Sun Oct 13 16:14:14 UTC 2024 I: starting to build gubbins/trixie/i386 on jenkins on '2024-10-13 16:14' Sun Oct 13 16:14:14 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_14/46472/console.log Sun Oct 13 16:14:14 UTC 2024 I: Downloading source for trixie/gubbins=3.3.5-1 --2024-10-13 16:14:14-- http://deb.debian.org/debian/pool/main/g/gubbins/gubbins_3.3.5-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2422 (2.4K) [text/prs.lines.tag] Saving to: ‘gubbins_3.3.5-1.dsc’ 0K .. 100% 190M=0s 2024-10-13 16:14:14 (190 MB/s) - ‘gubbins_3.3.5-1.dsc’ saved [2422/2422] Sun Oct 13 16:14:14 UTC 2024 I: gubbins_3.3.5-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 3.3.5-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://sanger-pathogens.github.io/gubbins/ Standards-Version: 4.6.2 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: 6841558ea0c950b1e825ba2e711294649cf63c7a 2872452 gubbins_3.3.5.orig.tar.gz edfe47ecdbfc56e4fa35db0b97deb613561efc3b 9524 gubbins_3.3.5-1.debian.tar.xz Checksums-Sha256: 4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774 2872452 gubbins_3.3.5.orig.tar.gz bbddd5af4f016a1a091446637b3296a411ff47f6dc32293d350e5759912d8514 9524 gubbins_3.3.5-1.debian.tar.xz Files: 3b51c573afa3c287b8594246bad7681c 2872452 gubbins_3.3.5.orig.tar.gz ad46716a8872e227e2c88898347c9c5f 9524 gubbins_3.3.5-1.debian.tar.xz Dgit: 763aabb5cb171c4c0c3b6adec190f29b63f9ce53 debian archive/debian/3.3.5-1 https://git.dgit.debian.org/gubbins -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZOVMsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrneA//Q2JGG+1ZtMieBPfXtaKrESaApaTf 9kgpp4YV8K4qVUPWfXbtfDcd4sc8uRcl2he04xZNY6uvKQ/SAsSdUnBD/h70iyjX n9XV5/BDkkCLIK4yQO7wmV8elcsFDw5uuwPglM1WcojpsDa6wP45XURf1todpcuq S9j4jvN4xAEzgpbbOJsVnT/ZToA51ri24Gd+zCl+XPemskl7DCY40BjPNZoC5dzc uuxx/x49eJqn+XSmJ601/7mYxcXJ45Wk+j5AzlRwiEPORtCkRck3mZQ5YptUc7Jc Dg20Hf0/bgWG1qdrUpDySdxUR9YnIkNHOdUzf/EtnddJMBLgc8XdF5Zi4hKd4+PB 8TmE+Dl2IODknGR7SmCbnQ8Qnpfe75149cufbw/9Z0Mb+jfDRQ2VVNDNWR+zffgO I6mxbZUG95U3nI5loPp17aDpLHHhBCEXWHo2iKQeo+LiW/3dNSMolEbWx9ODZZbd djvjT6l4KlJzbi0FXIlNpQujM2prlRVYgXp8z3z/zOZHUhWRydtROCt9I6uin/bb t4zn+AuKS74ILyn5Z2EAEaC0kbN1LNRA3Sn0sxY0UJZfcpXOKtjndcxY8GVDYvQc rhpIeg/pauNMzvmqSVNhGwpsSygs9X8Bx7OKWC1gs1fhD25+CnLg2solwsliFC56 pyzkDB2tyRqamAg= =RNA7 -----END PGP SIGNATURE----- Sun Oct 13 16:14:14 UTC 2024 I: Checking whether the package is not for us Sun Oct 13 16:14:14 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net. Sun Oct 13 16:14:14 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net. Sun Oct 13 16:16:20 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 15 10:37:13 -12 2025 I: pbuilder-time-stamp: 1763246233 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [gubbins_3.3.5-1.dsc] I: copying [./gubbins_3.3.5.orig.tar.gz] I: copying [./gubbins_3.3.5-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 22 20:25:47 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gubbins_3.3.5-1.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.3.5 dpkg-source: info: unpacking gubbins_3.3.5.orig.tar.gz dpkg-source: info: unpacking gubbins_3.3.5-1.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/27857/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='12f4efbfac5649828a21eb3b8656e6b0' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='27857' 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.ybea9FZZ/pbuilderrc_0J6n --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ybea9FZZ/b1 --logfile b1/build.log gubbins_3.3.5-1.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom08-i386 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27857/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19774 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} intltool-debian{a} iqtree{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhwloc15{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmpich12{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{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-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-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{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-wheel-whl{a} python3-zipp{a} python3.12{a} python3.12-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 javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libhwloc-plugins libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-dev python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 154 newly installed, 0 to remove and 0 not upgraded. Need to get 92.5 MB of archives. After unpacking 343 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.6-1 [813 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.3-1 [107 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.6-1 [2242 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 13 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.6-1 [1961 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.6-1 [669 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-1 [1386 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3 [42.9 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-9 [102 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libsubunit0 i386 1.4.2-3 [6288 B] Get: 43 http://deb.debian.org/debian trixie/main i386 libsubunit-dev i386 1.4.2-3 [7348 B] Get: 44 http://deb.debian.org/debian trixie/main i386 check i386 0.15.2-2+b1 [116 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.1 [733 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 65 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.20.2-1 [10.3 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 74.1.2-2 [736 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240824 [109 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.44-2 [288 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 xfonts-utils i386 1:7.7+7 [95.1 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 81 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-6 [735 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libhwloc15 i386 2.11.2-1 [177 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libmpich12 i386 4.2.0-14 [1518 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 iqtree i386 2.0.7+dfsg-1+b2 [3229 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2 [116 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2 [105 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.82.1-1 [1570 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 9.0.0-1 [500 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1+b1 [35.9 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-3 [38.2 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.4.0-0.1 [111 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.4.0-0.1 [125 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-3 [30.3 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-3 [26.1 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.26.4+ds-11 [4299 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 python3-pil i386 10.4.0-1 [503 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 python3-cairo i386 1.26.1-2 [116 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 python3-freetype all 2.5.1-1 [89.3 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 130 http://deb.debian.org/debian trixie/main i386 python3-reportlab all 4.2.5-1 [1117 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 python3-biopython i386 1.83+dfsg1-5 [1604 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 python3-cachetools all 5.3.3-1 [13.2 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 python3-colorama all 0.4.6-4 [36.2 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 python3-dendropy all 4.6.1-1 [277 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 python3-dill all 0.3.8-1 [81.7 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 python3-distlib all 0.3.8-1 [257 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 python3-filelock all 3.15.4-1 [12.6 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 python3-multiprocess all 0.70.16-2 [105 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.1-1 [45.8 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 python3-pip-whl all 24.2+dfsg-1 [1494 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 python3-pyproject-api all 1.8.0-1 [51.7 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 python3-scipy i386 1.13.1-5 [16.6 MB] Get: 148 http://deb.debian.org/debian trixie/main i386 python3-setuptools-whl all 74.1.2-2 [1262 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 python3-wheel-whl all 0.44.0-2 [70.1 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 python3-virtualenv all 20.26.2+ds-1 [70.8 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 python3-wheel all 0.44.0-2 [53.4 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 raxml i386 8.2.13+dfsg-1+b1 [992 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 tox all 4.21.2-1 [392 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Fetched 92.5 MB in 1s (82.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19774 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../libpython3.12-minimal_3.12.6-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.6-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.3-1_i386.deb ... Unpacking libexpat1:i386 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_i386.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:i386 (3.12.6-1) ... Setting up libexpat1:i386 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21276 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-3_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_i386.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22348 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-1_i386.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-9_i386.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../012-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gubbins-3.3.5/ && 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_3.3.5-1_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.3.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.5' 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-3.3.5' 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=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a 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 how to create a pax tar archive... gnutar checking build system type... i686-pc-linux-gnu checking host system type... i686-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/ld checking if the linker (/usr/bin/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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(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... 3.12 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/python3.12/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.12/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 -j6 make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.5' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.3.5' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5/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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o string_cat.lo string_cat.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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o /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 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csv_of_snp_sites.c -o csv_of_snp_sites.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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/i386-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 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/src' Making all in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' make[1]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.5' # 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 -j6 check "TESTSUITEFLAGS=-j6 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gubbins-3.3.5' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5/src' make run_all_tests make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.5/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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -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-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/src' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.5/src' make[5]: Entering directory '/build/reproducible-path/gubbins-3.3.5/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-3.3.5/src' make[4]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/src' Making check in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' rm -rf tests/data mv tests/data.save tests/data make[1]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.5' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.3.5/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gubbins-3.3.5' Making install in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.5/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-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-3.3.5/debian/gubbins/usr/lib/i386-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-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: ranlib /build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.3.5/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/src' Making install in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5/release' make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.5/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-3.3.5/release' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.5' make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.5' 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-3.3.5' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.3.5' # 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:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py creating build creating build/lib creating build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins copying gubbins/pyjar.py -> build/lib/gubbins copying gubbins/run_gubbins.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> 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_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.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_pre_process_fasta.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.12 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.12 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.12 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.12 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.12 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.12 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.12 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.12 changing mode of build/scripts-3.12/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.12/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.12/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.12/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.12/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.12/count_recombinations_per_gene.py from 644 to 755 running install_lib creating ../debian/gubbins/usr/share creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../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_treebuilders.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_utils.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_validate_starting_tree.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/__init__.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_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-312.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-3.3.5.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R 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_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_ska_alignment.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/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-3.3.5' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.5' 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-3.3.5' dh_installdocs dh_installchangelogs dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 54912 new size 55670 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/i386-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-dbgsym' in '../gubbins-dbgsym_3.3.5-1_i386.deb'. dpkg-deb: building package 'gubbins' in '../gubbins_3.3.5-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.3.5-1_i386.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.3.5-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/27857 and its subdirectories I: Current time: Sat Nov 15 10:39:14 -12 2025 I: pbuilder-time-stamp: 1763246354 Sun Oct 13 16:16:21 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net. Sun Oct 13 16:16:21 UTC 2024 I: Preparing to do remote build '2' on infom07-i386.debian.net. Sun Oct 13 16:18:43 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. Sun Oct 13 16:18:44 UTC 2024 I: gubbins_3.3.5-1_i386.changes: Format: 1.8 Date: Wed, 22 May 2024 22:19:47 +0200 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: i386 Version: 3.3.5-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: gubbins - phylogenetic analysis of genome sequences Closes: 1058474 Changes: gubbins (3.3.5-1) unstable; urgency=medium . * New upstream version 3.3.5 * iqtree2.patch: unfuzz. * python3-shebang.patch: new. This fixes a couple of occurrences of unversioned Python interpreter declared in the shebang of a couple of scripts. * d/control: move to pkgconf. * remove-numba-temporarily.patch: new. Remove temporarily numba-accelerated pyjar.py functions decorators. This allows decorellation of gubbins from numba until the latter is available again in trixie. The change may affect performances, but should not affect gubbins results and functionalities otherwise. * d/control: promote and comment out dependency on python3-numba. This prepares the field for when it will be possible to bring numba support back to gubbins, once numba 0.59 or later makes it to trixie. * d/t/control: autopkgtests do not depend on python3-numba anymore. (Closes: #1058474) Checksums-Sha1: 4409d453440cb7388aefcbda6f058d50f3587edf 64700 gubbins-dbgsym_3.3.5-1_i386.deb f56ae0f974de7c4d31f8c0b59b537872e23acedb 8678 gubbins_3.3.5-1_i386.buildinfo 8a6a918b4e8680e4650ae12265e2fadaa39c90de 93088 gubbins_3.3.5-1_i386.deb Checksums-Sha256: 9e6cecad04a255acbaaf988121ffb34bc6e123c9b4b85b85e0140cea3936e26e 64700 gubbins-dbgsym_3.3.5-1_i386.deb 5782aa7c9c3d4e3702060b20816cfb60b9f932c99087ed74f1fb74bc72f14e5a 8678 gubbins_3.3.5-1_i386.buildinfo 607964b592ebf40e9904568bc9b2855d01183974beb618b724b2f5cb29420b69 93088 gubbins_3.3.5-1_i386.deb Files: 07b700961b97a76f598d3627ab01a8e2 64700 debug optional gubbins-dbgsym_3.3.5-1_i386.deb 8d1ae22915f2a2757a9c4d5e16f3dc91 8678 science optional gubbins_3.3.5-1_i386.buildinfo c53e42d21c75af298973ea7086f15e53 93088 science optional gubbins_3.3.5-1_i386.deb Sun Oct 13 16:18:45 UTC 2024 I: diffoscope 280 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_14-46472.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ybea9FZZ/gubbins_3.3.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ybea9FZZ/gubbins_3.3.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ybea9FZZ/gubbins_3.3.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ybea9FZZ/b1/gubbins_3.3.5-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.ybea9FZZ/b2/gubbins_3.3.5-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.472s) 0.472s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 862ms CPU time consumed: 862ms Sun Oct 13 16:18:46 UTC 2024 I: diffoscope 280 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 13 16:18:46 UTC 2024 I: gubbins from trixie built successfully and reproducibly on i386. Sun Oct 13 16:18:49 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Oct 13 16:18:49 UTC 2024 I: Submitting 12K b1/gubbins_3.3.5-1_i386.buildinfo.asc Sun Oct 13 16:18:49 UTC 2024 I: Submitting 12K b2/gubbins_3.3.5-1_i386.buildinfo.asc Sun Oct 13 16:18:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Oct 13 16:18:50 UTC 2024 I: Done submitting .buildinfo files. Sun Oct 13 16:18:50 UTC 2024 I: Removing signed gubbins_3.3.5-1_i386.buildinfo.asc files: removed './b1/gubbins_3.3.5-1_i386.buildinfo.asc' removed './b2/gubbins_3.3.5-1_i386.buildinfo.asc'