Thu May 9 23:16:35 UTC 2024 I: starting to build gubbins/trixie/amd64 on jenkins on '2024-05-09 23:16' Thu May 9 23:16:35 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_2/6211/console.log Thu May 9 23:16:35 UTC 2024 I: Downloading source for trixie/gubbins=3.3.3-1 --2024-05-09 23:16:35-- http://deb.debian.org/debian/pool/main/g/gubbins/gubbins_3.3.3-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2440 (2.4K) [text/prs.lines.tag] Saving to: ‘gubbins_3.3.3-1.dsc’ 0K .. 100% 376M=0s 2024-05-09 23:16:35 (376 MB/s) - ‘gubbins_3.3.3-1.dsc’ saved [2440/2440] Thu May 9 23:16:35 UTC 2024 I: gubbins_3.3.3-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 3.3.3-1 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, python3-numba Build-Depends: debhelper-compat (= 13), dh-sequence-python3, autoconf-archive, pkg-config, 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: 9f13b8279a192cd0612d446542b4ff681cfc384a 2872362 gubbins_3.3.3.orig.tar.gz 7da972a8a84d304a04dec80ff4972a71c92972fa 7568 gubbins_3.3.3-1.debian.tar.xz Checksums-Sha256: b1d878130a6f07ff133efa55f0d6ed2ec3bcfa64029352ce5050c6a162b9a0b2 2872362 gubbins_3.3.3.orig.tar.gz 3dc983118e6c6da1e042dfcac905e2d7f1165d9ab2908bf296dfb5f792605f68 7568 gubbins_3.3.3-1.debian.tar.xz Files: 8d5502031f849fd3d94beb1bd237f927 2872362 gubbins_3.3.3.orig.tar.gz f603af3198a354a3fc067dbc53d4d768 7568 gubbins_3.3.3-1.debian.tar.xz Dgit: 0664cc0c7dedf3796cd61cc93354fd113b9984f5 debian archive/debian/3.3.3-1 https://git.dgit.debian.org/gubbins -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmW/wHUUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpxQRAAqLDkkKo0+D4QQqyyttsb6q7ah/qI qm7vKldVmXHXqZc7LX8LoUl4ikowwWV74/PVVn8vDQErYKg093krCnsOaFZPIDKo AU2KxamtADNjquZw2H2VuBk3bU9kczdr3yw4hhayWAA5R2OMy/2gXvC9JhvptXEy rfj0rDMewsXmweYHx7H/7qOY8KunbooF1F/yv998jdbvUa0uNhyB8q1lsda+8Rsv xBh5xalqGO6MrJVp8IRxKhwo/XXM6XDa4FwzS8LSAkG9yqRQSgtEHvff3J3XvafM Tq9+zmrUtYV5L9kyDXBd3wpZAzK9ysoDQRYl+5Qpu9cR8hEzFQYWtQYamd4q1gXA dmoCDF6KGG1Xr7HvtVTv6VEAnThAXfxceOwnlJyRsYTqSPsdQKGq5sYs1r9bbSQ+ 2rgzLh0CNmjBfXxozzHsw9NRkKhcIYOA55qTFGt9PRldW3lMqRcunrsw3IsE091a x/qXaUSk0ezU7EMrOeVMJ6rhW65xuAv+bUAy/dffwfQ4aaV6+YYgYAmergv8LijP hbmiyRRFGt+TU7lEHd1itP0MMbWSoP7Npidy5CRcmoUetBfhpkDc/Wl+t0SmrymU rVH55GBU3rfqfzWCwm5q/Qe/BhiiryrlwZxCR0/aigHQadaBL9VoE6rsHAuEelB1 M3PfeNNvhygeFBY= =yzYI -----END PGP SIGNATURE----- Thu May 9 23:16:35 UTC 2024 I: Checking whether the package is not for us Thu May 9 23:16:35 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu May 9 23:16:35 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu May 9 23:19:45 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 11 17:39:37 -12 2025 I: pbuilder-time-stamp: 1749706777 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: Copying source file I: copying [gubbins_3.3.3-1.dsc] I: copying [./gubbins_3.3.3.orig.tar.gz] I: copying [./gubbins_3.3.3-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 4 16:51:01 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_3.3.3-1.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.3.3 dpkg-source: info: unpacking gubbins_3.3.3.orig.tar.gz dpkg-source: info: unpacking gubbins_3.3.3-1.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2817542/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='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3b7cc82423e54f6bb8c7e43ce703e4e9' 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='2817542' 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.bQNkKiWZ/pbuilderrc_g0CB --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.bQNkKiWZ/b1 --logfile b1/build.log gubbins_3.3.3-1.dsc' SUDO_GID='110' 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 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 10 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2817542/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, pkg-config, 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 ... 19699 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 pkg-config; however: Package pkg-config 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} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{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} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenjp2-7{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix2t64{a} libpng16-16t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} librdmacm1t64{a} libreadline8t64{a} libsharpyuv0{a} libsub-override-perl{a} libsubunit-dev{a} libsubunit0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{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} libxnvctrl0{a} libxrender1{a} libz3-4{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{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-distutils{a} python3-filelock{a} python3-freetype{a} python3-lib2to3{a} python3-minimal{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-virtualenv{a} python3-wheel{a} python3-wheel-whl{a} python3.11{a} python3.11-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 libarchive-cpio-perl libglib2.0-data 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, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 155 MB of archives. After unpacking 638 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libsubunit0 amd64 1.4.2-3 [6160 B] Get: 34 http://deb.debian.org/debian trixie/main amd64 libsubunit-dev amd64 1.4.2-3 [7080 B] Get: 35 http://deb.debian.org/debian trixie/main amd64 check amd64 0.15.2-2+b1 [113 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 67 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 98 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.2 [2428 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 iqtree amd64 2.0.7+dfsg-1+b1 [3671 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.1-1 [1485 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.3.2-0.4+b1 [107 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.3.2-0.4+b1 [120 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.1.0-4 [1113 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-cachetools all 5.3.0-2 [13.3 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-dendropy all 4.6.1-1 [277 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-dill all 0.3.8-1 [81.7 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-distlib all 0.3.8-1 [257 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-filelock all 3.14.0-1 [10.9 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-multiprocess all 0.70.16-2 [105 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-pip-whl all 24.0+dfsg-2 [1774 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.2.1-1 [16.0 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-api all 1.6.1-1 [55.6 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-setuptools-whl all 68.1.2-2 [797 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-wheel-whl all 0.43.0-1 [68.8 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-virtualenv all 20.26.1+ds-1 [70.7 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 tox all 4.15.0-2 [375 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 155 MB in 2s (85.0 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 ... 19699 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21197 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22189 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... 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_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libsubunit0:amd64. Preparing to unpack .../019-libsubunit0_1.4.2-3_amd64.deb ... Unpacking libsubunit0:amd64 (1.4.2-3) ... Selecting previously unselected package libsubunit-dev:amd64. Preparing to unpack .../020-libsubunit-dev_1.4.2-3_amd64.deb ... Unpacking libsubunit-dev:amd64 (1.4.2-3) ... Selecting previously unselected package check:amd64. Preparing to unpack .../021-check_0.15.2-2+b1_amd64.deb ... Unpacking check:amd64 (0.15.2-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../022-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../023-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../024-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../025-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../026-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../027-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../028-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../029-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../030-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../031-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../032-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../033-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../034-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../035-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../036-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../037-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../038-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../039-python3-distutils_3.12.3-1_all.deb ... Unpacking python3-distutils (3.12.3-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../040-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../041-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package fasttree. Preparing to unpack .../042-fasttree_2.1.11-2_amd64.deb ... Unpacking fasttree (2.1.11-2) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../043-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../044-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../045-libfontenc1_1%3a1.1.8-1_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../046-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../047-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../048-libfreetype6_2.13.2+dfsg-1+b4_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package x11-common. Preparing to unpack .../049-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../050-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../051-xfonts-utils_1%3a7.7+6_amd64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../052-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../053-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../054-libnl-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../055-libnl-route-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../056-libibverbs1_50.0-2+b1_amd64.deb ... Unpacking libibverbs1:amd64 (50.0-2+b1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../057-ibverbs-providers_50.0-2+b1_amd64.deb ... Unpacking ibverbs-providers:amd64 (50.0-2+b1) ... Selecting previously unselected package libevent-core-2.1-7t64:amd64. Preparing to unpack .../058-libevent-core-2.1-7t64_2.1.12-stable-8.1+b3_amd64.deb ... Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. Preparing to unpack .../059-libevent-pthreads-2.1-7t64_2.1.12-stable-8.1+b3_amd64.deb ... Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../060-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../061-libnuma1_2.0.18-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.18-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../062-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1t64:amd64. Preparing to unpack .../063-librdmacm1t64_50.0-2+b1_amd64.deb ... Unpacking librdmacm1t64:amd64 (50.0-2+b1) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../064-libfabric1_1.17.0-3+b1_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3+b1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../065-libhwloc15_2.10.0-1+b1_amd64.deb ... Unpacking libhwloc15:amd64 (2.10.0-1+b1) ... Selecting previously unselected package libmunge2:amd64. Preparing to unpack .../066-libmunge2_0.5.15-4_amd64.deb ... Unpacking libmunge2:amd64 (0.5.15-4) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../067-libpciaccess0_0.17-3+b1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-3+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../068-libxau6_1%3a1.0.9-1+b1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1+b1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../069-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../070-libxdmcp6_1%3a1.1.2-3+b1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../071-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../073-libx11-6_2%3a1.8.7-1+b1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../074-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../075-libxnvctrl0_535.171.04-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (535.171.04-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../076-ocl-icd-libopencl1_2.3.2-1+b1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../077-libhwloc-plugins_2.10.0-1+b1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.10.0-1+b1) ... Selecting previously unselected package libpmix2t64:amd64. Preparing to unpack .../078-libpmix2t64_5.0.2-3_amd64.deb ... Unpacking libpmix2t64:amd64 (5.0.2-3) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../079-libedit2_3.1-20230828-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20230828-1+b1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../080-libz3-4_4.8.12-3.1+b2_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm17t64:amd64. Preparing to unpack .../081-libllvm17t64_1%3a17.0.6-11_amd64.deb ... Unpacking libllvm17t64:amd64 (1:17.0.6-11) ... Selecting previously unselected package libamd-comgr2:amd64. Preparing to unpack .../082-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1_amd64.deb ... Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../083-libdrm-common_2.4.120-2_all.deb ... Unpacking libdrm-common (2.4.120-2) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../084-libdrm2_2.4.120-2_amd64.deb ... Unpacking libdrm2:amd64 (2.4.120-2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../085-libdrm-amdgpu1_2.4.120-2_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) ... Selecting previously unselected package libhsakmt1:amd64. Preparing to unpack .../086-libhsakmt1_5.7.0-1_amd64.deb ... Unpacking libhsakmt1:amd64 (5.7.0-1) ... Selecting previously unselected package libhsa-runtime64-1. Preparing to unpack .../087-libhsa-runtime64-1_5.7.1-2_amd64.deb ... Unpacking libhsa-runtime64-1 (5.7.1-2) ... Selecting previously unselected package libamdhip64-5. Preparing to unpack .../088-libamdhip64-5_5.7.1-3_amd64.deb ... Unpacking libamdhip64-5 (5.7.1-3) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../089-libucx0_1.16.0+ds-5_amd64.deb ... Unpacking libucx0:amd64 (1.16.0+ds-5) ... Selecting previously unselected package libopenmpi3t64:amd64. Preparing to unpack .../090-libopenmpi3t64_4.1.6-13.2_amd64.deb ... Unpacking libopenmpi3t64:amd64 (4.1.6-13.2) ... Selecting previously unselected package iqtree. Preparing to unpack .../091-iqtree_2.0.7+dfsg-1+b1_amd64.deb ... Unpacking iqtree (2.0.7+dfsg-1+b1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../092-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../093-libfontconfig1_2.15.0-1.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../094-libpixman-1-0_0.42.2-1+b1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1+b1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../095-libxcb-render0_1.15-1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../096-libxcb-shm0_1.15-1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.15-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../097-libxrender1_1%3a0.9.10-1.1+b1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../098-libcairo2_1.18.0-3+b1_amd64.deb ... Unpacking libcairo2:amd64 (1.18.0-3+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../099-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../100-libfribidi0_1.0.13-3+b1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.13-3+b1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../101-libgfortran5_14-20240330-1_amd64.deb ... Unpacking libgfortran5:amd64 (14-20240330-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../102-libglib2.0-0t64_2.80.1-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.80.1-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../103-libgraphite2-3_1.3.14-2_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../104-libharfbuzz0b_8.3.0-2+b1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (8.3.0-2+b1) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../105-libimagequant0_2.18.0-1+b1_amd64.deb ... Unpacking libimagequant0:amd64 (2.18.0-1+b1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../106-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../107-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../108-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../109-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../110-libjs-sphinxdoc_7.2.6-6_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../111-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package liblbfgsb0:amd64. Preparing to unpack .../112-liblbfgsb0_3.0+dfsg.4-1+b1_amd64.deb ... Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../113-liblcms2-2_2.14-2+b1_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2+b1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../114-liblerc4_4.0.0+ds-4+b1_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../115-libopenjp2-7_2.5.0-2+b3_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.0-2+b3) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../116-libpkgconf3_1.8.1-1+b2_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1+b2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../117-libraqm0_0.10.1-1+b1_amd64.deb ... Unpacking libraqm0:amd64 (0.10.1-1+b1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../118-libsharpyuv0_1.3.2-0.4+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../119-libwebp7_1.3.2-0.4+b1_amd64.deb ... Unpacking libwebp7:amd64 (1.3.2-0.4+b1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../120-libtiff6_4.5.1+git230720-4_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-4) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../121-libwebpdemux2_1.3.2-0.4+b1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.3.2-0.4+b1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../122-libwebpmux3_1.3.2-0.4+b1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.3.2-0.4+b1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../123-pkgconf-bin_1.8.1-1+b2_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../124-pkgconf_1.8.1-1+b2_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1+b2) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../125-pkg-config_1.8.1-1+b2_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1+b2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../126-python3-numpy_1%3a1.26.4+ds-8_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-8) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../127-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../128-python3-pil_10.3.0-2_amd64.deb ... Unpacking python3-pil:amd64 (10.3.0-2) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../129-python3-cairo_1.26.0-1_amd64.deb ... Unpacking python3-cairo (1.26.0-1) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../130-python3-freetype_2.4.0-1_all.deb ... Unpacking python3-freetype (2.4.0-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../131-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../132-python3-reportlab_4.1.0-4_all.deb ... Unpacking python3-reportlab (4.1.0-4) ... Selecting previously unselected package xml-core. Preparing to unpack .../133-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../134-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../135-python3-biopython_1.83+dfsg1-2_amd64.deb ... Unpacking python3-biopython (1.83+dfsg1-2) ... Selecting previously unselected package python3-cachetools. Preparing to unpack .../136-python3-cachetools_5.3.0-2_all.deb ... Unpacking python3-cachetools (5.3.0-2) ... Selecting previously unselected package python3-colorama. Preparing to unpack .../137-python3-colorama_0.4.6-4_all.deb ... Unpacking python3-colorama (0.4.6-4) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../138-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-dendropy. Preparing to unpack .../139-python3-dendropy_4.6.1-1_all.deb ... Unpacking python3-dendropy (4.6.1-1) ... Selecting previously unselected package python3-dill. Preparing to unpack .../140-python3-dill_0.3.8-1_all.deb ... Unpacking python3-dill (0.3.8-1) ... Selecting previously unselected package python3-distlib. Preparing to unpack .../141-python3-distlib_0.3.8-1_all.deb ... Unpacking python3-distlib (0.3.8-1) ... Selecting previously unselected package python3-filelock. Preparing to unpack .../142-python3-filelock_3.14.0-1_all.deb ... Unpacking python3-filelock (3.14.0-1) ... Selecting previously unselected package python3-multiprocess. Preparing to unpack .../143-python3-multiprocess_0.70.16-2_all.deb ... Unpacking python3-multiprocess (0.70.16-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../144-python3-packaging_24.0-1_all.deb ... Unpacking python3-packaging (24.0-1) ... Selecting previously unselected package python3-pip-whl. Preparing to unpack .../145-python3-pip-whl_24.0+dfsg-2_all.deb ... Unpacking python3-pip-whl (24.0+dfsg-2) ... Selecting previously unselected package python3-platformdirs. Preparing to unpack .../146-python3-platformdirs_4.2.1-1_all.deb ... Unpacking python3-platformdirs (4.2.1-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../147-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pyproject-api. Preparing to unpack .../148-python3-pyproject-api_1.6.1-1_all.deb ... Unpacking python3-pyproject-api (1.6.1-1) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../149-python3-scipy_1.11.4-6_amd64.deb ... Unpacking python3-scipy (1.11.4-6) ... Selecting previously unselected package python3-setuptools-whl. Preparing to unpack .../150-python3-setuptools-whl_68.1.2-2_all.deb ... Unpacking python3-setuptools-whl (68.1.2-2) ... Selecting previously unselected package python3-wheel-whl. Preparing to unpack .../151-python3-wheel-whl_0.43.0-1_all.deb ... Unpacking python3-wheel-whl (0.43.0-1) ... Selecting previously unselected package python3-virtualenv. Preparing to unpack .../152-python3-virtualenv_20.26.1+ds-1_all.deb ... Unpacking python3-virtualenv (20.26.1+ds-1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../153-python3-wheel_0.43.0-1_all.deb ... Unpacking python3-wheel (0.43.0-1) ... Selecting previously unselected package raxml. Preparing to unpack .../154-raxml_8.2.13+dfsg-1_amd64.deb ... Unpacking raxml (8.2.13+dfsg-1) ... Selecting previously unselected package tox. Preparing to unpack .../155-tox_4.15.0-2_all.deb ... Unpacking tox (4.15.0-2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../156-zlib1g-dev_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Setting up libpciaccess0:amd64 (0.17-3+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up python3-setuptools-whl (68.1.2-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.45-3) ... Setting up libsubunit0:amd64 (1.4.2-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jun 12 05:40:56 UTC 2025. Universal Time is now: Thu Jun 12 05:40:56 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.80.1-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... 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 (1.8.1-1+b2) ... Setting up libmunge2:amd64 (0.5.15-4) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libhwloc15:amd64 (2.10.0-1+b1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:amd64 (1.3.2-0.4+b1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up python3-wheel-whl (0.43.0-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up raxml (8.2.13+dfsg-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.4+b1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libsubunit-dev:amd64 (1.4.2-3) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libllvm17t64:amd64 (1:17.0.6-11) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up check:amd64 (0.15.2-2+b1) ... Setting up pkg-config:amd64 (1.8.1-1+b2) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libibverbs1:amd64 (50.0-2+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Setting up python3-pip-whl (24.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-distlib (0.3.8-1) ... Setting up python3-freetype (2.4.0-1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-platformdirs (4.2.1-1) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-dill (0.3.8-1) ... Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up python3-multiprocess (0.70.16-2) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-filelock (3.14.0-1) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-cachetools (5.3.0-2) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-pyproject-api (1.6.1-1) ... Setting up python3-virtualenv (20.26.1+ds-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-reportlab (4.1.0-4) ... Setting up python3-dendropy (4.6.1-1) ... Setting up dh-python (6.20240422) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... Setting up python3-scipy (1.11.4-6) ... Setting up tox (4.15.0-2) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.2) ... Setting up iqtree (2.0.7+dfsg-1+b1) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Processing triggers for ca-certificates (20240203) ... 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-3.3.3/ && 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_3.3.3-1_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.3.3-1 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-3.3.3' 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-3.3.3' 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 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... 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/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... 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/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 ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib 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/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/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/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/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... 3.11 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/python3.11/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.11/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-3.3.3' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.3.3' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3/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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parse_phylip.lo parse_phylip.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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -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 -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-3.3.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-3.3.3=. -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 make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/src' Making all in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' make[1]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.3' # 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-3.3.3' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3/src' make run_all_tests make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.3/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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -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-3.3.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-3.3.3=. -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 make[4]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/src' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.3/src' make[5]: Entering directory '/build/reproducible-path/gubbins-3.3.3/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-3.3.3/src' make[4]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/src' Making check in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' rm -rf tests/data mv tests/data.save tests/data make[1]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.3' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.3.3/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gubbins-3.3.3' Making install in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.3/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.3.3/debian/gubbins/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.3.3/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.3.3/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.3.3/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-3.3.3/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-3.3.3/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.3.3/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/reproducible-path/gubbins-3.3.3/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/reproducible-path/gubbins-3.3.3/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-3.3.3/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.3.3/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-3.3.3/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/src' Making install in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3/release' make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.3/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-3.3.3/release' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.3.3' make[4]: Entering directory '/build/reproducible-path/gubbins-3.3.3' 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-3.3.3' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.3.3' # 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 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/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-3.11 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.11 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.11 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.11 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.11 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.11 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.11 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.11 changing mode of build/scripts-3.11/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.11/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.11/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.11/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.11/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.11/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/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-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-311.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-3.3.1.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.11/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.11/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.11/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.11/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.11/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.11/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/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-3.3.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.3.3' 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-3.3.3' dh_installdocs dh_installchangelogs dh_installman dh_python3 I: dh_python3 tools:113: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins/pyjar.py I: dh_python3 tools:113: 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 70552 new size 71216 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 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 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_3.3.3-1_amd64.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.3.3-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.3.3-1_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.3.3-1_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: 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/2817542 and its subdirectories I: Current time: Wed Jun 11 17:42:44 -12 2025 I: pbuilder-time-stamp: 1749706964 Thu May 9 23:19:46 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu May 9 23:19:46 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu May 9 23:24:26 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu May 9 23:24:27 UTC 2024 I: gubbins_3.3.3-1_amd64.changes: Format: 1.8 Date: Sun, 04 Feb 2024 17:45:59 +0100 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: amd64 Version: 3.3.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: gubbins - phylogenetic analysis of genome sequences Changes: gubbins (3.3.3-1) unstable; urgency=medium . * New upstream version * iqtree2.patch: unfuzz. * autoupdate_configure.ac.patch: forwarding not needed. Checksums-Sha1: 5a4f24aa1a7895871f5db000f91060396c036ddc 76492 gubbins-dbgsym_3.3.3-1_amd64.deb b705fdb6aae5ac5f98cda3a80f35cbe895ee8c68 9589 gubbins_3.3.3-1_amd64.buildinfo 0440b57c11637ee87d47cb3c46cd5f9f0e7ddf2c 91508 gubbins_3.3.3-1_amd64.deb Checksums-Sha256: 3679d0fde2e7ae0ad0f6b9f530f01848ec379ac43bdfd7973b5fa363afcc57d0 76492 gubbins-dbgsym_3.3.3-1_amd64.deb db40abd64cf8b173f6d5f50e6137a227c6e13283037476cb0bb72c5f96b6e247 9589 gubbins_3.3.3-1_amd64.buildinfo 3a0c110afc0584306519fb53fc196cbd83f9c3ec512d65581670ab46b995d9cd 91508 gubbins_3.3.3-1_amd64.deb Files: 0530e318762ac61d85a0e9775917c228 76492 debug optional gubbins-dbgsym_3.3.3-1_amd64.deb 9d0f1a519dfee8f1a3d9cace4e20bb6c 9589 science optional gubbins_3.3.3-1_amd64.buildinfo 3d81155df3ec099749d1fd5730aa8105 91508 science optional gubbins_3.3.3-1_amd64.deb Thu May 9 23:24:28 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_2-6211.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bQNkKiWZ/gubbins_3.3.3-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bQNkKiWZ/gubbins_3.3.3-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bQNkKiWZ/gubbins_3.3.3-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bQNkKiWZ/b1/gubbins_3.3.3-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bQNkKiWZ/b2/gubbins_3.3.3-1_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 abc.DotChangesFile ## main (total time: 0.367s) 0.367s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 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: 695ms CPU time consumed: 695ms Thu May 9 23:24:29 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 23:24:29 UTC 2024 I: gubbins from trixie built successfully and reproducibly on amd64. Thu May 9 23:24:31 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 23:24:31 UTC 2024 I: Submitting 12K b1/gubbins_3.3.3-1_amd64.buildinfo.asc Thu May 9 23:24:32 UTC 2024 I: Submitting 12K b2/gubbins_3.3.3-1_amd64.buildinfo.asc Thu May 9 23:24:33 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 23:24:33 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 23:24:33 UTC 2024 I: Removing signed gubbins_3.3.3-1_amd64.buildinfo.asc files: removed './b1/gubbins_3.3.3-1_amd64.buildinfo.asc' removed './b2/gubbins_3.3.3-1_amd64.buildinfo.asc'