Running as unit: rb-build-amd64_18-53061.service; invocation ID: 00cab672384e49ed84b17891a473f6ad ==================================================================================== Tue Sep 16 09:41:52 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_18) on jenkins, called using "ionos5-amd64 ionos1-amd64" as arguments. Tue Sep 16 09:41:52 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-c0nRYXYj" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 09:41:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Sep 16 09:41:53 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-rEkvA1' Tue Sep 16 09:41:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Tue Sep 16 09:41:53 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-uAyi4c' ok, let's check if gubbins is building anywhere yet… ok, gubbins is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of gubbins in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Tue Sep 16 09:42:15 UTC 2025 I: starting to build gubbins/unstable/amd64 on jenkins on '2025-09-16 09:41' Tue Sep 16 09:42:16 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_18/53061/console.log 1758015736 amd64 unstable gubbins Tue Sep 16 09:42:16 UTC 2025 I: Downloading source for unstable/gubbins=3.4-2 --2025-09-16 09:42:16-- http://deb.debian.org/debian/pool/main/g/gubbins/gubbins_3.4-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2410 (2.4K) [text/prs.lines.tag] Saving to: ‘gubbins_3.4-2.dsc’ 0K .. 100% 231M=0s 2025-09-16 09:42:16 (231 MB/s) - ‘gubbins_3.4-2.dsc’ saved [2410/2410] --2025-09-16 09:42:16-- http://deb.debian.org/debian/pool/main/g/gubbins/gubbins_3.4-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2410 (2.4K) [text/prs.lines.tag] Saving to: ‘gubbins_3.4-2.dsc’ 0K .. 100% 231M=0s 2025-09-16 09:42:16 (231 MB/s) - ‘gubbins_3.4-2.dsc’ saved [2410/2410] Tue Sep 16 09:42:16 UTC 2025 I: gubbins_3.4-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 3.4-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://sanger-pathogens.github.io/gubbins/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/gubbins Vcs-Git: https://salsa.debian.org/med-team/gubbins.git Testsuite: autopkgtest Testsuite-Triggers: iqtree Build-Depends: debhelper-compat (= 13), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox , python3-scipy , python3-multiprocess , python3-wheel Package-List: gubbins deb science optional arch=any Checksums-Sha1: 7af60a6e649cebff6772e3089a8eb8578be91198 2878089 gubbins_3.4.orig.tar.gz d35c87d09ebc60341335c36d02e62471928bfe4d 10608 gubbins_3.4-2.debian.tar.xz Checksums-Sha256: ff134b7c1d06eee548e94f417394fb67229caf1b0d35b097a71309017ac7a91d 2878089 gubbins_3.4.orig.tar.gz eda1745e97e55163d3a1e91432edcc3fec8f5f2479cb589ccc0d8d923601ce1c 10608 gubbins_3.4-2.debian.tar.xz Files: 3c8e6a0d6d119a0b535615747cb76b28 2878089 gubbins_3.4.orig.tar.gz 84c8941c934809255d2719131f9fb966 10608 gubbins_3.4-2.debian.tar.xz Dgit: 2d395af20ba92da6c6cc13954e1cc196cc004dd7 debian archive/debian/3.4-2 https://git.dgit.debian.org/gubbins -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmfBjeIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr2ExAArWns8lVHh8SSVag5Gcp5y4sGz2ZZ krFgpaNX0O7xVk745t7JuY6Gjj2rFq2HEm8xFDib+qybYpTg7pO810YHF0MD3cgf 0khYrKsjAnVZm5B1PUvy+zLgQp/3w8OuTHPyw5V0jJiG7Lwpt9qUMVzVhlEHVhDw cIMAfT5zSI6BSzyyzx3kavn0iQ+5x6ORqLE5lOiP6YaillkB4mJpMvwnifxIfkAH 477WCUniajL62xaKhXSdO8LBc0w4mM2K3zcvontV7Vk1UXTblLoSF/kZN5Y64RkI n4v37dPxJeAbbK4uLeRb54/7o1j6D8l/Pm1vWWPdQn+Yd+LHXy1hXOWrPLb2pEBr CTfwyLrZGh2BWC2BnpdMfHSMD4EvoSZjmkKUWQn0icbfh/3ypenguD0Cc5p8jT1s iIlj7qPRF2VG+orvCXPs26sblpFxre6A9zZ8MVwHGsvw5pVcrZzMsF8IwQ+nTlnd WQBNsZKGRMO2IXzdMBDz5WB5tmLZC8tXfvYELVeHVMeNNskE6q/cVHVcwjk/cv9T cEMzPnRCpvQxjERwGQML+MjdvA+GAXt/oCo7hLxOy5ZrB9fqfpucbi//bjF1GkPX /jp4XygdnrKzlPDW9ccwvJDNpkXjf5f3Q+IDDqSh2MhxQXsP8E0DCRpdPLGrlwT0 iv1E883lsFpyBhA= =qf6J -----END PGP SIGNATURE----- Tue Sep 16 09:42:16 UTC 2025 I: Checking whether the package is not for us Tue Sep 16 09:42:16 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Sep 16 09:42:16 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Sep 16 09:42:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Sep 16 09:42:16 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-X2fPV6' ==================================================================================== Mon Oct 19 16:05:17 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 gubbins unstable /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU 3.4-2" as arguments. Mon Oct 19 16:05:17 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-CqMyxMdT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Oct 19 16:05:17 UTC 2026 I: Downloading source for unstable/gubbins=3.4-2 Reading package lists... NOTICE: 'gubbins' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gubbins.git Please use: git clone https://salsa.debian.org/med-team/gubbins.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2891 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (tar) [2878 kB] Get:3 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (diff) [10.6 kB] Fetched 2891 kB in 0s (55.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'gubbins' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gubbins.git Please use: git clone https://salsa.debian.org/med-team/gubbins.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2891 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (tar) [2878 kB] Get:3 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (diff) [10.6 kB] Fetched 2891 kB in 0s (55.9 MB/s) Download complete and in download only mode ============================================================================= Building gubbins in unstable on amd64 on ionos5-amd64 now. Date: Mon Oct 19 16:05:17 UTC 2026 Date UTC: Mon Oct 19 16:05:17 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 19 04:05:17 -12 2026 I: pbuilder-time-stamp: 1792425917 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 [gubbins_3.4-2.dsc] I: copying [./gubbins_3.4.orig.tar.gz] I: copying [./gubbins_3.4-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-2.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.4 dpkg-source: info: unpacking gubbins_3.4.orig.tar.gz dpkg-source: info: unpacking gubbins_3.4-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch dpkg-source: info: applying gubbins_exe_in_usr_lib.patch dpkg-source: info: applying iqtree2.patch dpkg-source: info: applying autoupdate_configure.ac.patch dpkg-source: info: applying python3-shebang.patch dpkg-source: info: applying remove-numba-temporarily.patch dpkg-source: info: applying numpy2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2920459/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='51a33e633d884bee8fb421f0cff5eaa2' 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='2920459' 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.Q8PzurSU/pbuilderrc_cCrn --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.Q8PzurSU/b1 --logfile b1/build.log gubbins_3.4-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2920459/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), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox, python3-scipy, python3-multiprocess, python3-wheel dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on iqtree; however: Package iqtree is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-reportlab; however: Package python3-reportlab is not installed. pbuilder-satisfydepends-dummy depends on tox; however: Package tox is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-multiprocess; however: Package python3-multiprocess is not installed. pbuilder-satisfydepends-dummy depends on python3-wheel; however: Package python3-wheel is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} iqtree{a} libabsl20240722{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs1{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-sphinxdoc{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenjp2-7{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libxrender1{a} libyuv0{a} libz3-4{a} libze1{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-biopython{a} python3-cachetools{a} python3-cairo{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-decorator{a} python3-dendropy{a} python3-dill{a} python3-distlib{a} python3-filelock{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pip-whl{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyproject-api{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-whl{a} python3-typeguard{a} python3-typing-extensions{a} python3-virtualenv{a} python3-wheel{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sgml-base{a} tox{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-dev python3-olefile python3-pooch python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 153 MB of archives. After unpacking 615 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libsubunit0 amd64 1.4.2-3+b1 [6436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsubunit-dev amd64 1.4.2-3+b1 [7352 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 check amd64 0.15.2-3 [113 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 67 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 84 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 iqtree amd64 2.0.7+dfsg-1+b2 [3652 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 python3-cachetools all 5.3.3-1 [13.2 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 python3-dill all 0.4.0-1 [83.7 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 python3-distlib all 0.4.0-1 [257 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-filelock all 3.19.1-1 [12.6 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-multiprocess all 0.70.17-1 [107 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-pip-whl all 25.2+dfsg-1 [1428 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-api all 1.9.1-1 [42.3 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-setuptools-whl all 78.1.1-0.1 [1268 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-virtualenv all 20.34.0+ds-1 [75.9 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 tox all 4.25.0-1 [401 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 153 MB in 32s (4815 kB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... 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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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 19 16:07:55 UTC 2026. Universal Time is now: Mon Oct 19 16:07:55 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.1-7) ... 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 libpkgconf3:amd64 (1.8.1-4) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (4.4.0-3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.50-1) ... 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Setting up python3-cachetools (5.3.3-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-charset-normalizer (3.4.3-1) ... Setting up python3-pyproject-api (1.9.1-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-virtualenv (20.34.0+ds-1) ... Setting up debhelper (13.26) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-wheel (0.46.1-2) ... Setting up python3-pil:amd64 (11.3.0-1) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.4.3-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up tox (4.25.0-1) ... Setting up libamdhip64-5:amd64 (5.7.1-6) ... Setting up libucx0:amd64 (1.19.0+ds-1) ... Setting up libopenmpi40:amd64 (5.0.8-9) ... Setting up iqtree (2.0.7+dfsg-1+b2) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-5) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/gubbins-3.4/ && 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 > ../gubbins_3.4-2_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete rm -rf python/output_alignment python/tmp* tests/.deps make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:29: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking how to create a pax tar archive... gnutar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/x86_64-linux-gnu-ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/x86_64-linux-gnu-ld -m elf_x86_64 checking if the linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether to build with code coverage support... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for zlib.h... yes checking for math.h... yes checking for a Python interpreter with version >= 3.8... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.13 checking for python3 platform... linux checking for GNU default python3 prefix... ${prefix} checking for GNU default python3 exec_prefix... ${exec_prefix} checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.13/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.13/site-packages checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o main.o main.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o Newickform.lo Newickform.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alignment_file.lo alignment_file.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o block_tab_file.lo block_tab_file.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o branch_sequences.lo branch_sequences.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o string_cat.lo string_cat.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time 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-I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parse_vcf.lo parse_vcf.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o seqUtil.lo seqUtil.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o snp_searching.lo snp_searching.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o snp_sites.lo snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tree_statistics.lo tree_statistics.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tree_scaling.lo tree_scaling.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o vcf.lo vcf.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o csv_of_snp_sites.lo csv_of_snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -fPIC -DPIC -o .libs/vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -fPIC -DPIC -o .libs/csv_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -o string_cat.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -o gff_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -o csv_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -o gubbins.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -o snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -o vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -o snp_searching.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c alignment_file.c -o alignment_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -o Newickform.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o .libs/csv_of_snp_sites.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o csv_of_snp_sites.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm -pthread make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making all in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' # make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test) cp -a tests/data tests/data.save dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make run_all_tests make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[5]: Entering directory '/build/reproducible-path/gubbins-3.4/src' PASS: run_all_tests ============================================================================ Testsuite summary for gubbins package_version ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making check in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' rm -rf tests/data mv tests/data.save tests/data make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.4/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making install in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making install in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' # pybuild --install --system=distutils cd python && \ python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License (GPL) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() 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 build running build_py creating build/lib/gubbins copying gubbins/run_gubbins.py -> build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/pyjar.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.13 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.13 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.13 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.13 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.13 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.13 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.13 copying and adjusting scripts/extract_recombinant_sequences.py -> build/scripts-3.13 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.13 changing mode of build/scripts-3.13/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.13/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.13/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.13/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.13/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.13/count_recombinations_per_gene.py from 644 to 755 changing mode of build/scripts-3.13/extract_recombinant_sequences.py from 644 to 755 running install_lib creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-313.pyc running install_egg_info running egg_info creating gubbins.egg-info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing entry points to gubbins.egg-info/entry_points.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt writing manifest file 'gubbins.egg-info/SOURCES.txt' reading manifest file 'gubbins.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-3.4.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.13/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 755 changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py to 755 Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_install find debian -name "*.la" -delete find debian -name "*.a" -delete mkdir -p debian/gubbins/usr/lib/gubbins mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' dh_installdocs dh_installchangelogs dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/generate_ska_alignment.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/run_gubbins.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/pyjar.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 78450 new size 79316 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gubbins' in '../gubbins_3.4-2_amd64.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.4-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.4-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.4-2_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/2920459 and its subdirectories I: Current time: Mon Oct 19 04:12:04 -12 2026 I: pbuilder-time-stamp: 1792426324 Mon Oct 19 16:12:04 UTC 2026 I: Signing ./b1/gubbins_3.4-2_amd64.buildinfo as gubbins_3.4-2_amd64.buildinfo.asc Mon Oct 19 16:12:04 UTC 2026 I: Signed ./b1/gubbins_3.4-2_amd64.buildinfo as ./b1/gubbins_3.4-2_amd64.buildinfo.asc Mon Oct 19 16:12:04 UTC 2026 - build #1 for gubbins/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Mon Oct 19 16:12:04 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-CqMyxMdT, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:49 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:42 b2 -rw-rw-r-- 1 jenkins jenkins 2410 Feb 28 2025 gubbins_3.4-2.dsc -rw------- 1 jenkins jenkins 3500 Sep 16 09:42 rbuildlog.EycyhnO /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b1: total 364 -rw-r--r-- 1 jenkins jenkins 125772 Sep 16 09:49 build.log -rw-r--r-- 1 jenkins jenkins 85076 Sep 16 09:49 gubbins-dbgsym_3.4-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 10608 Sep 16 09:49 gubbins_3.4-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2410 Sep 16 09:49 gubbins_3.4-2.dsc -rw-r--r-- 1 jenkins jenkins 9625 Sep 16 09:49 gubbins_3.4-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 10507 Sep 16 09:49 gubbins_3.4-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1483 Sep 16 09:49 gubbins_3.4-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 95436 Sep 16 09:49 gubbins_3.4-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1356 Sep 16 09:49 gubbins_3.4-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2: total 0 Tue Sep 16 09:49:04 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 19 04:05:17 -12 2026 I: pbuilder-time-stamp: 1792425917 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 [gubbins_3.4-2.dsc] I: copying [./gubbins_3.4.orig.tar.gz] I: copying [./gubbins_3.4-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-2.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.4 dpkg-source: info: unpacking gubbins_3.4.orig.tar.gz dpkg-source: info: unpacking gubbins_3.4-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch dpkg-source: info: applying gubbins_exe_in_usr_lib.patch dpkg-source: info: applying iqtree2.patch dpkg-source: info: applying autoupdate_configure.ac.patch dpkg-source: info: applying python3-shebang.patch dpkg-source: info: applying remove-numba-temporarily.patch dpkg-source: info: applying numpy2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2920459/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='51a33e633d884bee8fb421f0cff5eaa2' 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='2920459' 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.Q8PzurSU/pbuilderrc_cCrn --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.Q8PzurSU/b1 --logfile b1/build.log gubbins_3.4-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2920459/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), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox, python3-scipy, python3-multiprocess, python3-wheel dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on iqtree; however: Package iqtree is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-reportlab; however: Package python3-reportlab is not installed. pbuilder-satisfydepends-dummy depends on tox; however: Package tox is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-multiprocess; however: Package python3-multiprocess is not installed. pbuilder-satisfydepends-dummy depends on python3-wheel; however: Package python3-wheel is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} iqtree{a} libabsl20240722{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs1{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-sphinxdoc{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenjp2-7{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libxrender1{a} libyuv0{a} libz3-4{a} libze1{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-biopython{a} python3-cachetools{a} python3-cairo{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-decorator{a} python3-dendropy{a} python3-dill{a} python3-distlib{a} python3-filelock{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pip-whl{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyproject-api{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-whl{a} python3-typeguard{a} python3-typing-extensions{a} python3-virtualenv{a} python3-wheel{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sgml-base{a} tox{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-dev python3-olefile python3-pooch python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 153 MB of archives. After unpacking 615 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libsubunit0 amd64 1.4.2-3+b1 [6436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsubunit-dev amd64 1.4.2-3+b1 [7352 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 check amd64 0.15.2-3 [113 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 67 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 84 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 iqtree amd64 2.0.7+dfsg-1+b2 [3652 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 python3-cachetools all 5.3.3-1 [13.2 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 python3-dill all 0.4.0-1 [83.7 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 python3-distlib all 0.4.0-1 [257 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-filelock all 3.19.1-1 [12.6 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-multiprocess all 0.70.17-1 [107 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-pip-whl all 25.2+dfsg-1 [1428 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-api all 1.9.1-1 [42.3 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-setuptools-whl all 78.1.1-0.1 [1268 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-virtualenv all 20.34.0+ds-1 [75.9 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 tox all 4.25.0-1 [401 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 153 MB in 32s (4815 kB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... 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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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gubbins-3.4/ && 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 > ../gubbins_3.4-2_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete rm -rf python/output_alignment python/tmp* tests/.deps make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:29: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking how to create a pax tar archive... gnutar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... 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Makefile config.status: creating src/Makefile config.status: creating release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o main.o main.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong 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-Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o .libs/csv_of_snp_sites.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o csv_of_snp_sites.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm -pthread make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making all in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' # make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test) cp -a tests/data tests/data.save dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make run_all_tests make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[5]: Entering directory '/build/reproducible-path/gubbins-3.4/src' PASS: run_all_tests ============================================================================ Testsuite summary for gubbins package_version ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making check in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' rm -rf tests/data mv tests/data.save tests/data make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.4/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making install in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making install in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' # pybuild --install --system=distutils cd python && \ python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License (GPL) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() 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 build running build_py creating build/lib/gubbins copying gubbins/run_gubbins.py -> build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/pyjar.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.13 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.13 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.13 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.13 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.13 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.13 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.13 copying and adjusting scripts/extract_recombinant_sequences.py -> build/scripts-3.13 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.13 changing mode of build/scripts-3.13/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.13/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.13/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.13/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.13/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.13/count_recombinations_per_gene.py from 644 to 755 changing mode of build/scripts-3.13/extract_recombinant_sequences.py from 644 to 755 running install_lib creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-313.pyc running install_egg_info running egg_info creating gubbins.egg-info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing entry points to gubbins.egg-info/entry_points.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt writing manifest file 'gubbins.egg-info/SOURCES.txt' reading manifest file 'gubbins.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-3.4.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.13/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 755 changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py to 755 Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_install find debian -name "*.la" -delete find debian -name "*.a" -delete mkdir -p debian/gubbins/usr/lib/gubbins mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' dh_installdocs dh_installchangelogs dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/generate_ska_alignment.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/run_gubbins.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/pyjar.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 78450 new size 79316 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gubbins' in '../gubbins_3.4-2_amd64.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.4-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.4-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.4-2_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/2920459 and its subdirectories I: Current time: Mon Oct 19 04:12:04 -12 2026 I: pbuilder-time-stamp: 1792426324 Tue Sep 16 09:49:05 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Sep 16 09:49:05 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Sep 16 09:49:05 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Tue Sep 16 09:49:05 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-j41Wlb' ==================================================================================== Tue Sep 16 09:49:05 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 gubbins unstable /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU 3.4-2" as arguments. Tue Sep 16 09:49:05 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-91hazt7W" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 09:49:05 UTC 2025 I: Downloading source for unstable/gubbins=3.4-2 Reading package lists... NOTICE: 'gubbins' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gubbins.git Please use: git clone https://salsa.debian.org/med-team/gubbins.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2891 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (tar) [2878 kB] Get:3 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (diff) [10.6 kB] Fetched 2891 kB in 0s (78.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'gubbins' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gubbins.git Please use: git clone https://salsa.debian.org/med-team/gubbins.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2891 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (tar) [2878 kB] Get:3 http://deb.debian.org/debian unstable/main gubbins 3.4-2 (diff) [10.6 kB] Fetched 2891 kB in 0s (78.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building gubbins in unstable on amd64 on ionos1-amd64 now. Date: Tue Sep 16 09:49:05 UTC 2025 Date UTC: Tue Sep 16 09:49:05 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/pbuilderrc_pbDm + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' gubbins = debian-installer -o gubbins = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' gubbins = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/pbuilderrc_pbDm --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2 --logfile b2/build.log gubbins_3.4-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 23:49:05 +14 2025 I: pbuilder-time-stamp: 1758016145 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 [gubbins_3.4-2.dsc] I: copying [./gubbins_3.4.orig.tar.gz] I: copying [./gubbins_3.4-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-2.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.4 dpkg-source: info: unpacking gubbins_3.4.orig.tar.gz dpkg-source: info: unpacking gubbins_3.4-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch dpkg-source: info: applying gubbins_exe_in_usr_lib.patch dpkg-source: info: applying iqtree2.patch dpkg-source: info: applying autoupdate_configure.ac.patch dpkg-source: info: applying python3-shebang.patch dpkg-source: info: applying remove-numba-temporarily.patch dpkg-source: info: applying numpy2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/556391/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 16 09:49 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/556391/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/556391/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=5ff7e303c53e417faf09c92c7a0e7cc3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=556391 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/pbuilderrc_pbDm --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2 --logfile b2/build.log gubbins_3.4-2.dsc' SUDO_GID=110 SUDO_HOME=/var/lib/jenkins SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/556391/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), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox, python3-scipy, python3-multiprocess, python3-wheel dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on iqtree; however: Package iqtree is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-reportlab; however: Package python3-reportlab is not installed. pbuilder-satisfydepends-dummy depends on tox; however: Package tox is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-multiprocess; however: Package python3-multiprocess is not installed. pbuilder-satisfydepends-dummy depends on python3-wheel; however: Package python3-wheel is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} iqtree{a} libabsl20240722{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs1{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-sphinxdoc{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenjp2-7{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libxrender1{a} libyuv0{a} libz3-4{a} libze1{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-biopython{a} python3-cachetools{a} python3-cairo{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-decorator{a} python3-dendropy{a} python3-dill{a} python3-distlib{a} python3-filelock{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pip-whl{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyproject-api{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-whl{a} python3-typeguard{a} python3-typing-extensions{a} python3-virtualenv{a} python3-wheel{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sgml-base{a} tox{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-dev python3-olefile python3-pooch python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 153 MB of archives. After unpacking 615 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libsubunit0 amd64 1.4.2-3+b1 [6436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsubunit-dev amd64 1.4.2-3+b1 [7352 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 check amd64 0.15.2-3 [113 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 67 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 84 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 iqtree amd64 2.0.7+dfsg-1+b2 [3652 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.4.3-1 [1168 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-5 [1674 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 python3-cachetools all 5.3.3-1 [13.2 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 python3-dill all 0.4.0-1 [83.7 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 python3-distlib all 0.4.0-1 [257 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-filelock all 3.19.1-1 [12.6 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-multiprocess all 0.70.17-1 [107 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-pip-whl all 25.2+dfsg-1 [1428 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-api all 1.9.1-1 [42.3 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-setuptools-whl all 78.1.1-0.1 [1268 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-virtualenv all 20.34.0+ds-1 [75.9 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 tox all 4.25.0-1 [401 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 153 MB in 1s (107 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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-5) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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: user script /srv/workspace/pbuilder/556391/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/556391/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gubbins-3.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gubbins_3.4-2_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete rm -rf python/output_alignment python/tmp* tests/.deps make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:29: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking how to create a pax tar archive... gnutar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/x86_64-linux-gnu-ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/x86_64-linux-gnu-ld -m elf_x86_64 checking if the linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether to build with code coverage support... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for zlib.h... yes checking for math.h... yes checking for a Python interpreter with version >= 3.8... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.13 checking for python3 platform... linux checking for GNU default python3 prefix... ${prefix} checking for GNU default python3 exec_prefix... ${exec_prefix} checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.13/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.13/site-packages checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o main.o main.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o Newickform.lo Newickform.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alignment_file.lo alignment_file.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o block_tab_file.lo block_tab_file.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o branch_sequences.lo branch_sequences.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o string_cat.lo string_cat.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o gff_file.lo gff_file.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o gubbins.lo gubbins.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parse_phylip.lo parse_phylip.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time 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-DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o snp_searching.lo snp_searching.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o snp_sites.lo snp_sites.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tree_statistics.lo tree_statistics.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tree_scaling.lo tree_scaling.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o vcf.lo vcf.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o csv_of_snp_sites.lo csv_of_snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -fPIC -DPIC -o .libs/csv_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -fPIC -DPIC -o .libs/vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -o string_cat.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -o gff_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -o csv_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -o gubbins.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -o snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -o vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -o snp_searching.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c alignment_file.c -o alignment_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -o Newickform.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o .libs/csv_of_snp_sites.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o csv_of_snp_sites.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm -pthread make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making all in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' # make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test) cp -a tests/data tests/data.save dh_auto_test make -j40 check "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make run_all_tests make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[5]: Entering directory '/build/reproducible-path/gubbins-3.4/src' PASS: run_all_tests ============================================================================ Testsuite summary for gubbins package_version ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making check in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' rm -rf tests/data mv tests/data.save tests/data make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.4/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making install in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making install in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' # pybuild --install --system=distutils cd python && \ python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License (GPL) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() 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 build running build_py creating build/lib/gubbins copying gubbins/pyjar.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/run_gubbins.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.13 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.13 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.13 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.13 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.13 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.13 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.13 copying and adjusting scripts/extract_recombinant_sequences.py -> build/scripts-3.13 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.13 changing mode of build/scripts-3.13/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.13/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.13/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.13/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.13/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.13/count_recombinations_per_gene.py from 644 to 755 changing mode of build/scripts-3.13/extract_recombinant_sequences.py from 644 to 755 running install_lib creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-313.pyc running install_egg_info running egg_info creating gubbins.egg-info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing entry points to gubbins.egg-info/entry_points.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt writing manifest file 'gubbins.egg-info/SOURCES.txt' reading manifest file 'gubbins.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-3.4.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.13/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 775 changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_install find debian -name "*.la" -delete find debian -name "*.a" -delete mkdir -p debian/gubbins/usr/lib/gubbins mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' dh_installdocs dh_installchangelogs dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/generate_ska_alignment.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/run_gubbins.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/pyjar.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 78450 new size 79316 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gubbins' in '../gubbins_3.4-2_amd64.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.4-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.4-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.4-2_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: user script /srv/workspace/pbuilder/556391/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/556391/tmp/hooks/B01_cleanup finished 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/556391 and its subdirectories I: Current time: Tue Sep 16 23:51:19 +14 2025 I: pbuilder-time-stamp: 1758016279 + false + set +x Tue Sep 16 09:51:19 UTC 2025 I: Signing ./b2/gubbins_3.4-2_amd64.buildinfo as gubbins_3.4-2_amd64.buildinfo.asc Tue Sep 16 09:51:19 UTC 2025 I: Signed ./b2/gubbins_3.4-2_amd64.buildinfo as ./b2/gubbins_3.4-2_amd64.buildinfo.asc Tue Sep 16 09:51:19 UTC 2025 - build #2 for gubbins/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Tue Sep 16 09:51:19 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-91hazt7W, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU: total 144 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:49 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:51 b2 -rw-rw-r-- 1 jenkins jenkins 2410 Feb 28 2025 gubbins_3.4-2.dsc -rw------- 1 jenkins jenkins 129558 Sep 16 09:49 rbuildlog.EycyhnO /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b1: total 364 -rw-r--r-- 1 jenkins jenkins 125772 Sep 16 09:49 build.log -rw-r--r-- 1 jenkins jenkins 85076 Sep 16 09:49 gubbins-dbgsym_3.4-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 10608 Sep 16 09:49 gubbins_3.4-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2410 Sep 16 09:49 gubbins_3.4-2.dsc -rw-r--r-- 1 jenkins jenkins 9625 Sep 16 09:49 gubbins_3.4-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 10507 Sep 16 09:49 gubbins_3.4-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1483 Sep 16 09:49 gubbins_3.4-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 95436 Sep 16 09:49 gubbins_3.4-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1356 Sep 16 09:49 gubbins_3.4-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2: total 368 -rw-rw-r-- 1 jenkins jenkins 127640 Sep 16 09:51 build.log -rw-r--r-- 1 jenkins jenkins 85076 Sep 16 09:51 gubbins-dbgsym_3.4-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 10608 Sep 16 09:51 gubbins_3.4-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2410 Sep 16 09:51 gubbins_3.4-2.dsc -rw-rw-r-- 1 jenkins jenkins 9625 Sep 16 09:51 gubbins_3.4-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 10507 Sep 16 09:51 gubbins_3.4-2_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1483 Sep 16 09:51 gubbins_3.4-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 95436 Sep 16 09:51 gubbins_3.4-2_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1356 Sep 16 09:51 gubbins_3.4-2_source.changes Tue Sep 16 09:51:19 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Sep 16 09:51:19 UTC 2025 I: gubbins_3.4-2_amd64.changes: Format: 1.8 Date: Fri, 28 Feb 2025 11:09:34 +0100 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: amd64 Version: 3.4-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: gubbins - phylogenetic analysis of genome sequences Closes: 1098693 Changes: gubbins (3.4-2) unstable; urgency=medium . * d/control: gubbins depends on python3-pkg-resources. * numpy2.patch: new: fix further autopkgtest failure with numpy 2. (Closes: #1098693) * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: 1abce4e12e3ce1c66a486beec94b0154270bf276 85076 gubbins-dbgsym_3.4-2_amd64.deb 388ef068bb6b9202781a2932a978e8412353fdcd 9625 gubbins_3.4-2_amd64.buildinfo b048e17b608659a8697442feecbd40f084cd54cc 95436 gubbins_3.4-2_amd64.deb Checksums-Sha256: 0eb9927f9dfbcd166cac5afbbca028495b9ce0b2bf171b4d7d85ff733937a890 85076 gubbins-dbgsym_3.4-2_amd64.deb cea823fae2fbb22838aeab468872ed3cbc192697d9258c76ad1dbf6748c28f34 9625 gubbins_3.4-2_amd64.buildinfo 1ae2b5751621dcc277a1faaaac034c9ae8789bc13ed78bc02e9024f61a0d2033 95436 gubbins_3.4-2_amd64.deb Files: 489748841aaaab6ba4a11b5a78d9227a 85076 debug optional gubbins-dbgsym_3.4-2_amd64.deb 1fed0790ce5a60a3598d9ca5a5136c98 9625 science optional gubbins_3.4-2_amd64.buildinfo 37059022323ad989630277b0d56bdbdc 95436 science optional gubbins_3.4-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/gubbins_3.4-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/gubbins_3.4-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/gubbins_3.4-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/gubbins_3.4-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/gubbins_3.4-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/gubbins_3.4-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-16 09:49:04.762377903 +0000 +++ b2/build.log 2025-09-16 09:51:19.598543981 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Oct 19 04:05:17 -12 2026 -I: pbuilder-time-stamp: 1792425917 +I: Current time: Tue Sep 16 23:49:05 +14 2025 +I: pbuilder-time-stamp: 1758016145 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,53 +30,85 @@ dpkg-source: info: applying numpy2.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2920459/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 16 09:49 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/556391/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=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='51a33e633d884bee8fb421f0cff5eaa2' - 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='2920459' - PS1='# ' - PS2='> ' + INVOCATION_ID=5ff7e303c53e417faf09c92c7a0e7cc3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=556391 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.Q8PzurSU/pbuilderrc_cCrn --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.Q8PzurSU/b1 --logfile b1/build.log gubbins_3.4-2.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/pbuilderrc_pbDm --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2 --logfile b2/build.log gubbins_3.4-2.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2920459/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -327,7 +359,7 @@ Get: 179 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.13+dfsg-2+b1 [1514 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 tox all 4.25.0-1 [401 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 153 MB in 32s (4815 kB/s) +Fetched 153 MB in 1s (107 MB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -924,8 +956,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Oct 19 16:07:55 UTC 2026. -Universal Time is now: Mon Oct 19 16:07:55 UTC 2026. +Local time is now: Tue Sep 16 09:50:00 UTC 2025. +Universal Time is now: Tue Sep 16 09:50:00 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... @@ -1091,7 +1123,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gubbins-3.4/ && 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 > ../gubbins_3.4-2_source.changes +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gubbins-3.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gubbins_3.4-2_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.4-2 dpkg-buildpackage: info: source distribution unstable @@ -1260,58 +1296,58 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j42 + make -j40 make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o main.o main.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o Newickform.lo Newickform.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alignment_file.lo alignment_file.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o block_tab_file.lo block_tab_file.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o branch_sequences.lo branch_sequences.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o string_cat.lo string_cat.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o gff_file.lo gff_file.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o gubbins.lo gubbins.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-fcf-protection -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -fPIC -DPIC -o .libs/vcf.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -fPIC -DPIC -o .libs/csv_of_snp_sites.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -o string_cat.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -o gff_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -o csv_of_snp_sites.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -o gubbins.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -o snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -o vcf.o >/dev/null 2>&1 @@ -1321,14 +1357,14 @@ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -o Newickform.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o .libs/csv_of_snp_sites.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o csv_of_snp_sites.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm -pthread make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making all in release @@ -1344,7 +1380,7 @@ # make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test) cp -a tests/data tests/data.save dh_auto_test - make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 + make -j40 check "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' @@ -1365,7 +1401,7 @@ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit +/bin/sh ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make check-TESTS @@ -1407,7 +1443,7 @@ make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) @@ -1417,7 +1453,7 @@ libtool: install: ranlib /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. @@ -1472,26 +1508,26 @@ running build running build_py creating build/lib/gubbins -copying gubbins/run_gubbins.py -> build/lib/gubbins -copying gubbins/treebuilders.py -> build/lib/gubbins -copying gubbins/common.py -> build/lib/gubbins copying gubbins/pyjar.py -> build/lib/gubbins +copying gubbins/common.py -> build/lib/gubbins +copying gubbins/run_gubbins.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins +copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins +copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins -copying gubbins/PreProcessFasta.py -> build/lib/gubbins creating build/lib/gubbins/tests -copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests +copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests -copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests +copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests +copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests -copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests -copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests +copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests -copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests +copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.13 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.13 @@ -1512,45 +1548,45 @@ running install_lib creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-313.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-313.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-313.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-313.pyc running install_egg_info running egg_info creating gubbins.egg-info @@ -1566,22 +1602,22 @@ Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-3.4.egg-info Skipping SOURCES.txt running install_scripts -copying build/scripts-3.13/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins -copying build/scripts-3.13/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins -copying build/scripts-3.13/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins +copying build/scripts-3.13/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins +copying build/scripts-3.13/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.13/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins -changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755 +copying build/scripts-3.13/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py to 755 -changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 755 -changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755 -changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 +changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 775 changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.py to 755 +changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755 +changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py to 755 +changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_install @@ -1618,9 +1654,9 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol @@ -1635,12 +1671,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/556391/tmp/hooks/B01_cleanup finished 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/2920459 and its subdirectories -I: Current time: Mon Oct 19 04:12:04 -12 2026 -I: pbuilder-time-stamp: 1792426324 +I: removing directory /srv/workspace/pbuilder/556391 and its subdirectories +I: Current time: Tue Sep 16 23:51:19 +14 2025 +I: pbuilder-time-stamp: 1758016279 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/gubbins_3.4-2.diff: 87.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/gubbins_3.4-2.diff.gz b2/build.log: 84.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.5% -- replaced with stdout Tue Sep 16 09:51:20 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_gubbins_unstable_amd64_1758016280 + touch /var/log/reproducible-builds/diffoscope_stamp_gubbins_unstable_amd64_1758016280 + RESULT=0 + systemd-run '--description=diffoscope on gubbins/3.4-2 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_18-53061 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU --run-session -c jenkins-reproducible-unstable-diffoscope-edc90482-ee13-4427-8d20-0c597e78d449 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/dbd-tmp-oU66VBw ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/gubbins_3.4-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/gubbins_3.4-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/gubbins_3.4-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b1/gubbins_3.4-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2/gubbins_3.4-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_18-53061.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/gubbins_3.4-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/gubbins_3.4-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/gubbins_3.4-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b1/gubbins_3.4-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Q8PzurSU/b2/gubbins_3.4-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 241ms CPU time consumed: 197ms Memory peak: 18.8M (swap: 0B) _ _ _ __ _ _ _| |__ | |__ (_)_ __ ___ / _` | | | | '_ \| '_ \| | '_ \/ __| | (_| | |_| | |_) | |_) | | | | \__ \ \__, |\__,_|_.__/|_.__/|_|_| |_|___/ |___/ Tue Sep 16 09:56:49 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 16 09:56:49 UTC 2025 I: gubbins from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-16 09:56:50] INFO: Starting at 2025-09-16 09:56:50.349887 [2025-09-16 09:56:50] INFO: Generating the pages of 1 package(s) [2025-09-16 09:56:51] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/gubbins didn't produce a buildlog, even though it has been built. [2025-09-16 09:56:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/gubbins_3.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/gubbins_3.4-2.diff.gz is missing [2025-09-16 09:56:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/gubbins_3.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/gubbins_3.4-2.diff.gz is missing [2025-09-16 09:56:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/gubbins_3.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/gubbins_3.4-2.diff.gz is missing [2025-09-16 09:56:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/gubbins_2.4.1-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/gubbins_2.4.1-5.diff.gz is missing [2025-09-16 09:56:51] INFO: Finished at 2025-09-16 09:56:51.570924, took: 0:00:01.221040 Tue Sep 16 09:56:51 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/gubbins.html Tue Sep 16 09:56:51 UTC 2025 I: Removing signed gubbins_3.4-2_amd64.buildinfo.asc files: removed './b1/gubbins_3.4-2_amd64.buildinfo.asc' removed './b2/gubbins_3.4-2_amd64.buildinfo.asc' 1758016612 amd64 unstable gubbins Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/gubbins_3.4-2.rbuild.log: 82.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/gubbins_3.4-2.rbuild.log.gz [2025-09-16 09:56:52] INFO: Starting at 2025-09-16 09:56:52.367729 [2025-09-16 09:56:52] INFO: Generating the pages of 1 package(s) [2025-09-16 09:56:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/gubbins_3.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/gubbins_3.4-2.diff.gz is missing [2025-09-16 09:56:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/gubbins_3.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/gubbins_3.4-2.diff.gz is missing [2025-09-16 09:56:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/gubbins_3.4-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/gubbins_3.4-2.diff.gz is missing [2025-09-16 09:56:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/gubbins_2.4.1-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/gubbins_2.4.1-5.diff.gz is missing [2025-09-16 09:56:52] INFO: Finished at 2025-09-16 09:56:52.995590, took: 0:00:00.627866 All cleanup done. Tue Sep 16 09:56:53 UTC 2025 - total duration: 0h 14m 56s. Tue Sep 16 09:56:53 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-c0nRYXYj, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 15min 250ms CPU time consumed: 5.038s Memory peak: 64.1M (swap: 0B)