Tue Apr 22 07:59:08 UTC 2025 I: starting to build consensuscore/unstable/amd64 on jenkins on '2025-04-22 07:58' Tue Apr 22 07:59:08 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/52393/console.log Tue Apr 22 07:59:08 UTC 2025 I: Downloading source for unstable/consensuscore=1.1.1+dfsg-8 --2025-04-22 07:59:08-- http://deb.debian.org/debian/pool/main/c/consensuscore/consensuscore_1.1.1%2bdfsg-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2372 (2.3K) [text/prs.lines.tag] Saving to: ‘consensuscore_1.1.1+dfsg-8.dsc’ 0K .. 100% 356M=0s 2025-04-22 07:59:08 (356 MB/s) - ‘consensuscore_1.1.1+dfsg-8.dsc’ saved [2372/2372] Tue Apr 22 07:59:08 UTC 2025 I: consensuscore_1.1.1+dfsg-8.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-8 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, python3-numpy-dev, 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 295d4089d3f91afce437f8da9d4e96e85a8e4355 10280 consensuscore_1.1.1+dfsg-8.debian.tar.xz Checksums-Sha256: 47865e3769e2d6647003f70ffce68f8a5b2f69a6ae04ff27d106b3ec84660d82 363936 consensuscore_1.1.1+dfsg.orig.tar.xz c6bca19d3f472d6c97567c42c6c677b2183a2d8086fd369e80cf46e9d781ef83 10280 consensuscore_1.1.1+dfsg-8.debian.tar.xz Files: 17991299008d1c01e25ce3984b7fe7bd 363936 consensuscore_1.1.1+dfsg.orig.tar.xz 5d616d8f06b526982012d298c45aa7d6 10280 consensuscore_1.1.1+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmgGNmIRHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBq4XA//bcI91SPBNTxHy/quKBMfF4T3ZZiWAHAF FVfbF6EbJqJILDeaXYGh38hdhXzTco/obJG7M7vH2SewPmF0A0juo7gOaWo/RO9o ovi13jIXzyYaYd0GOlUL1YJ5THSphPK0Mv9nwhRUZ6FjWCA6jI9ejzvzfcmPf++n sruEvyW0dTr+/921DUgMDRy0PbLs0V1sPZk3/OpqiRoMOPpiTLXU/SSIQDeZN0qX YJpgGs1SuOaAiu8hQo3vcM6xF4XDVxE5FP4OHENS807gDesbGIjisAuYDks2vZyj WZErGEgB9BoKwvbPUEWgJkiD6niuhvJUwSupz5I9TgO86zNspahW/V/SVHXbIl+D 7iaou+b3cFKVZ+u3hICuGNYVrOyFwQWrOwLKALatvDOtn7D253dlI6dftnGCjhs5 vJ3D3ezkNDRb/vrzoIIMROqtMfkd0kVDC/mbTWCceYbxdXQZovzOlc6Ms2Cw5xDZ 6QeAJ6owWy4Mzd5MX2K1xf+YsIh/et2C9BaEx6u1aIjPUoIu5o8XfItYcelD8YTY XAE3eRz+77+slNC1BcxgD9mll+oK6Fb9xCM5OhCwBscBw0ZyhO1ERN9NwD9YvT22 wOVn+EwkhzzLkjSxXRQ6EqrCVpcfNrI0g0J9CqwDoCjf2n+E8GsJ0skHwRjrA312 VptyoWtLIA8= =CHSG -----END PGP SIGNATURE----- Tue Apr 22 07:59:08 UTC 2025 I: Checking whether the package is not for us Tue Apr 22 07:59:08 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Tue Apr 22 07:59:09 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Tue Apr 22 08:04:57 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 21 19:59:10 -12 2025 I: pbuilder-time-stamp: 1745308750 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: Copying source file I: copying [consensuscore_1.1.1+dfsg-8.dsc] I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz] I: copying [./consensuscore_1.1.1+dfsg-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-8.dsc: unsupported subcommand 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-8.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/774675/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='191faedf0ee741c1964df560b6092233' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='774675' 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.CmI7CoVl/pbuilderrc_KHBy --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.CmI7CoVl/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-8.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-33-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.133-1 (2025-04-10) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/774675/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, python3-numpy-dev, 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 ... 19839 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-64-bit; however: Package architecture-is-64-bit 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 python3-numpy-dev; however: Package python3-numpy-dev 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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{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-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-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, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 49.6 MB of archives. After unpacking 329 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-2 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 31 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.3-2 [2156 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.3-2 [5015 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.3-1 [10.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.3-1 [1068 B] Get: 63 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.3-1 [1048 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.3-2 [508 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.3-1 [26.1 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.3-1 [1068 B] Get: 68 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.0-1.2 [224 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.0-1.2 [738 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-1 [1503 kB] Fetched 49.6 MB in 4s (12.4 MB/s) Preconfiguring packages ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libboost1.83-dev:amd64 (1.83.0-4.2) ... Setting up swig (4.3.0-1) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 22 07:59:38 UTC 2025. Universal Time is now: Tue Apr 22 07:59:38 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.7.1-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-1) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up libpython3.13:amd64 (3.13.3-2) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... 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Setting up python3-all-dev (3.13.3-1) ... Setting up python3-setuptools (78.1.0-1.2) ... Processing triggers for libc-bin (2.41-7) ... 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-8_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild debian/rules execute_before_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' ! test -f src/SWIG/numpy.i.orig || mv -v src/SWIG/numpy.i.orig src/SWIG/numpy.i make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 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_3.13_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' 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: python3.13 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' test -f src/SWIG/numpy.i.orig || mv -v src/SWIG/numpy.i src/SWIG/numpy.i.orig renamed 'src/SWIG/numpy.i' -> 'src/SWIG/numpy.i.orig' cp /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/numpy.i src/SWIG/numpy.i make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_auto_build -O--buildsystem=pybuild 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/4.3.0 PYTHON_INCLUDE = /usr/include/python3.13 NUMPY_INCLUDE = /usr/lib/x86_64-linux-gnu/python3-numpy/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 190 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 191 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:192:16: required from here 192 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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::SimpleRecursor; EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:193:16: required from here 193 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:194:16: required from here 194 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:195:16: required from here 195 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:196:16: required from here 196 | template class MutationScorer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } catch (AlphaBetaMismatchException e) { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ar crs /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.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++/LinearAlignment.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/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp: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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/python3.13 -I /usr/lib/x86_64-linux-gnu/python3-numpy/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/TestQvEvaluator.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/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.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. [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (33 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (35 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (38 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (27 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (2 ms) [----------] 5 tests from QvEvaluatorTest (135 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 (1 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 (2 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 (2 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 (2 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (11 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (11 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (12 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (18 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (17 ms) [----------] 5 tests from RecursorFuzzTest/0 (69 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (35 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (36 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (36 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (17 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (17 ms) [----------] 5 tests from RecursorFuzzTest/1 (142 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (36 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (38 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (43 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (12 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (13 ms) [----------] 5 tests from RecursorFuzzTest/2 (142 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (34 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (35 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (35 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (13 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (12 ms) [----------] 5 tests from RecursorFuzzTest/3 (129 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (0 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (1 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (1 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 (0 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (487 ms) [----------] 8 tests from PoaConsensus (492 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) [----------] 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) [----------] 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 (0 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 (1 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 (3 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) [----------] 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 (1 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 (1 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 (5 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 (5 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 (1 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 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 (2 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 (0 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (2 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (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 (2 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 (9 ms) [----------] 2 tests from AffineAlignmentTests (9 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 (1 ms) [----------] 1 test from LinearAlignmentTests (1 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (1148 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' /usr/bin/make test-python make[2]: Entering 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/Python SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp: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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/python3.13 -I /usr/lib/x86_64-linux-gnu/python3-numpy/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 1.0.2 Python3 build is OK! 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 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/4.3.0 PYTHON_INCLUDE = /usr/include/python3.13 NUMPY_INCLUDE = /usr/lib/x86_64-linux-gnu/python3-numpy/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/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp: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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/python3.13 -I /usr/lib/x86_64-linux-gnu/python3-numpy/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:90: 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_3.13_pbconsensuscore/build copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages/ConsensusCore.py to ConsensusCore.cpython-313.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/python3.13/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:421: renaming _ConsensusCore.so to _ConsensusCore.cpython-313-x86_64-linux-gnu.so debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. dh_numpy3: warning: skipping binary package libconsensuscore-dev which does not depend on the NumPy C ABI 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 dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-8_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-8_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/774675 and its subdirectories I: Current time: Mon Apr 21 20:04:56 -12 2025 I: pbuilder-time-stamp: 1745309096 Tue Apr 22 08:04:57 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Apr 22 08:04:57 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Apr 22 08:10:56 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Apr 22 08:10:56 UTC 2025 I: consensuscore_1.1.1+dfsg-8_amd64.changes: Format: 1.8 Date: Mon, 21 Apr 2025 13:40:07 +0200 Source: consensuscore Binary: libconsensuscore-dev python3-pbconsensuscore python3-pbconsensuscore-dbgsym Architecture: amd64 Version: 1.1.1+dfsg-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Alexandre Detiste 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-8) unstable; urgency=medium . * Team upload. * Re-enable Python test after py2 -> py3 transition * Clean better * Fix dh_numpy invocation Checksums-Sha1: 59be435fb467051a759407c699d81ed67ed6ed19 6934 consensuscore_1.1.1+dfsg-8_amd64.buildinfo 5cacd6e219a7f389e9d2c91028de676a4750a4a1 486080 libconsensuscore-dev_1.1.1+dfsg-8_amd64.deb 38d50b9e46177d47993f98fd4c2115d18b5d6419 9235656 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-8_amd64.deb 5da1f47cde1e92fe245f677ceca2241e21a33724 723788 python3-pbconsensuscore_1.1.1+dfsg-8_amd64.deb Checksums-Sha256: 62ec6df905d4f4e60b3708168ffc0b0d86e5bcdca7da6060a18e6651601cfb97 6934 consensuscore_1.1.1+dfsg-8_amd64.buildinfo 155cdf903331775ff67ad666011cf7542b1d6edcb7235316d75851a83eda7ba2 486080 libconsensuscore-dev_1.1.1+dfsg-8_amd64.deb 5f87d8158ca92d9117342a213c632105fa9cc2039c82d05fdb90c3b65afb9a15 9235656 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-8_amd64.deb 9885d156699f1042f930eb717f495f058e71af5701a95ca200b76720c771328d 723788 python3-pbconsensuscore_1.1.1+dfsg-8_amd64.deb Files: 4ab64ead7453c1e9bfc68079e1cab6f1 6934 science optional consensuscore_1.1.1+dfsg-8_amd64.buildinfo 1a48c914ce94cfba970ac7722bf8529e 486080 libdevel optional libconsensuscore-dev_1.1.1+dfsg-8_amd64.deb 0d1d65e297087b31f320179b06565321 9235656 debug optional python3-pbconsensuscore-dbgsym_1.1.1+dfsg-8_amd64.deb a37ee48e72ba62e406767f879db877c1 723788 python optional python3-pbconsensuscore_1.1.1+dfsg-8_amd64.deb Tue Apr 22 08:10:57 UTC 2025 I: diffoscope 294 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_27-52393.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.CmI7CoVl/consensuscore_1.1.1+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.CmI7CoVl/consensuscore_1.1.1+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.CmI7CoVl/consensuscore_1.1.1+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.CmI7CoVl/b1/consensuscore_1.1.1+dfsg-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.CmI7CoVl/b2/consensuscore_1.1.1+dfsg-8_amd64.changes ## close_archive (total time: 0.000s) 0.000s 26 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## command (total time: 459.252s) 222.722s 959 calls readelf 208.493s 119 calls diff 24.510s 165 calls objdump 1.626s 2 calls objcopy 1.059s 26 calls xz 0.577s 22 calls strings 0.199s 11 calls nm 0.031s 14 calls cmp 0.030s 14 calls cmp (external) 0.005s 61 calls cmp (internal) ## compare_files (cumulative) (total time: 1441.941s) 276.556s 1 call abc.DotChangesFile 276.514s 3 calls abc.DebFile 276.375s 6 calls abc.XzFile 275.605s 3 calls abc.DebDataTarFile 268.429s 2 calls abc.ElfFile 58.687s 10 calls diffoscope.comparators.elf.ElfCodeSection 6.091s 1 call abc.ArFile 2.547s 33 calls diffoscope.comparators.elf.ElfSection 0.974s 3 calls diffoscope.comparators.elf.ElfStringSection 0.112s 3 calls abc.TarFile 0.021s 3 calls abc.Md5sumsFile 0.019s 1 call abc.TextFile 0.011s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 1.332s) 1.061s 26 calls diffoscope.comparators.xz.XzContainer 0.131s 126 calls diffoscope.comparators.deb.DebTarContainer 0.097s 32 calls diffoscope.comparators.deb.DebContainer 0.029s 66 calls diffoscope.comparators.ar.ArContainer 0.014s 28 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 6.908s) 6.908s 1518 calls linediff ## has_same_content_as (total time: 0.041s) 0.034s 35 calls abc.ElfFile 0.003s 3 calls abc.DebDataTarFile 0.001s 8 calls abc.TextFile 0.001s 6 calls abc.Md5sumsFile 0.001s 6 calls abc.XzFile 0.000s 3 calls abc.TarFile 0.000s 3 calls abc.DebFile 0.000s 33 calls diffoscope.comparators.elf.ElfSection 0.000s 1 call abc.ArFile 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 3 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 317.607s) 317.606s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 26 calls diffoscope.comparators.xz.XzContainer 0.000s 18 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## output (total time: 40.593s) 22.520s 1 call html 10.695s 1 call text 7.379s 1 call json ## recognizes (total time: 1.225s) 0.528s 1160 calls diffoscope.comparators.utils.archive.ArchiveMember 0.517s 4500 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.108s 12 calls diffoscope.comparators.binary.FilesystemFile 0.072s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.787s) 0.787s 114 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 5min 17.964s CPU time consumed: 6min 27.996s Tue Apr 22 08:16:20 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Apr 22 08:16:20 UTC 2025 E: consensuscore failed to build reproducibly in unstable on amd64. Tue Apr 22 08:20:15 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Apr 22 08:20:15 UTC 2025 I: Submitting 8.0K b1/consensuscore_1.1.1+dfsg-8_amd64.buildinfo.asc Tue Apr 22 08:20:20 UTC 2025 I: Submitting 8.0K b2/consensuscore_1.1.1+dfsg-8_amd64.buildinfo.asc Tue Apr 22 08:20:25 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 22 08:20:25 UTC 2025 I: Done submitting .buildinfo files. Tue Apr 22 08:20:25 UTC 2025 I: Removing signed consensuscore_1.1.1+dfsg-8_amd64.buildinfo.asc files: removed './b1/consensuscore_1.1.1+dfsg-8_amd64.buildinfo.asc' removed './b2/consensuscore_1.1.1+dfsg-8_amd64.buildinfo.asc'