/consensuscore_1.1.1+dfsg-7_i386.buildinfo.asc Mon May 20 20:36:45 UTC 2024 I: Submitting 8.0K b2/consensuscore_1.1.1+dfsg-7_i386.buildinfo.asc Mon May 20 20:36:45 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 20 20:36:45 UTC 2024 I: Done submitting .buildinfo files. Mon May 20 20:36:45 UTC 2024 I: Removing signed consensuscore_1.1.1+dfsg-7_i386.buildinfo.asc files: removed './b1/consensuscore_1.1.1+dfsg-7_i386.buildinfo.asc' removed './b2/consensuscore_1.1.1+dfsg-7_i386.buildinfo.asc'