Thu May 2 02:24:41 UTC 2024 I: starting to build macsyfinder/trixie/arm64 on jenkins on '2024-05-02 02:24' Thu May 2 02:24:41 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_11/41922/console.log Thu May 2 02:24:41 UTC 2024 I: Downloading source for trixie/macsyfinder=2.1.3-1 --2024-05-02 02:24:41-- http://deb.debian.org/debian/pool/main/m/macsyfinder/macsyfinder_2.1.3-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2460 (2.4K) [text/prs.lines.tag] Saving to: ‘macsyfinder_2.1.3-1.dsc’ 0K .. 100% 263M=0s 2024-05-02 02:24:41 (263 MB/s) - ‘macsyfinder_2.1.3-1.dsc’ saved [2460/2460] Thu May 2 02:24:41 UTC 2024 I: macsyfinder_2.1.3-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: macsyfinder Binary: macsyfinder Architecture: amd64 i386 arm64 Version: 2.1.3-1 Maintainer: Debian Med Packaging Team Uploaders: bertrand Neron Homepage: https://github.com/gem-pasteur/macsyfinder Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/macsyfinder Vcs-Git: https://salsa.debian.org/med-team/macsyfinder.git Testsuite: autopkgtest Testsuite-Triggers: python3-setuptools Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, pybuild-plugin-pyproject, python3-setuptools, python3-sphinx, python3-networkx , python3-yaml , python3-colorlog , python3-colorama, python3-pandas , python3-sphinx-rtd-theme , tex-gyre , texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer, debhelper Package-List: macsyfinder deb science optional arch=amd64,i386,arm64 Checksums-Sha1: 7b38e2828d2f36fb3aa6ed5b6a6cd2e1360ad80c 37844961 macsyfinder_2.1.3.orig.tar.gz db8874cc68f973b0c2d8aaee322bf3f5b5760d17 10012 macsyfinder_2.1.3-1.debian.tar.xz Checksums-Sha256: 64dbcfd5d466349e2f9008ef6d7fc687b66eb84754c09108abc92d535f21aaf0 37844961 macsyfinder_2.1.3.orig.tar.gz 27c871c88d7a83bbf30ccc54a3ebf57458454eda87705277364b16096e4d874b 10012 macsyfinder_2.1.3-1.debian.tar.xz Files: f8c2d2509063f9a894a453dc8efcf85a 37844961 macsyfinder_2.1.3.orig.tar.gz ded6a6123a9ea70a39f6de166b8d33c8 10012 macsyfinder_2.1.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmXgnJsACgkQPCZ2P2xn 5uLSWg//QhcjEBLLgovwFjJn4hRYaWS5jBZCIVTOaVagF8/ZuCub1SNkVpE+RDsl 42WEW3sIiPnH5K/EjqZbu3R8cYsptyLT7eOwSS5pBAdd09fCrtDfzQVuQBXCRE4V QJvPv0qRF2/rXpK6fEn2upSnk5QQ5iiSGFGDw0/7b/4WkqRmmjUdJS6Rog1SOTO5 pavWa6illyt4gJv9NczJHAI4R4GXYOr+DdxXPsuFfge7frq15lKa/ScmnR4SO5Az p2tgnStGBaszIU4lwnHOOyw+0SerIwq0rAaM13O+cH41U7Ho+jzREQEVhSApwPXh lGjPWgmVr7ZxiUSKD1IgBy4xIunnD/IWPl5OZR7kypGmsG/OFRfo9XQiRgnN9BEq FhJrSEoKryTt/IiQ7S7Y/8rGqprqMzqODoju3vzNJGJryQ1HhJwhrAt+rLgS7MG+ ZY6f9lnFgGJHeNugP56SgJIuThPou47bXRZBYYxZwGfVw6K/5ImNuY54jgAWb8Xi iZX+gqEc7pe7DU5lazWk/6F/diunGzY9T7yCOkHurShKUedKnTEJRdGjP6HVWlOl 4MR2O7FUb+nTF7Z9CZTEk0T1Ac0ZmouNDESONoNFN2o30Mz4ICo9zf9ZwvJTPlHl Fh9YrM4bAeRIXwq4Xos+xLtRYDtgqIGTY4z/eWnjzXwb7ZmIiKY= =M9vW -----END PGP SIGNATURE----- Thu May 2 02:24:41 UTC 2024 I: Checking whether the package is not for us Thu May 2 02:24:41 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Thu May 2 02:24:41 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Thu May 2 02:35:15 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 3 20:47:44 -12 2025 I: pbuilder-time-stamp: 1749026864 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 [macsyfinder_2.1.3-1.dsc] I: copying [./macsyfinder_2.1.3.orig.tar.gz] I: copying [./macsyfinder_2.1.3-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 29 15:02:51 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.1.3-1.dsc: no acceptable signature found dpkg-source: info: extracting macsyfinder in macsyfinder-2.1.3 dpkg-source: info: unpacking macsyfinder_2.1.3.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.1.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying privacy dpkg-source: info: applying fix-test-parse.patch dpkg-source: info: applying do_not_test_parse_model_old_syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2160584/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='2872e68b8e2a4dc3a08d7496ce813803' 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='2160584' 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.L8L7wnrJ/pbuilderrc_Rr8Y --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.L8L7wnrJ/b1 --logfile b1/build.log macsyfinder_2.1.3-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 24 13:38 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2160584/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: arm64 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, python3, pybuild-plugin-pyproject, python3-setuptools, python3-sphinx, python3-networkx, python3-yaml, python3-colorlog, python3-colorama, python3-pandas, python3-sphinx-rtd-theme, tex-gyre, texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19915 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 python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-colorlog; however: Package python3-colorlog is not installed. pbuilder-satisfydepends-dummy depends on python3-colorama; however: Package python3-colorama is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-plain-generic; however: Package texlive-plain-generic is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on latexmk; however: Package latexmk is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} hmmer{a} intltool-debian{a} latexmk{a} libabsl20230802{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libkpathsea6{a} liblab-gamut1{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} librav1e0{a} libsharpyuv0{a} libsm6{a} libsub-override-perl{a} libsvtav1enc1d1{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libzzip-0-13t64{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-recommended{a} texlive-plain-generic{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} The following packages are RECOMMENDED but will NOT be installed: apvlv atril curl dvisvgm evince fonts-liberation2 fonts-texgyre fonts-texgyre-math ghostscript gv libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx mupdf okular qpdfview qpdfview-ps-plugin shared-mime-info tipa viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 126 MB of archives. After unpacking 398 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-sequence-python3 which is a virtual package, provided by: - dh-python (6.20240422), but it is not installable Depends: python3 but it is not installable Depends: pybuild-plugin-pyproject but it is not installable Depends: python3-setuptools but it is not installable Depends: python3-sphinx but it is not installable Depends: python3-networkx but it is not installable Depends: python3-yaml but it is not installable Depends: python3-colorlog but it is not installable Depends: python3-colorama but it is not installable Depends: python3-pandas but it is not installable Depends: python3-sphinx-rtd-theme but it is not installable Depends: texlive-latex-extra but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) ca-certificates [20240203 (testing)] 4) dh-python [6.20240422 (testing)] 5) docutils-common [0.20.1+dfsg-3 (testing)] 6) fonts-font-awesome [5.0.10+really4.7.0~dfsg-4.1 (testing)] 7) fonts-lato [2.015-1 (testing)] 8) libapache-pom-java [29-2 (testing)] 9) libblis4-serial [0.9.0-1+b2 (testing)] 10) libcommons-logging-java [1.3.0-1 (testing)] 11) libcommons-parent-java [56-1 (testing)] 12) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 13) libfontbox-java [1:1.8.16-5 (testing)] 14) libgfortran5 [14-20240330-1 (testing)] 15) libjs-jquery [3.6.1+dfsg+~3.5.14-1 (testing)] 16) libjs-sphinxdoc [7.2.6-6 (testing)] 17) libjs-underscore [1.13.4~dfsg+~1.11.4-3 (testing)] 18) libjson-perl [4.10000-1 (testing)] 19) liblapack3 [3.12.0-3 (testing)] 20) libpdfbox-java [1:1.8.16-5 (testing)] 21) libpython3-stdlib [3.11.8-1 (testing)] 22) libpython3.11-minimal [3.11.9-1 (testing)] 23) libpython3.11-stdlib [3.11.9-1 (testing)] 24) libpython3.12-minimal [3.12.3-1 (testing)] 25) libpython3.12-stdlib [3.12.3-1 (testing)] 26) libreadline8t64 [8.2-4 (testing)] 27) libssl3t64 [3.2.1-3 (testing)] 28) libyaml-0-2 [0.2.5-1+b1 (testing)] 29) media-types [10.1.0 (testing)] 30) netbase [6.4 (testing)] 31) openssl [3.2.1-3 (testing)] 32) preview-latex-style [13.2-1 (testing)] 33) pybuild-plugin-pyproject [6.20240422 (testing)] 34) python-babel-localedata [2.14.0-1 (testing)] 35) python3 [3.11.8-1 (testing)] 36) python3-alabaster [0.7.12-1 (testing)] 37) python3-babel [2.14.0-1 (testing)] 38) python3-build [1.1.1-1 (testing)] 39) python3-certifi [2023.11.17-1 (testing)] 40) python3-chardet [5.2.0+dfsg-1 (testing)] 41) python3-charset-normalizer [3.3.2-1 (testing)] 42) python3-colorama [0.4.6-4 (testing)] 43) python3-colorlog [6.8.2-1 (testing)] 44) python3-dateutil [2.9.0-2 (testing)] 45) python3-distutils [3.12.3-1 (testing)] 46) python3-docutils [0.20.1+dfsg-3 (testing)] 47) python3-idna [3.6-2 (testing)] 48) python3-imagesize [1.4.1-1 (testing)] 49) python3-installer [0.7.0+dfsg1-3 (testing)] 50) python3-jinja2 [3.1.3-1 (testing)] 51) python3-lib2to3 [3.12.3-1 (testing)] 52) python3-markupsafe [2.1.5-1 (testing)] 53) python3-minimal [3.11.8-1 (testing)] 54) python3-networkx [2.8.8-2 (testing)] 55) python3-numpy [1:1.24.2-2 (testing)] 56) python3-packaging [24.0-1 (testing)] 57) python3-pandas [2.1.4+dfsg-5 (testing)] 58) python3-pandas-lib [2.1.4+dfsg-5 (testing)] 59) python3-pkg-resources [68.1.2-2 (testing)] 60) python3-pygments [2.17.2+dfsg-1 (testing)] 61) python3-pyproject-hooks [1.0.0-2 (testing)] 62) python3-requests [2.31.0+dfsg-1 (testing)] 63) python3-roman [3.3-3 (testing)] 64) python3-setuptools [68.1.2-2 (testing)] 65) python3-six [1.16.0-6 (testing)] 66) python3-snowballstemmer [2.2.0-4 (testing)] 67) python3-sphinx [7.2.6-6 (testing)] 68) python3-sphinx-rtd-theme [2.0.0+dfsg-1 (testing)] 69) python3-sphinxcontrib.jquery [4.1-5 (testing)] 70) python3-toml [0.10.2-1 (testing)] 71) python3-tz [2024.1-2 (testing)] 72) python3-urllib3 [1.26.18-2 (testing)] 73) python3-wheel [0.43.0-1 (testing)] 74) python3-yaml [6.0.1-2 (testing)] 75) python3.11 [3.11.9-1 (testing)] 76) python3.11-minimal [3.11.9-1 (testing)] 77) python3.12 [3.12.3-1 (testing)] 78) python3.12-minimal [3.12.3-1 (testing)] 79) readline-common [8.2-4 (testing)] 80) sgml-base [1.31 (testing)] 81) sphinx-common [7.2.6-6 (testing)] 82) sphinx-rtd-theme-common [2.0.0+dfsg-1 (testing)] 83) texlive-latex-extra [2023.20240207-1 (testing)] 84) texlive-pictures [2023.20240207-1 (testing)] 85) tzdata [2024a-3 (testing)] 86) xml-core [0.19 (testing)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lmodern{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} hmmer{a} intltool-debian{a} latexmk{a} libabsl20230802{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavif16{a} libblis4-serial{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdav1d7{a} libdb5.3t64{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libkpathsea6{a} liblab-gamut1{a} liblapack3{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libssl3t64{a} libsub-override-perl{a} libsvtav1enc1d1{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyaml-0-2{a} libyuv0{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} preview-latex-style{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-colorlog{a} python3-dateutil{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-installer{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pygments{a} python3-pyproject-hooks{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-toml{a} python3-tz{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-plain-generic{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: apvlv atril curl default-jre dvisvgm evince fonts-liberation2 fonts-texgyre fonts-texgyre-math ghostscript gv javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx mupdf okular python3-bottleneck python3-bs4 python3-gdal python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-pydot python3-pygraphviz python3-scipy python3-tables qpdfview qpdfview-ps-plugin ruby shared-mime-info tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 210 newly installed, 2 to remove and 0 not upgraded. Need to get 218 MB of archives. After unpacking 805 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [625 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 16 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 45 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libann0 arm64 1.1.2+doc-9+b1 [23.6 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libcdt5 arm64 2.42.2-8 [38.3 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libcgraph6 arm64 2.42.2-8 [60.3 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libaom3 arm64 3.8.2-2 [1528 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libdav1d7 arm64 1.4.1-1 [251 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libgav1-1 arm64 0.19.0-2+b1 [481 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 librav1e0 arm64 0.7.1-2 [630 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libsvtav1enc1d1 arm64 1.7.0+dfsg-2+b1 [1083 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libyuv0 arm64 0.0~git202401110.af6ac82-1 [123 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libavif16 arm64 1.0.4-2 [99.4 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-dav1d arm64 1.17.6-1+b2 [9888 B] Get: 84 http://deb.debian.org/debian trixie/main arm64 libde265-0 arm64 1.0.15-1+b1 [151 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-libde265 arm64 1.17.6-1+b2 [13.0 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libheif1 arm64 1.17.6-1+b2 [247 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libgd3 arm64 2.3.3-9+b3 [114 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2 [141 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-1+b1 [478 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.52.1+ds-1 [204 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.52.1+ds-1 [45.4 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.52.1+ds-1 [33.1 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libpathplan4 arm64 2.42.2-8 [40.3 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libgvc6 arm64 2.42.2-8 [615 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libgvpr2 arm64 2.42.2-8 [179 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 liblab-gamut1 arm64 2.42.2-8 [198 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 graphviz arm64 2.42.2-8 [571 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libdivsufsort3 arm64 2.0.1-6 [39.1 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 hmmer arm64 3.4+dfsg-2 [955 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 tex-common all 6.18 [32.5 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 134 http://deb.debian.org/debian trixie/main arm64 libkpathsea6 arm64 2023.20230311.66589-9+b2 [151 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libptexenc1 arm64 2023.20230311.66589-9+b2 [46.3 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libsynctex2 arm64 2023.20230311.66589-9+b2 [59.8 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libtexlua53-5 arm64 2023.20230311.66589-9+b2 [105 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libpotrace0 arm64 1.16-2+b1 [23.1 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libteckit0 arm64 2.5.12+ds1-1 [300 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.1-1 [77.5 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2+b1 [56.7 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 texlive-binaries arm64 2023.20230311.66589-9+b2 [7353 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 146 http://deb.debian.org/debian trixie/main arm64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 latexmk all 1:4.85-1 [501 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 149 http://deb.debian.org/debian trixie/main arm64 libblis4-serial arm64 0.9.0-1+b2 [791 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-build all 1.1.1-1 [32.5 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2023.11.17-1 [155 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-colorlog all 6.8.2-1 [27.2 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-roman all 3.3-3 [9880 B] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.6-2 [37.0 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1 [14.6 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 2.8.8-2 [1425 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.24.2-2 [4122 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.1.4+dfsg-5 [6620 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 7.2.6-6 [702 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 7.2.6-6 [552 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 208 http://deb.debian.org/debian trixie/main arm64 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 209 http://deb.debian.org/debian trixie/main arm64 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Get: 210 http://deb.debian.org/debian trixie/main arm64 texlive-plain-generic all 2023.20240207-1 [29.0 MB] Fetched 218 MB in 2s (113 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. libpam-modules:arm64 depends on libdb5.3. (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 ... 19915 files and directories currently installed.) Removing libdb5.3:arm64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:arm64. (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 ... 19908 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_arm64.deb ... Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19914 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (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 ... 19901 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package fonts-lato. (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 ... 19916 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (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 ... 20258 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.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-3_all.deb ... Unpacking tzdata (2024a-3) ... 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:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 21250 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.2.1-3_arm64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-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 .../021-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... 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 ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libfontbox-java (1:1.8.16-5) ... Setting up liblab-gamut1:arm64 (2.42.2-8) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... 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:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libblis4-serial:arm64 (0.9.0-1+b2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blis-serial/libblis.so.4 to provide /usr/lib/aarch64-linux-gnu/libblis.so.4 (libblis.so.4-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/blis-serial/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libsvtav1enc1d1:arm64 (1.7.0+dfsg-2+b1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up librav1e0:arm64 (0.7.1-2) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jun 4 08:49:18 UTC 2025. Universal Time is now: Wed Jun 4 08:49:18 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.2+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:arm64 (2.5.12+ds1-1) ... Setting up libpathplan4:arm64 (2.42.2-8) ... Setting up libapache-pom-java (29-2) ... Setting up libann0 (1.1.2+doc-9+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.13-3+b1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:arm64 (2023.20230311.66589-9+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libltdl7:arm64 (2.4.7-7+b1) ... Setting up libkpathsea6:arm64 (2023.20230311.66589-9+b2) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.3.2-0.4+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:arm64 (1.4.1-1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libjson-perl (4.10000-1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:arm64 (20230802.1-4) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2) ... Setting up sgml-base (1.31) ... Setting up libcdt5:arm64 (2.42.2-8) ... Setting up libcgraph6:arm64 (2.42.2-8) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:arm64 (1.0.15-1+b1) ... Setting up libdivsufsort3:arm64 (2.0.1-6) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libyuv0:arm64 (0.0~git202401110.af6ac82-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:arm64 (2023.20230311.66589-9+b2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (1.16-2+b1) ... 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 python3.12-minimal (3.12.3-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libptexenc1:arm64 (2023.20230311.66589-9+b2) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libgav1-1:arm64 (0.19.0-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libgvpr2:arm64 (2.42.2-8) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up libpaper1:arm64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libavif16:arm64 (1.0.4-2) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libxpm4:arm64 (1:3.5.17-1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpango-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-1+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up sphinx-common (7.2.6-6) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libpangoft2-1.0-0:arm64 (1.52.1+ds-1) ... Setting up tex-gyre (20180621-6) ... Setting up libpangocairo-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxmu6:arm64 (2:1.1.3-3+b2) ... Setting up libxi6:arm64 (2:1.8.1-1) ... Setting up preview-latex-style (13.2-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libxaw7:arm64 (2:1.0.14-1+b2) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.6-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up texlive-binaries (2023.20230311.66589-9+b2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-dateutil (2.9.0-2) ... Setting up python3-build (1.1.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up texlive-base (2023.20240207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.6-4) ... Setting up python3-colorlog (6.8.2-1) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up texlive-plain-generic (2023.20240207-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-networkx (2.8.8-2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up texlive-pictures (2023.20240207-1) ... Setting up texlive-fonts-recommended (2023.20240207-1) ... Setting up dh-python (6.20240422) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-5) ... Setting up latexmk (1:4.85-1) ... Setting up texlive-latex-extra (2023.20240207-1) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Setting up libheif-plugin-dav1d:arm64 (1.17.6-1+b2) ... Setting up libheif-plugin-libde265:arm64 (1.17.6-1+b2) ... Setting up libheif1:arm64 (1.17.6-1+b2) ... Setting up libgd3:arm64 (2.3.3-9+b3) ... Setting up libgvc6 (2.42.2-8) ... Setting up graphviz (2.42.2-8) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... 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. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... 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/macsyfinder-2.1.3/ && 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 > ../macsyfinder_2.1.3-1_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.1.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11 * Building wheel... running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/macsypy copying macsypy/utils.py -> build/lib/macsypy copying macsypy/system.py -> build/lib/macsypy copying macsypy/solution.py -> build/lib/macsypy copying macsypy/serialization.py -> build/lib/macsypy copying macsypy/search_genes.py -> build/lib/macsypy copying macsypy/report.py -> build/lib/macsypy copying macsypy/registries.py -> build/lib/macsypy copying macsypy/profile.py -> build/lib/macsypy copying macsypy/package.py -> build/lib/macsypy copying macsypy/model_conf_parser.py -> build/lib/macsypy copying macsypy/model.py -> build/lib/macsypy copying macsypy/licenses.py -> build/lib/macsypy copying macsypy/hit.py -> build/lib/macsypy copying macsypy/gene.py -> build/lib/macsypy copying macsypy/error.py -> build/lib/macsypy copying macsypy/definition_parser.py -> build/lib/macsypy copying macsypy/database.py -> build/lib/macsypy copying macsypy/config.py -> build/lib/macsypy copying macsypy/cluster.py -> build/lib/macsypy copying macsypy/__init__.py -> build/lib/macsypy creating build/lib/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsydata.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyconfig.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsy_merge_results.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsy_gembase_split.py -> build/lib/macsypy/scripts copying macsypy/scripts/__init__.py -> build/lib/macsypy/scripts installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64 creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/macsypy creating build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/__init__.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsy_gembase_split.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsy_merge_results.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsyconfig.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsydata.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsyfinder.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsyprofile.py -> build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/__init__.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/cluster.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/config.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/database.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/definition_parser.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/error.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/gene.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/hit.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/licenses.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/model.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/model_conf_parser.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/package.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/profile.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/registries.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/report.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/search_genes.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/serialization.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/solution.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/system.py -> build/bdist.linux-aarch64/wheel/macsypy copying build/lib/macsypy/utils.py -> build/bdist.linux-aarch64/wheel/macsypy running install_data creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.data creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.data/data creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.data/data/share creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.data/data/share/macsyfinder creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.data/data/share/macsyfinder/models copying data/models/README -> build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.data/data/share/macsyfinder/models running install_egg_info running egg_info creating MacSyFinder.egg-info writing MacSyFinder.egg-info/PKG-INFO writing dependency_links to MacSyFinder.egg-info/dependency_links.txt writing entry points to MacSyFinder.egg-info/entry_points.txt writing requirements to MacSyFinder.egg-info/requires.txt writing top-level names to MacSyFinder.egg-info/top_level.txt writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' reading manifest file 'MacSyFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'doc/build/html' warning: no files found matching 'doc/build/latex/macsyfinder.pdf' warning: no files found matching 'etc/macsyfinder.conf' warning: no previously-included files matching '*' found under directory 'tests/__pycache__/' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no previously-included files found matching '.coverage' warning: no previously-included files found matching 'coverage_html/' warning: no previously-included files found matching '.gitignore' warning: no previously-included files found matching '.travis.yml' warning: no previously-included files found matching '.github/' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' adding license file 'COPYING' writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' Copying MacSyFinder.egg-info to build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.3.dist-info/WHEEL creating '/build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/.tmp-k8114nn0/MacSyFinder-2.1.3-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'MacSyFinder-2.1.3.data/data/share/macsyfinder/models/README' adding 'macsypy/__init__.py' adding 'macsypy/cluster.py' adding 'macsypy/config.py' adding 'macsypy/database.py' adding 'macsypy/definition_parser.py' adding 'macsypy/error.py' adding 'macsypy/gene.py' adding 'macsypy/hit.py' adding 'macsypy/licenses.py' adding 'macsypy/model.py' adding 'macsypy/model_conf_parser.py' adding 'macsypy/package.py' adding 'macsypy/profile.py' adding 'macsypy/registries.py' adding 'macsypy/report.py' adding 'macsypy/search_genes.py' adding 'macsypy/serialization.py' adding 'macsypy/solution.py' adding 'macsypy/system.py' adding 'macsypy/utils.py' adding 'macsypy/scripts/__init__.py' adding 'macsypy/scripts/macsy_gembase_split.py' adding 'macsypy/scripts/macsy_merge_results.py' adding 'macsypy/scripts/macsyconfig.py' adding 'macsypy/scripts/macsydata.py' adding 'macsypy/scripts/macsyfinder.py' adding 'macsypy/scripts/macsyprofile.py' adding 'MacSyFinder-2.1.3.dist-info/COPYING' adding 'MacSyFinder-2.1.3.dist-info/METADATA' adding 'MacSyFinder-2.1.3.dist-info/WHEEL' adding 'MacSyFinder-2.1.3.dist-info/entry_points.txt' adding 'MacSyFinder-2.1.3.dist-info/top_level.txt' adding 'MacSyFinder-2.1.3.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Successfully built MacSyFinder-2.1.3-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build; python3.11 -m unittest discover -v test_Config (tests.test_Config.TestConfig.test_Config) ... ok test_Config_args (tests.test_Config.TestConfig.test_Config_args) ... ok test_Config_conf_file_virtualenv (tests.test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok test_Config_default_conf_file (tests.test_Config.TestConfig.test_Config_default_conf_file) ... ok test_Config_file_bad_values (tests.test_Config.TestConfig.test_Config_file_bad_values) ... ok test_Config_file_n_args (tests.test_Config.TestConfig.test_Config_file_n_args) ... ok test_bad_db_type (tests.test_Config.TestConfig.test_bad_db_type) ... ok test_bad_models_dir (tests.test_Config.TestConfig.test_bad_models_dir) ... ok test_bad_sequence_db (tests.test_Config.TestConfig.test_bad_sequence_db) ... ok test_bad_topology (tests.test_Config.TestConfig.test_bad_topology) ... ok test_bad_topology_file (tests.test_Config.TestConfig.test_bad_topology_file) ... ok test_bad_values (tests.test_Config.TestConfig.test_bad_values) ... ok test_cmd_config_file (tests.test_Config.TestConfig.test_cmd_config_file) ... ok test_config_file_2_dict (tests.test_Config.TestConfig.test_config_file_2_dict) ... ok test_cut_ga (tests.test_Config.TestConfig.test_cut_ga) ... ok test_e_value_search (tests.test_Config.TestConfig.test_e_value_search) ... ok test_hit_weights (tests.test_Config.TestConfig.test_hit_weights) ... ok test_hmmsearch (tests.test_Config.TestConfig.test_hmmsearch) ... ok test_hmmsearch_set_by_user (tests.test_Config.TestConfig.test_hmmsearch_set_by_user) ... ok test_model_conf (tests.test_Config.TestConfig.test_model_conf) ... ok test_models_dir (tests.test_Config.TestConfig.test_models_dir) ... ok test_no_hmmsearch (tests.test_Config.TestConfig.test_no_hmmsearch) ... ok test_out_dir (tests.test_Config.TestConfig.test_out_dir) ... ok test_previous_n_sequence_db (tests.test_Config.TestConfig.test_previous_n_sequence_db) ... ok test_previous_wo_cfg (tests.test_Config.TestConfig.test_previous_wo_cfg) ... ok test_project_config_file (tests.test_Config.TestConfig.test_project_config_file) ... ok test_save (tests.test_Config.TestConfig.test_save) ... ok test_set_log_level (tests.test_Config.TestConfig.test_set_log_level) ... ok test_set_option (tests.test_Config.TestConfig.test_set_option) ... ok test_str_2_tuple (tests.test_Config.TestConfig.test_str_2_tuple) ... ok test_working_dir (tests.test_Config.TestConfig.test_working_dir) ... ok test_NoneConfig (tests.test_Config.TestNoneConfig.test_NoneConfig) ... ok test_bad_exchangeable_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... ok test_bad_gene_inter_gene_max_space_2 (tests.test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) ... ok test_bad_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... ok test_bad_max_nb_genes (tests.test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... ok test_bad_min_genes_required (tests.test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... ok test_bad_min_genes_required_2 (tests.test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... ok test_bad_min_mandatory_genes_required (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... ok test_bad_min_mandatory_genes_required_2 (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... ok test_bad_min_mandatory_genes_required_4 (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... ok test_exchangeable_inheritance (tests.test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... ok test_gene_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... ok test_gene_no_name (tests.test_DefinitionParser.TestModelParser.test_gene_no_name) ... ok test_gene_w_unkown_attr (tests.test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... ok test_inter_gene_max_space_cfg (tests.test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... ok test_invalid_homolog (tests.test_DefinitionParser.TestModelParser.test_invalid_homolog) ... ok test_invalid_homolog_2 (tests.test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... ok test_invalid_presence (tests.test_DefinitionParser.TestModelParser.test_invalid_presence) ... ok test_loner (tests.test_DefinitionParser.TestModelParser.test_loner) ... ok test_max_nb_genes_cfg (tests.test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... ok test_min_genes_required_cfg (tests.test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... ok test_min_mandatory_genes_required_cfg (tests.test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... ok test_min_mandatory_genes_required_lesser_than_mandatory_genes (tests.test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... ok test_model_w_unkown_attr (tests.test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... ok test_multi_loci_cfg (tests.test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... ok test_multi_model (tests.test_DefinitionParser.TestModelParser.test_multi_model) ... ok test_multi_system (tests.test_DefinitionParser.TestModelParser.test_multi_system) ... ok test_no_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... ok test_only_one_accessory (tests.test_DefinitionParser.TestModelParser.test_only_one_accessory) ... ok test_parse_model_old_syntax (tests.test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails' test_parse_with_exchangeable (tests.test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... ok test_wo_presence (tests.test_DefinitionParser.TestModelParser.test_wo_presence) ... ok test_add_exchangeable (tests.test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok test_alternate_of (tests.test_Exchangeable.TestExchangeable.test_alternate_of) ... ok test_is_exchangeable (tests.test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok test_loner (tests.test_Exchangeable.TestExchangeable.test_loner) ... ok test_model (tests.test_Exchangeable.TestExchangeable.test_model) ... ok test_multi_system (tests.test_Exchangeable.TestExchangeable.test_multi_system) ... ok test_add_get_gene (tests.test_GeneBank.Test.test_add_get_gene) ... ok test_contains (tests.test_GeneBank.Test.test_contains) ... ok test_genes_fqn (tests.test_GeneBank.Test.test_genes_fqn) ... ok test_get_uniq_object (tests.test_GeneBank.Test.test_get_uniq_object) ... ok test_iter (tests.test_GeneBank.Test.test_iter) ... ok test_fasta_iter (tests.test_Indexes.TestFastaIter.test_fasta_iter) ... ok test_fasta_iter_bad_fasta (tests.test_Indexes.TestFastaIter.test_fasta_iter_bad_fasta) ... ok test_build_force (tests.test_Indexes.TestIndex.test_build_force) ... ok test_build_idx_gzip_seq (tests.test_Indexes.TestIndex.test_build_idx_gzip_seq) ... ok test_build_idx_older_than_fasta (tests.test_Indexes.TestIndex.test_build_idx_older_than_fasta) ... ok test_build_idx_point_wrong_fasta (tests.test_Indexes.TestIndex.test_build_idx_point_wrong_fasta) ... ok test_build_my_indexes (tests.test_Indexes.TestIndex.test_build_my_indexes) ... ok test_build_no_idx (tests.test_Indexes.TestIndex.test_build_no_idx) ... ok test_build_not_writable (tests.test_Indexes.TestIndex.test_build_not_writable) ... ok test_build_with_idx (tests.test_Indexes.TestIndex.test_build_with_idx) ... ok test_empty_fasta (tests.test_Indexes.TestIndex.test_empty_fasta) ... ok test_find_my_indexes (tests.test_Indexes.TestIndex.test_find_my_indexes) ... ok test_index_dir (tests.test_Indexes.TestIndex.test_index_dir) ... ok test_iter (tests.test_Indexes.TestIndex.test_iter) ... ok test_allowed_hits (tests.test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok test_forbidden_hits (tests.test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok test_hits (tests.test_LikelySystem.LikelySystemTest.test_hits) ... ok test_init (tests.test_LikelySystem.LikelySystemTest.test_init) ... ok test_str (tests.test_LikelySystem.LikelySystemTest.test_str) ... ok test_hits (tests.test_LikelySystem.UnlikelySystemTest.test_hits) ... ok test_init (tests.test_LikelySystem.UnlikelySystemTest.test_init) ... ok test_reason (tests.test_LikelySystem.UnlikelySystemTest.test_reason) ... ok test_str (tests.test_LikelySystem.UnlikelySystemTest.test_str) ... ok test_MacsyDefaults_no_virtual_env (tests.test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok test_MacsyDefaults_virtual_env (tests.test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok test_ordered_match (tests.test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok test_sort_hits_by_status (tests.test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... ok test_unordered_match (tests.test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok test_accessor_mutator (tests.test_Model.TestModel.test_accessor_mutator) ... ok test_eq (tests.test_Model.TestModel.test_eq) ... ok test_filter (tests.test_Model.TestModel.test_filter) ... ok test_fqn (tests.test_Model.TestModel.test_fqn) ... ok test_get_gene (tests.test_Model.TestModel.test_get_gene) ... ok test_gt (tests.test_Model.TestModel.test_gt) ... ok test_hash (tests.test_Model.TestModel.test_hash) ... ok test_inter_gene_max_space (tests.test_Model.TestModel.test_inter_gene_max_space) ... ok test_lt (tests.test_Model.TestModel.test_lt) ... ok test_max_nb_genes (tests.test_Model.TestModel.test_max_nb_genes) ... ok test_min_genes_required (tests.test_Model.TestModel.test_min_genes_required) ... ok test_min_mandatory_genes_required (tests.test_Model.TestModel.test_min_mandatory_genes_required) ... ok test_multi_loci (tests.test_Model.TestModel.test_multi_loci) ... ok test_str (tests.test_Model.TestModel.test_str) ... ok test_add_get_model (tests.test_ModelBank.Test.test_add_get_model) ... ok test_contains (tests.test_ModelBank.Test.test_contains) ... ok test_get_uniq_object (tests.test_ModelBank.Test.test_get_uniq_object) ... ok test_iter (tests.test_ModelBank.Test.test_iter) ... ok test_execute_hmm_protected_path (tests.test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok test_execute_hmm_w_GA_n_nocutga (tests.test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok test_execute_hmm_with_GA (tests.test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping' test_execute_hmm_wo_GA (tests.test_Profile.TestProfile.test_execute_hmm_wo_GA) ... ok test_execute_hmmer_failed (tests.test_Profile.TestProfile.test_execute_hmmer_failed) ... ok test_execute_unknown_binary (tests.test_Profile.TestProfile.test_execute_unknown_binary) ... ok test_ga_threshold (tests.test_Profile.TestProfile.test_ga_threshold) ... ok test_len (tests.test_Profile.TestProfile.test_len) ... ok test_str (tests.test_Profile.TestProfile.test_str) ... ok test_get_profile (tests.test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok test_get_uniq_object (tests.test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok test_unknow_profile (tests.test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok test_hits (tests.test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok test_init (tests.test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok test_str (tests.test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok test_fill_gembase_min_max_default_topology (tests.test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok test_fill_gembase_min_max_with_topology (tests.test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok test_fill_ordered_replicon_min_max (tests.test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok test_fill_topology (tests.test_RepliconDB.Test.test_fill_topology) ... ok test_get (tests.test_RepliconDB.Test.test_get) ... ok test_getitem (tests.test_RepliconDB.Test.test_getitem) ... ok test_guess_if_really_gembase (tests.test_RepliconDB.Test.test_guess_if_really_gembase) ... ok test_in (tests.test_RepliconDB.Test.test_in) ... ok test_items (tests.test_RepliconDB.Test.test_items) ... ok test_iteritems (tests.test_RepliconDB.Test.test_iteritems) ... ok test_names (tests.test_RepliconDB.Test.test_names) ... ok test_replicon_infos (tests.test_RepliconDB.Test.test_replicon_infos) ... ok test_extract (tests.test_Report.TestGembaseHMMReport.test_extract) ... ok test_extract_concurent (tests.test_Report.TestGembaseHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_extract (tests.test_Report.TestGeneralHMMReport.test_extract) ... ok test_extract_concurent (tests.test_Report.TestGeneralHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/tests/test_Report.py:541: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_HMMReport (tests.test_Report.TestHMMReport.test_HMMReport) ... ok test_best_hit (tests.test_Report.TestHMMReport.test_best_hit) ... ok test_build_my_db (tests.test_Report.TestHMMReport.test_build_my_db) ... ok test_fill_my_db (tests.test_Report.TestHMMReport.test_fill_my_db) ... ok test_hit_start (tests.test_Report.TestHMMReport.test_hit_start) ... ok test_parse_hmm_body (tests.test_Report.TestHMMReport.test_parse_hmm_body) ... ok test_parse_hmm_header (tests.test_Report.TestHMMReport.test_parse_hmm_header) ... ok test_save_extract (tests.test_Report.TestHMMReport.test_save_extract) ... ok test_str (tests.test_Report.TestHMMReport.test_str) ... ok test_extract (tests.test_Report.TestOrderedHMMReport.test_extract) ... ok test_extract_concurent (tests.test_Report.TestOrderedHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/tests/test_Report.py:461: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_HitSystemTracker (tests.test_System.SystemTest.test_HitSystemTracker) ... ok test_count (tests.test_System.SystemTest.test_count) ... ok test_fulfilled_function (tests.test_System.SystemTest.test_fulfilled_function) ... ok test_get_hits_encoding_multisystem (tests.test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok test_get_loners (tests.test_System.SystemTest.test_get_loners) ... ok test_get_multisystems (tests.test_System.SystemTest.test_get_multisystems) ... ok test_hits (tests.test_System.SystemTest.test_hits) ... ok test_init (tests.test_System.SystemTest.test_init) ... ok test_is_compatible (tests.test_System.SystemTest.test_is_compatible) ... ok test_loci_nb (tests.test_System.SystemTest.test_loci_nb) ... ok test_loci_num (tests.test_System.SystemTest.test_loci_num) ... ok test_multi_loci (tests.test_System.SystemTest.test_multi_loci) ... ok test_occurrence (tests.test_System.SystemTest.test_occurrence) ... ok test_position (tests.test_System.SystemTest.test_position) ... ok test_score (tests.test_System.SystemTest.test_score) ... ok test_wholeness (tests.test_System.SystemTest.test_wholeness) ... ok test_build_clusters (tests.test_cluster.TestBuildCluster.test_build_clusters) ... ok test_clusterize (tests.test_cluster.TestBuildCluster.test_clusterize) ... ok test_colocates (tests.test_cluster.TestBuildCluster.test_colocates) ... ok test_get_true_loners (tests.test_cluster.TestBuildCluster.test_get_true_loners) ... ok test_contains (tests.test_cluster.TestCluster.test_contains) ... ok test_fulfilled_function (tests.test_cluster.TestCluster.test_fulfilled_function) ... ok test_init (tests.test_cluster.TestCluster.test_init) ... ok test_len (tests.test_cluster.TestCluster.test_len) ... ok test_loner (tests.test_cluster.TestCluster.test_loner) ... ok test_merge (tests.test_cluster.TestCluster.test_merge) ... ok test_multi_system (tests.test_cluster.TestCluster.test_multi_system) ... ok test_replace (tests.test_cluster.TestCluster.test_replace) ... ok test_replicon_name (tests.test_cluster.TestCluster.test_replicon_name) ... ok test_score (tests.test_cluster.TestCluster.test_score) ... ok test_str (tests.test_cluster.TestCluster.test_str) ... ok test_2_systems_not_compatible (tests.test_functional_test.Test.test_2_systems_not_compatible) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_cfg_n_previous_run (tests.test_functional_test.Test.test_cfg_n_previous_run) ... ok test_degenerated_systems (tests.test_functional_test.Test.test_degenerated_systems) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_force (tests.test_functional_test.Test.test_force) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_functional_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_gembase (tests.test_functional_test.Test.test_gembase) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_gzip (tests.test_functional_test.Test.test_gzip) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gzip/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_index_dir (tests.test_functional_test.Test.test_index_dir) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_model_unknown (tests.test_functional_test.Test.test_model_unknown) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_db_type (tests.test_functional_test.Test.test_no_db_type) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_models (tests.test_functional_test.Test.test_no_models) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_seq_db (tests.test_functional_test.Test.test_no_seq_db) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_sequence (tests.test_functional_test.Test.test_no_sequence) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_no_sequence/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_only_loners (tests.test_functional_test.Test.test_only_loners) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_cluster_3_loners (tests.test_functional_test.Test.test_ordered_1_cluster_3_loners) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_cluster_and_clusters_of_loners (tests.test_functional_test.Test.test_ordered_1_cluster_and_clusters_of_loners) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_and_clusters_of_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_clusters_3_loners_w_exchangeable (tests.test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_loner_exch_in_clust (tests.test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_loner_in_clust (tests.test_functional_test.Test.test_ordered_1_loner_in_clust) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_2_clusters_1_loner (tests.test_functional_test.Test.test_ordered_2_clusters_1_loner) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_2_clusters_3_loners (tests.test_functional_test.Test.test_ordered_2_clusters_3_loners) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_circular (tests.test_functional_test.Test.test_ordered_circular) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_linear (tests.test_functional_test.Test.test_ordered_linear) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_loci (tests.test_functional_test.Test.test_ordered_multi_loci) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_model (tests.test_functional_test.Test.test_ordered_multi_model) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_system (tests.test_functional_test.Test.test_ordered_multi_system) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_system_out_system (tests.test_functional_test.Test.test_ordered_multi_system_out_system) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_only_one_multi_model (tests.test_functional_test.Test.test_ordered_only_one_multi_model) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_single_loci (tests.test_functional_test.Test.test_ordered_single_loci) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_timeout (tests.test_functional_test.Test.test_timeout) ... ok test_uncomplete_degenerated_systems (tests.test_functional_test.Test.test_uncomplete_degenerated_systems) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_unordered (tests.test_functional_test.Test.test_unordered) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_unordered_no_hits (tests.test_functional_test.Test.test_unordered_no_hits) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_unordered_only_forbidden (tests.test_functional_test.Test.test_unordered_only_forbidden) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_working_dir_exists (tests.test_functional_test.Test.test_working_dir_exists) ... ok test_working_dir_exists_and_not_dir (tests.test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok test_core_gene (tests.test_gene.TestCoreGene.test_core_gene) ... ok test_str (tests.test_gene.TestGeneStatus.test_str) ... ok test_add_exchangeable (tests.test_gene.TestModelGene.test_add_exchangeable) ... ok test_alternate_of (tests.test_gene.TestModelGene.test_alternate_of) ... ok test_core_gene (tests.test_gene.TestModelGene.test_core_gene) test getter/setter for core_gene property ... ok test_exhangeables (tests.test_gene.TestModelGene.test_exhangeables) ... ok test_hash (tests.test_gene.TestModelGene.test_hash) ... ok test_init (tests.test_gene.TestModelGene.test_init) ... ok test_inter_gene_max_space (tests.test_gene.TestModelGene.test_inter_gene_max_space) test getter for inter_gene_max_space property ... ok test_is_Forbidden (tests.test_gene.TestModelGene.test_is_Forbidden) test if gene belong to model mandatory genes ... ok test_is_accessory (tests.test_gene.TestModelGene.test_is_accessory) test if gene belong to model mandatory genes ... ok test_is_exchangeable (tests.test_gene.TestModelGene.test_is_exchangeable) ... ok test_is_mandatory (tests.test_gene.TestModelGene.test_is_mandatory) test if gene belong to model mandatory genes ... ok test_loner (tests.test_gene.TestModelGene.test_loner) test getter for loner property ... ok test_model (tests.test_gene.TestModelGene.test_model) test getter/setter for model property ... ok test_multi_model (tests.test_gene.TestModelGene.test_multi_model) test getter for multi_modelproperty ... ok test_multi_system (tests.test_gene.TestModelGene.test_multi_system) test getter for multi_system property ... ok test_str (tests.test_gene.TestModelGene.test_str) ... ok test_unknown_attribute (tests.test_gene.TestModelGene.test_unknown_attribute) ... ok test_cmp (tests.test_hit.CoreHitTest.test_cmp) ... ok test_eq (tests.test_hit.CoreHitTest.test_eq) ... ok test_get_position (tests.test_hit.CoreHitTest.test_get_position) ... ok test_hash (tests.test_hit.CoreHitTest.test_hash) ... ok test_str (tests.test_hit.CoreHitTest.test_str) ... ok test_compute_best_MSHit (tests.test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok test_get_best_hits (tests.test_hit.GetBestHitTest.test_get_best_hits) ... ok test_get_best_hits_4_func (tests.test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok test_sort_multisystem_hits (tests.test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok test_hit_weight_default (tests.test_hit.HitWeightTest.test_hit_weight_default) ... ok test_hit_weight_not_default (tests.test_hit.HitWeightTest.test_hit_weight_not_default) ... ok test_counterpart (tests.test_hit.LonerMultiSystemTest.test_counterpart) ... ok test_init (tests.test_hit.LonerMultiSystemTest.test_init) ... ok test_loner (tests.test_hit.LonerMultiSystemTest.test_loner) ... ok test_multi_system (tests.test_hit.LonerMultiSystemTest.test_multi_system) ... ok test_str (tests.test_hit.LonerMultiSystemTest.test_str) ... ok test_counterpart (tests.test_hit.LonerTest.test_counterpart) ... ok test_init (tests.test_hit.LonerTest.test_init) ... ok test_len (tests.test_hit.LonerTest.test_len) ... ok test_loner (tests.test_hit.LonerTest.test_loner) ... ok test_multi_system (tests.test_hit.LonerTest.test_multi_system) ... ok test_str (tests.test_hit.LonerTest.test_str) ... ok test_delegation (tests.test_hit.ModelHitTest.test_delegation) ... ok test_eq (tests.test_hit.ModelHitTest.test_eq) ... ok test_hash (tests.test_hit.ModelHitTest.test_hash) ... ok test_init (tests.test_hit.ModelHitTest.test_init) ... ok test_loner (tests.test_hit.ModelHitTest.test_loner) ... ok test_multi_model (tests.test_hit.ModelHitTest.test_multi_model) ... ok test_multi_system (tests.test_hit.ModelHitTest.test_multi_system) ... ok test_counterpart (tests.test_hit.MultiSystemTest.test_counterpart) ... ok test_init (tests.test_hit.MultiSystemTest.test_init) ... ok test_len (tests.test_hit.MultiSystemTest.test_len) ... ok test_loner (tests.test_hit.MultiSystemTest.test_loner) ... ok test_multi_system (tests.test_hit.MultiSystemTest.test_multi_system) ... ok test_str (tests.test_hit.MultiSystemTest.test_str) ... ok test_functional_split (tests.test_macsy_gembase_split.TestSplit.test_functional_split) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpxwutneb3/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_functional_split_out_error (tests.test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... ok test_functional_split_out_not_writable (tests.test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... ok test_functional_merge (tests.test_macsy_merge_results.TestMerge.test_functional_merge) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmprc1j0gbe/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_functional_merge_one_results_empty (tests.test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp0_nmy6rf/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_functional_merge_out_error (tests.test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... ok test_functional_merge_out_not_writable (tests.test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... ok test_functional_merge_results_empty (tests.test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpije5xefd/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_get_warning (tests.test_macsy_merge_results.TestMerge.test_get_warning) ... ok test_merge_and_reindex_invalid_solid (tests.test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... ok test_add_comment (tests.test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok test_write (tests.test_macsyconfig.TestConfigParserWithComment.test_write) ... ok test_ask (tests.test_macsyconfig.TestMacsyconfig.test_ask) ... ok test_ask_bad_value (tests.test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok test_ask_default_is_sequence (tests.test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok test_ask_use_default (tests.test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok test_ask_value_is_sequence (tests.test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok test_check_bool (tests.test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok test_check_choice (tests.test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok test_check_dir (tests.test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok test_check_exe (tests.test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok test_check_file (tests.test_macsyconfig.TestMacsyconfig.test_check_file) ... ok test_check_float (tests.test_macsyconfig.TestMacsyconfig.test_check_float) ... ok test_check_positive_int (tests.test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok test_check_str (tests.test_macsyconfig.TestMacsyconfig.test_check_str) ... ok test_functional_dark_theme (tests.test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok test_functional_file_already_exists (tests.test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok test_parse_args (tests.test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok test_set_base_options (tests.test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok test_set_general_options (tests.test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok test_set_hmmer_options (tests.test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok test_set_path_options (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok test_set_path_options_with_system_models_dir (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok test_set_score_options (tests.test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok test_set_section (tests.test_macsyconfig.TestMacsyconfig.test_set_section) ... ok test_set_section_use_defaults (tests.test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok test_available (tests.test_macsydata.TestMacsydata.test_available) ... ok test_build_argparser (tests.test_macsydata.TestMacsydata.test_build_argparser) ... ok test_check (tests.test_macsydata.TestMacsydata.test_check) ... ok test_check_with_errors (tests.test_macsydata.TestMacsydata.test_check_with_errors) ... ok test_check_with_warnings (tests.test_macsydata.TestMacsydata.test_check_with_warnings) ... ok test_cite (tests.test_macsydata.TestMacsydata.test_cite) ... ok test_cmd_name (tests.test_macsydata.TestMacsydata.test_cmd_name) ... ok test_definition_all_def (tests.test_macsydata.TestMacsydata.test_definition_all_def) ... /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp580ajcp0/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp580ajcp0/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_definition_bad_def (tests.test_macsydata.TestMacsydata.test_definition_bad_def) ... ok test_definition_bad_pack (tests.test_macsydata.TestMacsydata.test_definition_bad_pack) ... ok test_definition_bad_subfamily (tests.test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... ok test_definition_models_dir (tests.test_macsydata.TestMacsydata.test_definition_models_dir) ... /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpt_9b4ozt/model_dir/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpt_9b4ozt/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_definition_one_def (tests.test_macsydata.TestMacsydata.test_definition_one_def) ... /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpzj8sdp2_/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.1.3/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpzj8sdp2_/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_download (tests.test_macsydata.TestMacsydata.test_download) ... ok test_freeze (tests.test_macsydata.TestMacsydata.test_freeze) ... ok test_help (tests.test_macsydata.TestMacsydata.test_help) ... ok test_info (tests.test_macsydata.TestMacsydata.test_info) ... ok test_init_package_complete (tests.test_macsydata.TestMacsydata.test_init_package_complete) ... ok test_init_package_minimal (tests.test_macsydata.TestMacsydata.test_init_package_minimal) ... ok test_install_bad_target (tests.test_macsydata.TestMacsydata.test_install_bad_target) ... ok test_install_installed_package_corrupted (tests.test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... ok test_install_local (tests.test_macsydata.TestMacsydata.test_install_local) ... ok test_install_local_already_installed (tests.test_macsydata.TestMacsydata.test_install_local_already_installed) ... ok test_install_local_already_installed_force (tests.test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... ok test_install_remote (tests.test_macsydata.TestMacsydata.test_install_remote) ... ok test_install_remote_already_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... ok test_install_remote_already_in_local_force (tests.test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... ok test_install_remote_lower_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... ok test_install_remote_permision_error (tests.test_macsydata.TestMacsydata.test_install_remote_permision_error) ... ok test_install_remote_spec_not_found (tests.test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... ok test_install_remote_upper_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... ok test_install_target (tests.test_macsydata.TestMacsydata.test_install_target) ... ok test_list (tests.test_macsydata.TestMacsydata.test_list) ... ok test_list_long (tests.test_macsydata.TestMacsydata.test_list_long) ... ok test_list_outdated (tests.test_macsydata.TestMacsydata.test_list_outdated) ... ok test_list_uptodate (tests.test_macsydata.TestMacsydata.test_list_uptodate) ... ok test_list_verbose (tests.test_macsydata.TestMacsydata.test_list_verbose) ... ok test_no_subcommand (tests.test_macsydata.TestMacsydata.test_no_subcommand) ... ok test_search_in_pack_desc (tests.test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok test_search_in_pack_desc_match_case (tests.test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok test_search_in_pack_name (tests.test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok test_search_in_pack_name_match_case (tests.test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok test_search_reach_limit (tests.test_macsydata.TestMacsydata.test_search_reach_limit) ... ok test_uninstall (tests.test_macsydata.TestMacsydata.test_uninstall) ... ok test_verbosity_to_log_level (tests.test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok test_likely_systems_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok test_likely_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok test_loners_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok test_multisystem_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok test_rejected_candidates_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok test_rejected_candidates_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok test_solutions_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok test_summary_best_solution (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok test_summary_best_solution_empty (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok test_summary_best_solution_lack_models (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok test_summary_best_solution_lack_models_replicons (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok test_summary_best_solution_lack_replicon (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok test_systems_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok test_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok test_unnlikely_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok test_LightHit (tests.test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok test_build_my_db (tests.test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok test_fill_my_db (tests.test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok test_functional (tests.test_macsyprofile.TestMacsyprofile.test_functional) ... ok test_functional_best_score (tests.test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok test_functional_coverage (tests.test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok test_functional_evalue (tests.test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok test_functional_no_hits (tests.test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok test_functional_no_previous_run (tests.test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... ok test_functional_out_exists (tests.test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... ok test_functional_pattern (tests.test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok test_getProfile_len (tests.test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok test_get_gene_name (tests.test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok test_header (tests.test_macsyprofile.TestMacsyprofile.test_header) ... ok test_hit_start (tests.test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok test_parse (tests.test_macsyprofile.TestMacsyprofile.test_parse) ... ok test_parse_hmm_body (tests.test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok test_parse_hmm_header (tests.test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok test_pasre_args (tests.test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok test_verbosity_to_log_level (tests.test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok test_init_logger_default (tests.test_macsypy.Test.test_init_logger_default) ... ok test_init_logger_logfile (tests.test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp3iwe0spe' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_init_logger_no_out (tests.test_macsypy.Test.test_init_logger_no_out) ... ok test_logger_set_level_bad_level (tests.test_macsypy.Test.test_logger_set_level_bad_level) ... ok test_logger_set_level_default (tests.test_macsypy.Test.test_logger_set_level_default) ... ok test_logger_set_level_error (tests.test_macsypy.Test.test_logger_set_level_error) ... ok test_logger_set_level_handlers (tests.test_macsypy.Test.test_logger_set_level_handlers) ... ok test_parse (tests.test_model_conf_parser.TestModelConfParser.test_parse) ... ok test_parse_bad_file (tests.test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... ok test_parse_filtering (tests.test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... ok test_parse_w_bad_value (tests.test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... ok test_parse_w_unkown_tag (tests.test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... ok test_parse_weights (tests.test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok test_parse_wo_filtering (tests.test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok test_parse_wo_weights (tests.test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok test_init (tests.test_package.TestLocalModelIndex.test_init) ... ok test_init (tests.test_package.TestModelIndex.test_init) ... ok test_check (tests.test_package.TestPackage.test_check) ... ok test_check_metadata (tests.test_package.TestPackage.test_check_metadata) ... ok test_check_model_conf (tests.test_package.TestPackage.test_check_model_conf) ... ok test_check_model_conf_bad_conf (tests.test_package.TestPackage.test_check_model_conf_bad_conf) ... ok test_check_model_conf_no_conf (tests.test_package.TestPackage.test_check_model_conf_no_conf) ... ok test_check_model_consistency (tests.test_package.TestPackage.test_check_model_consistency) ... ok test_check_model_consistency_bad_definitions (tests.test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok test_check_model_consistency_extra_profile (tests.test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok test_check_model_consistency_lack_one_profile (tests.test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok test_check_no_readme_n_no_license (tests.test_package.TestPackage.test_check_no_readme_n_no_license) ... ok test_check_structure (tests.test_package.TestPackage.test_check_structure) ... ok test_check_structure_bad_path (tests.test_package.TestPackage.test_check_structure_bad_path) ... ok test_check_structure_no_def (tests.test_package.TestPackage.test_check_structure_no_def) ... ok test_check_structure_no_license (tests.test_package.TestPackage.test_check_structure_no_license) ... ok test_check_structure_no_metadata (tests.test_package.TestPackage.test_check_structure_no_metadata) ... ok test_check_structure_no_profiles (tests.test_package.TestPackage.test_check_structure_no_profiles) ... ok test_check_structure_no_readme (tests.test_package.TestPackage.test_check_structure_no_readme) ... ok test_find_readme (tests.test_package.TestPackage.test_find_readme) ... ok test_help (tests.test_package.TestPackage.test_help) ... ok test_info (tests.test_package.TestPackage.test_info) ... ok test_init (tests.test_package.TestPackage.test_init) ... ok test_metadata (tests.test_package.TestPackage.test_metadata) ... ok test_parse_arch_path (tests.test_package.TestPackageFunc.test_parse_arch_path) ... ok test_download (tests.test_package.TestRemoteModelIndex.test_download) ... ok test_get_metadata (tests.test_package.TestRemoteModelIndex.test_get_metadata) ... ok test_init (tests.test_package.TestRemoteModelIndex.test_init) ... ok test_list_package_vers (tests.test_package.TestRemoteModelIndex.test_list_package_vers) ... ok test_list_packages (tests.test_package.TestRemoteModelIndex.test_list_packages) ... ok test_remote_exists (tests.test_package.TestRemoteModelIndex.test_remote_exists) ... ok test_unarchive (tests.test_package.TestRemoteModelIndex.test_unarchive) ... ok test_url_json (tests.test_package.TestRemoteModelIndex.test_url_json) ... ok test_url_json_reach_limit (tests.test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok test_DefinitionLocationn (tests.test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok test_add_submodel (tests.test_registries.DefinitionLocationTest.test_add_submodel) ... ok test_all (tests.test_registries.DefinitionLocationTest.test_all) ... ok test_eq (tests.test_registries.DefinitionLocationTest.test_eq) ... ok test_family_name (tests.test_registries.DefinitionLocationTest.test_family_name) ... ok test_greater (tests.test_registries.DefinitionLocationTest.test_greater) ... ok test_hash (tests.test_registries.DefinitionLocationTest.test_hash) ... ok test_lesser (tests.test_registries.DefinitionLocationTest.test_lesser) ... ok test_root_name (tests.test_registries.DefinitionLocationTest.test_root_name) ... ok test_separator (tests.test_registries.DefinitionLocationTest.test_separator) ... ok test_split_fqn (tests.test_registries.DefinitionLocationTest.test_split_fqn) ... ok test_str (tests.test_registries.DefinitionLocationTest.test_str) ... ok test_ModelLocation (tests.test_registries.ModelLocationTest.test_ModelLocation) ... ok test_get_all_definitions (tests.test_registries.ModelLocationTest.test_get_all_definitions) ... ok test_get_definition (tests.test_registries.ModelLocationTest.test_get_definition) ... ok test_get_definitions (tests.test_registries.ModelLocationTest.test_get_definitions) ... ok test_get_profile (tests.test_registries.ModelLocationTest.test_get_profile) ... ok test_get_profiles_names (tests.test_registries.ModelLocationTest.test_get_profiles_names) ... ok test_str (tests.test_registries.ModelLocationTest.test_str) ... ok test_version (tests.test_registries.ModelLocationTest.test_version) ... ok test_version_no_metadata (tests.test_registries.ModelLocationTest.test_version_no_metadata) ... ok test_add_get (tests.test_registries.ModelRegistryTest.test_add_get) ... ok test_models (tests.test_registries.ModelRegistryTest.test_models) ... ok test_scan_models_dir (tests.test_registries.ModelRegistryTest.test_scan_models_dir) ... ok test_str (tests.test_registries.ModelRegistryTest.test_str) ... ok test_join_def_path (tests.test_registries.RegitriesUtilsTest.test_join_def_path) ... ok test_split_def_name (tests.test_registries.RegitriesUtilsTest.test_split_def_name) ... ok test_search (tests.test_search_genes.TestSearchGenes.test_search) ... ok test_search_fail (tests.test_search_genes.TestSearchGenes.test_search_fail) ... ok test_search_recover (tests.test_search_genes.TestSearchGenes.test_search_recover) ... ok test_worker_cpu (tests.test_search_genes.TestSearchGenes.test_worker_cpu) ... ok test_LikelySystemSerializer_txt (tests.test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok test_RejectedClusters_tsv (tests.test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok test_SolutionSerializer_tsv (tests.test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok test_SpecialHitSerializer_tsv (tests.test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok test_SystemSerializer_str (tests.test_serialization.SerializationTest.test_SystemSerializer_str) ... ok test_SystemSerializer_tsv (tests.test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok test_UnlikelySystemSerializer_txt (tests.test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok test_combine_clusters (tests.test_solution.SolutionExplorerTest.test_combine_clusters) ... ok test_combine_multisystems (tests.test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok test_find_best_solution (tests.test_solution.SolutionExplorerTest.test_find_best_solution) ... ok test_average_wholeness (tests.test_solution.SolutionTest.test_average_wholeness) ... ok test_gt (tests.test_solution.SolutionTest.test_gt) ... ok test_hits_number (tests.test_solution.SolutionTest.test_hits_number) ... ok test_hits_positions (tests.test_solution.SolutionTest.test_hits_positions) ... ok test_iteration (tests.test_solution.SolutionTest.test_iteration) ... ok test_lt (tests.test_solution.SolutionTest.test_lt) ... ok test_score (tests.test_solution.SolutionTest.test_score) ... ok test_sorting (tests.test_solution.SolutionTest.test_sorting) ... ok test_systems (tests.test_solution.SolutionTest.test_systems) ... ok test_get_def_to_detect (tests.test_utils.TestUtils.test_get_def_to_detect) ... ok test_get_replicon_names_bad_type (tests.test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok test_get_replicon_names_gembase (tests.test_utils.TestUtils.test_get_replicon_names_gembase) ... ok test_get_replicon_names_ordered (tests.test_utils.TestUtils.test_get_replicon_names_ordered) ... ok test_get_replicon_names_unordered (tests.test_utils.TestUtils.test_get_replicon_names_unordered) ... ok test_parse_time (tests.test_utils.TestUtils.test_parse_time) ... ok test_threads_available (tests.test_utils.TestUtils.test_threads_available) ... ok ---------------------------------------------------------------------- Ran 509 tests in 44.007s OK (skipped=2) create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/macsyfinder/ -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.11 to destdir I: pybuild pybuild:334: cp -a /build/reproducible-path/macsyfinder-2.1.3/debian/etc /build/reproducible-path/macsyfinder-2.1.3/debian/macsyfinder/etc && cd /build/reproducible-path/macsyfinder-2.1.3/doc && make html latexpdf make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.1.3/doc' Running Sphinx v7.2.6 making output directory... done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 42 source files that are out of date updating environment: [new config] 42 added, 0 changed, 0 removed reading sources... 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[100%] user_guide/quickstart /build/reproducible-path/macsyfinder-2.1.3/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:8: ERROR: Unexpected indentation. /build/reproducible-path/macsyfinder-2.1.3/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:10: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.3/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:11: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.3/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:12: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.3/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: ERROR: Unexpected indentation. /build/reproducible-path/macsyfinder-2.1.3/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:4: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.3/macsypy/serialization.py:docstring of macsypy.serialization.TsvLikelySystemSerializer.serialize:3: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.3/macsypy/serialization.py:docstring of macsypy.serialization.TxtLikelySystemSerializer.serialize:3: WARNING: Definition list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying downloadable files... 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Running Sphinx v7.2.6 making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found copying TeX support files... copying TeX support files... done processing macsyfinder.tex... index user_guide/index user_guide/new_v2 user_guide/installation user_guide/quickstart user_guide/input user_guide/gembase_convention user_guide/outputs user_guide/big_data user_guide/model_definition user_guide/functioning user_guide/FAQ modeler_guide/index modeler_guide/package modeler_guide/modeling modeler_guide/helper_tools modeler_guide/publish_package modeler_guide/gallery modeler_guide/models_V1ToV2 modeler_guide/FAQ_modeler developer_guide/index developer_guide/overview developer_guide/api/index developer_guide/api/config developer_guide/api/model_conf_parser developer_guide/api/registries developer_guide/api/definition_parser developer_guide/api/model developer_guide/api/gene developer_guide/api/profile developer_guide/api/hit developer_guide/api/cluster developer_guide/api/system developer_guide/api/report developer_guide/api/search_genes developer_guide/api/solution developer_guide/api/serialization developer_guide/api/database developer_guide/api/error developer_guide/api/utils developer_guide/api/package developer_guide/api/scripts resolving references... done writing... done copying images... 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Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). make[2]: Entering directory '/build/reproducible-path/macsyfinder-2.1.3/doc/build/latex' latexmk -pdf -dvi- -ps- 'macsyfinder.tex' Rc files read: /etc/LatexMk latexmkrc Latexmk: This is Latexmk, John Collins, 7 Apr. 2024. Version 4.85. No existing .aux file, so I'll make a simple one, and require run of *latex. Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Category 'other': Rerun of 'pdflatex' forced or previously required: Reason or flag: 'Initial setup' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[10] [11] Underfull \hbox (badness 10000) in paragraph at lines 882--884 []\T1/txtt/m/n/10 macsyfinder [][]db[]type unordered [][]sequence[]db unordered _genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 893--895 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir Underfull \hbox (badness 10000) in paragraph at lines 905--907 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [12] Overfull \hbox (57.99365pt too wide) in paragraph at lines 969--973 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_ordered Overfull \hbox (68.49362pt too wide) in paragraph at lines 979--982 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_unordered Underfull \hbox (badness 10000) in paragraph at lines 979--982 [][]\T1/txtt/m/n/10 models TXSScan all [][]db[]type unordered []w 8 \T1/qtm/m/i t/10 # spec-i-fied out-put folder: mac- [13] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [14] Overfull \vbox (2.32195pt too high) detected at line 1179 [15] Underfull \vbox (badness 1226) detected at line 1201 [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 5417) in paragraph at lines 1810--1812 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file [23] [24] Underfull \vbox (badness 10000) detected at line 2023 Overfull \vbox (3.12196pt too high) detected at line 2023 [25] [26] [27] [28] [29] [30] Underfull \vbox (badness 1226) detected at line 2340 [31] Underfull \vbox (badness 10000) detected at line 2340 Underfull \vbox (badness 10000) detected at line 2340 [32] [33] [34] [35] [36] [37] [38] Underfull \vbox (badness 10000) detected at line 2695 Underfull \vbox (badness 10000) detected at line 2695 [39] [40] Overfull \vbox (1.52959pt too high) detected at line 2825 [41] [42] [43] [44] pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed [45] [46 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz- bb320290fa50a2c64c42d68cab416461f9843641.pdf pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag e >] [47] [48] [49] [50] [51] [52] [53] [54] [55 <./msf_functionning_step1.pdf>] [56 <./msf_functionning_step2.pdf>] [57] [58 <./msf_functionning_step3.pdf> <./ msf_functionning_step4.pdf pdfTeX warning: pdflatex (file ./msf_functionning_step4.pdf): PDF inclusion: mu ltiple pdfs with page group included in a single page >] [59 <./msf_functionning_step5.pdf>] [60] Underfull \hbox (badness 10000) in paragraph at lines 3997--3999 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4005--4007 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4013--4015 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4021--4023 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4032--4034 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir [61] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4110. 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Rule 'pdflatex': Reasons for rerun Changed files or newly in use/created: macsyfinder.aux macsyfinder.out macsyfinder.toc ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[10] [11] Underfull \hbox (badness 10000) in paragraph at lines 882--884 []\T1/txtt/m/n/10 macsyfinder [][]db[]type unordered [][]sequence[]db unordered _genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 893--895 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir Underfull \hbox (badness 10000) in paragraph at lines 905--907 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [12] Overfull \hbox (57.99365pt too wide) in paragraph at lines 969--973 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_ordered Overfull \hbox (68.49362pt too wide) in paragraph at lines 979--982 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_unordered Underfull \hbox (badness 10000) in paragraph at lines 979--982 [][]\T1/txtt/m/n/10 models TXSScan all [][]db[]type unordered []w 8 \T1/qtm/m/i t/10 # spec-i-fied out-put folder: mac- [13] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [14] Overfull \vbox (2.32195pt too high) detected at line 1179 [15] Underfull \vbox (badness 1226) detected at line 1201 [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 5417) in paragraph at lines 1810--1812 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file [23] [24] Underfull \vbox (badness 10000) detected at line 2023 Overfull \vbox (3.12196pt too high) detected at line 2023 [25] [26] [27] [28] [29] [30] Underfull \vbox (badness 1226) detected at line 2340 [31] Underfull \vbox (badness 10000) detected at line 2340 Underfull \vbox (badness 10000) detected at line 2340 [32] [33] [34] [35] [36] [37] [38] Underfull \vbox (badness 10000) detected at line 2695 Underfull \vbox (badness 10000) detected at line 2695 [39] [40] Overfull \vbox (1.52959pt too high) detected at line 2825 [41] [42] [43] [44] pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed [45] [46 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz- bb320290fa50a2c64c42d68cab416461f9843641.pdf pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag e >] [47] [48] [49] [50] [51] [52] [53] [54] [55 <./msf_functionning_step1.pdf>] [56 <./msf_functionning_step2.pdf>] [57] [58 <./msf_functionning_step3.pdf> <./ msf_functionning_step4.pdf pdfTeX warning: pdflatex (file ./msf_functionning_step4.pdf): PDF inclusion: mu ltiple pdfs with page group included in a single page >] [59 <./msf_functionning_step5.pdf>] [60] Underfull \hbox (badness 10000) in paragraph at lines 3997--3999 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4005--4007 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4013--4015 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4021--4023 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4032--4034 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir [61] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4110. 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Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' Latexmk: Examining 'macsyfinder.log' Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Log file says output to 'macsyfinder.pdf' Have index file 'macsyfinder.idx', macsyfinder.ind macsyfinder Latexmk: All targets (macsyfinder.pdf) are up-to-date make[2]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.3/doc/build/latex' make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.3/doc' dh_installdocs -O--buildsystem=pybuild dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.1.3' dh_fixperms find debian -name "test_*.fa" -executable -exec chmod -x \{\} \; find debian -name "*.prt" -executable -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.3' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'macsyfinder' in '../macsyfinder_2.1.3-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../macsyfinder_2.1.3-1_arm64.buildinfo dpkg-genchanges --build=binary -O../macsyfinder_2.1.3-1_arm64.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/2160584 and its subdirectories I: Current time: Tue Jun 3 20:58:11 -12 2025 I: pbuilder-time-stamp: 1749027491 Thu May 2 02:35:16 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Thu May 2 02:35:16 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Thu May 2 02:40:04 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Thu May 2 02:40:05 UTC 2024 I: macsyfinder_2.1.3-1_arm64.changes: Format: 1.8 Date: Thu, 29 Feb 2024 15:40:31 +0100 Source: macsyfinder Binary: macsyfinder Architecture: arm64 Version: 2.1.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: macsyfinder - detection of macromolecular systems in protein datasets Changes: macsyfinder (2.1.3-1) unstable; urgency=medium . * Team upload. * New upstream version * Mark patches as not needing forwarding upstream. Checksums-Sha1: a5902fd1ad7d743d49f32f604e0a43813adae2b5 10491 macsyfinder_2.1.3-1_arm64.buildinfo a30b3dd21b7a56bc33e2581c88a13c74a31a3521 14455440 macsyfinder_2.1.3-1_arm64.deb Checksums-Sha256: bd5fc0068a153ec795fefe95923a233f54b6acd1d65384bed879b06faec1c8f6 10491 macsyfinder_2.1.3-1_arm64.buildinfo 752763ec5fb347787e89db5fad0dc72eb9dc8f2e61cc6a1822f75d2478f7a3f9 14455440 macsyfinder_2.1.3-1_arm64.deb Files: 290991f88cba9d1e2fdc1312ba3e4369 10491 science optional macsyfinder_2.1.3-1_arm64.buildinfo 7ca5b0742b44e837b39fb3aae3150be0 14455440 science optional macsyfinder_2.1.3-1_arm64.deb Thu May 2 02:40:06 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_11-41922.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.L8L7wnrJ/macsyfinder_2.1.3-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.L8L7wnrJ/macsyfinder_2.1.3-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.L8L7wnrJ/macsyfinder_2.1.3-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.L8L7wnrJ/b1/macsyfinder_2.1.3-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.L8L7wnrJ/b2/macsyfinder_2.1.3-1_arm64.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.gzip.GzipContainer ## command (total time: 24.691s) 11.986s 14 calls dumppdf 9.106s 7 calls diff 2.816s 6 calls xz 0.612s 11 calls pdftotext 0.067s 2 calls gzip 0.050s 1 call cmp 0.050s 1 call cmp (external) 0.003s 36 calls cmp (internal) ## compare_files (cumulative) (total time: 1307.968s) 219.827s 1 call abc.DotChangesFile 219.785s 1 call abc.DebFile 219.660s 2 calls abc.XzFile 216.716s 1 call abc.DebDataTarFile 215.996s 1 call abc.GzipFile 215.909s 1 call abc.PdfFile 0.059s 1 call abc.TarFile 0.016s 1 call abc.Md5sumsFile ## container_extract (total time: 3.280s) 2.816s 6 calls diffoscope.comparators.xz.XzContainer 0.323s 534 calls diffoscope.comparators.deb.DebTarContainer 0.068s 2 calls diffoscope.comparators.gzip.GzipContainer 0.067s 8 calls diffoscope.comparators.deb.DebContainer 0.005s 12 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.577s) 0.577s 4 calls linediff ## has_same_content_as (total time: 0.056s) 0.051s 1 call abc.DebDataTarFile 0.003s 24 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.001s 6 calls abc.TextFile 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.DebFile 0.000s 1 call abc.PdfFile 0.000s 1 call abc.GzipFile ## main (total time: 221.160s) 221.159s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.gzip.GzipContainer ## output (total time: 0.831s) 0.825s 1 call html 0.003s 1 call text 0.002s 1 call json ## recognizes (total time: 0.345s) 0.161s 12 calls diffoscope.comparators.binary.FilesystemFile 0.110s 776 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.043s 364 calls diffoscope.comparators.utils.archive.ArchiveMember 0.031s 54 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.172s) 0.172s 40 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 3min 41.583s CPU time consumed: 3min 48.938s Thu May 2 02:43:48 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Thu May 2 02:43:48 UTC 2024 E: macsyfinder failed to build reproducibly in trixie on arm64. Thu May 2 02:43:51 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 2 02:43:51 UTC 2024 I: Submitting 12K b1/macsyfinder_2.1.3-1_arm64.buildinfo.asc Thu May 2 02:43:52 UTC 2024 I: Submitting 12K b2/macsyfinder_2.1.3-1_arm64.buildinfo.asc Thu May 2 02:43:53 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 2 02:43:53 UTC 2024 I: Done submitting .buildinfo files. Thu May 2 02:43:53 UTC 2024 I: Removing signed macsyfinder_2.1.3-1_arm64.buildinfo.asc files: removed './b1/macsyfinder_2.1.3-1_arm64.buildinfo.asc' removed './b2/macsyfinder_2.1.3-1_arm64.buildinfo.asc'