Sun Sep 8 07:24:05 UTC 2024 I: starting to build macsyfinder/unstable/i386 on jenkins on '2024-09-08 07:23' Sun Sep 8 07:24:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_14/40295/console.log Sun Sep 8 07:24:05 UTC 2024 I: Downloading source for unstable/macsyfinder=2.1.4-1 --2024-09-08 07:24:05-- http://deb.debian.org/debian/pool/main/m/macsyfinder/macsyfinder_2.1.4-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2430 (2.4K) [text/prs.lines.tag] Saving to: ‘macsyfinder_2.1.4-1.dsc’ 0K .. 100% 354M=0s 2024-09-08 07:24:05 (354 MB/s) - ‘macsyfinder_2.1.4-1.dsc’ saved [2430/2430] Sun Sep 8 07:24:05 UTC 2024 I: macsyfinder_2.1.4-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: macsyfinder Binary: macsyfinder Architecture: amd64 i386 arm64 Version: 2.1.4-1 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-pkg-pybuild 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: 535dcd1d942b4f98f327c486b71e57b670f943a9 37873754 macsyfinder_2.1.4.orig.tar.gz 9803bdf2d82287ec4472cf25269454a4c64a078c 9924 macsyfinder_2.1.4-1.debian.tar.xz Checksums-Sha256: 023d51bfa842d81adf919a0555b05df6ccb7a486d572eb5acd0aa29b50b22869 37873754 macsyfinder_2.1.4.orig.tar.gz 6e1f471c32686de9cd00543191bc2cebfe92d07c9caba4abc61a51e4c0cc325e 9924 macsyfinder_2.1.4-1.debian.tar.xz Files: ed501360fbf14625dc71c6edd81cb764 37873754 macsyfinder_2.1.4.orig.tar.gz 399d3b4946cf9d791bfb42b36b4d16ee 9924 macsyfinder_2.1.4-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbcuCwACgkQPCZ2P2xn 5uLnIA//W1sZ0JZPGbSXk7A4KOncMqvHX91PZ1jtvxXzEGvPh+I6wI0kfYPOlrVv 9NiJZ4UGt0mCH6uc1srLFnsix4N5mKCNspa7d8XgtImG7eENmwwf9NYYOE2raKKz a//L8G7pqIVMUxLOEgjSpYi2H3JanW6dUqZfcxtMgQzeD4gPjHnysy20ttc5YPbv qulZE2xtKumBnKHLeiZxm3Ow0eEMz+Ut7/Del9vC+SSnt4WKf0TGrnYGLy400OtR uw6x5EQwfCzyGY2dxgMYqQJcz1d+ShgTNjl9a/bzS/A3M3JtZTlTspSg1F5vYwOY EuhloviZ8Tow4Psoivi7uySEFWoMjVA/60ua43zgr15iCN9cHMsoRPpmIWRXz2Nj 2+VxcSE5uHw9jM9N1lfU5/0ESZrWiwTPcJl6XG76NHiaAQ4kip7QXL3/1BgU243b 4QsEdEj0hjyBWqnZ4dIGOx+JWG2jp71oyI7cbwLCDoJIGnmbJNn9Lfw6eWCoYqhr 9zXcyz/WwVX6lWCFBehAiz96D2u4sosu73GPDpIDDdRwgOXjRTFOKoOL291wjXwo zMQnEeYIF9DpFq2C8nEntHEuvg+ExpOhh7mfe2rM5A5M0HZX74GBscPUA27waySb oaFt0LRLKVmjpBs2knWrJZgTKTjbd4m55bF7TE/edxw21U/zrcc= =5BeW -----END PGP SIGNATURE----- Sun Sep 8 07:24:05 UTC 2024 I: Checking whether the package is not for us Sun Sep 8 07:24:05 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net. Sun Sep 8 07:24:05 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net. Sun Sep 8 07:28:41 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Oct 11 01:47:04 -12 2025 I: pbuilder-time-stamp: 1760190424 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [macsyfinder_2.1.4-1.dsc] I: copying [./macsyfinder_2.1.4.orig.tar.gz] I: copying [./macsyfinder_2.1.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 7 20:31:40 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.1.4-1.dsc: no acceptable signature found dpkg-source: info: extracting macsyfinder in macsyfinder-2.1.4 dpkg-source: info: unpacking macsyfinder_2.1.4.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.1.4-1.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 adjust_test dpkg-source: info: applying privacy 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/16556/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='71a7cf9cecc5404181bfda11f70b6b07' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='16556' 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.zmfZpgds/pbuilderrc_wjly --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zmfZpgds/b1 --logfile b1/build.log macsyfinder_2.1.4-1.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom08-i386 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/16556/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, 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 ... 19757 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} 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} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdav1d7{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} libgssapi-krb5-2{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} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack3{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libnsl2{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} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsvtav1enc2{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{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-autocommand{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-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{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-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{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 are RECOMMENDED but will NOT be installed: apvlv atril curl default-jre dvisvgm evince fonts-liberation fonts-texgyre fonts-texgyre-math ghostscript gv javascript-common krb5-locales 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 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, 220 newly installed, 0 to remove and 0 not upgraded. Need to get 226 MB of archives. After unpacking 825 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.6-1 [813 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.3-1 [107 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.6-1 [2242 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.5-1 [26.7 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 13 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.6-1 [1961 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.6-1 [669 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.5-1 [9588 B] Get: 23 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.5-1 [27.6 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-1 [1386 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-7 [101 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3+b1 [704 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-1 [42.2 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 73.0.1-1 [212 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.20.1-1 [10.2 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 73.0.1-1 [748 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240824 [109 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-1.1 [462 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libcdt5 i386 2.42.4-2 [40.6 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libcgraph6 i386 2.42.4-2 [67.9 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libaom3 i386 3.9.1-1 [1902 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libdav1d7 i386 1.4.3-1 [327 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libabsl20230802 i386 20230802.1-4 [521 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libgav1-1 i386 0.19.0-2+b1 [325 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 librav1e0.7 i386 0.7.1-7 [654 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libsvtav1enc2 i386 2.1.0+dfsg-2 [1021 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libyuv0 i386 0.0.1888.20240710-3 [109 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libavif16 i386 1.1.0-3 [122 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libheif-plugin-dav1d i386 1.18.1-2 [11.0 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libde265-0 i386 1.0.15-1+b2 [199 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libheif-plugin-libde265 i386 1.18.1-2 [14.6 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libheif1 i386 1.18.1-2 [327 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b1 [35.9 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.0-1 [1568 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 9.0.0-1 [500 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.21-1 [48.0 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libxpm4 i386 1:3.5.17-1+b1 [57.8 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libgd3 i386 2.3.3-12 [130 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libgts-0.7-5t64 i386 0.7.6+darcs121130-5.2 [158 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2 [116 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2 [105 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-1 [591 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-7+b1 [395 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.54.0+ds-2 [230 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.54.0+ds-2 [57.9 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.54.0+ds-2 [36.0 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libpathplan4 i386 2.42.4-2 [42.5 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libgvc6 i386 2.42.4-2 [717 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libgvpr2 i386 2.42.4-2 [203 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 liblab-gamut1 i386 2.42.4-2 [198 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.0.10-1+b1 [58.6 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.3-1+b1 [33.9 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2 [193 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 libxmu6 i386 2:1.1.3-3+b2 [60.5 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 libxaw7 i386 2:1.0.14-1+b2 [208 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 graphviz i386 2.42.4-2 [579 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libdivsufsort3 i386 2.0.1-6 [48.9 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 hmmer i386 3.4+dfsg-2 [1094 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 tex-common all 6.18 [32.5 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libpaper1 i386 1.1.29+b1 [13.0 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 libpaper-utils i386 1.1.29+b1 [9280 B] Get: 144 http://deb.debian.org/debian unstable/main i386 libkpathsea6 i386 2024.20240313.70630+ds-4 [160 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 libptexenc1 i386 2024.20240313.70630+ds-4 [50.0 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 libsynctex2 i386 2024.20240313.70630+ds-4 [65.5 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 libtexlua53-5 i386 2024.20240313.70630+ds-4 [129 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 libmpfi0 i386 1.5.4+ds-3 [38.5 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 libpotrace0 i386 1.16-2+b1 [24.2 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 libteckit0 i386 2.5.12+ds1-1 [284 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 libzzip-0-13t64 i386 0.13.72+dfsg.1-1.3 [58.0 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 texlive-binaries i386 2024.20240313.70630+ds-4 [8377 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 texlive-base all 2024.20240829-2 [22.7 MB] Get: 157 http://deb.debian.org/debian unstable/main i386 texlive-latex-base all 2024.20240829-2 [1273 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 latexmk all 1:4.85-1 [501 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libapache-pom-java all 29-2 [5276 B] Get: 160 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-4 [735 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-1+b1 [55.2 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 preview-latex-style all 13.2-1 [350 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.1-1 [45.8 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 python3-pyproject-hooks all 1.1.0-2 [11.3 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 python3-toml all 0.10.2-1 [16.2 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 python3-wheel all 0.44.0-2 [53.4 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 python3-build all 1.2.1-1 [34.1 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 pybuild-plugin-pyproject all 6.20240824 [11.2 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.14.0-1 [111 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2024.6.2-1 [157 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.3.2-2 [118 kB] Get: 188 http://deb.debian.org/debian unstable/main i386 python3-colorama all 0.4.6-4 [36.2 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 python3-colorlog all 6.8.2-1 [27.2 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 python3-six all 1.16.0-7 [16.4 kB] Get: 191 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 python3-roman all 3.3-3 [9880 B] Get: 194 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.6-2.1 [38.6 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 197 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1+b1 [13.7 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 python3-networkx all 3.2.1-4 [14.2 MB] Get: 200 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-11 [4299 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.2+dfsg-4+b1 [3998 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 204 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.0.7-2 [111 kB] Get: 205 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 sphinx-common all 7.4.7-3 [731 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 7.4.7-3 [588 kB] Get: 209 http://deb.debian.org/debian unstable/main i386 sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1021 kB] Get: 210 http://deb.debian.org/debian unstable/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 211 http://deb.debian.org/debian unstable/main i386 python3-sphinx-rtd-theme all 2.0.0+dfsg-2 [28.5 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 python3-yaml i386 6.0.2-1 [134 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 tex-gyre all 20180621-6 [6209 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 texlive-fonts-recommended all 2024.20240829-2 [4990 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 texlive-pictures all 2024.20240829-2 [17.0 MB] Get: 219 http://deb.debian.org/debian unstable/main i386 texlive-latex-extra all 2024.20240829-1 [20.9 MB] Get: 220 http://deb.debian.org/debian unstable/main i386 texlive-plain-generic all 2024.20240829-1 [28.6 MB] Fetched 226 MB in 4s (56.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19757 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 libpython3.12-minimal:i386. Preparing to unpack .../libpython3.12-minimal_3.12.6-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.6-1) ... Selecting previously unselected package libexpat1:i386. 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Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 11 13:47:51 UTC 2025. Universal Time is now: Sat Oct 11 13:47:51 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:i386 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.82.0-1) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.1.5-3) ... Setting up libzzip-0-13t64:i386 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libsvtav1enc2:i386 (2.1.0+dfsg-2) ... Setting up libteckit0:i386 (2.5.12+ds1-1) ... Setting up libpathplan4:i386 (2.42.4-2) ... Setting up libapache-pom-java (29-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:i386 (1.0.15-1) ... 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Setting up dh-autoreconf (20) ... Setting up libthai0:i386 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libptexenc1:i386 (2024.20240313.70630+ds-4) ... Setting up libfreetype6:i386 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libgav1-1:i386 (0.19.0-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:i386 (2.42.4-2) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libharfbuzz0b:i386 (9.0.0-1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up libsm6:i386 (2:1.2.3-1+b1) ... Setting up libpaper1:i386 (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:i386 (1.1.0-3) ... Setting up libxi6:i386 (2:1.8.1-1) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:i386 (1.54.0+ds-2) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.2-1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libraqm0:i386 (0.10.1-1+b1) ... Setting up sphinx-common (7.4.7-3) ... Setting up libxt6t64:i386 (1:1.2.1-1.2) ... Setting up libnsl2:i386 (1.3.0-3+b2) ... Setting up libpangoft2-1.0-0:i386 (1.54.0+ds-2) ... Setting up tex-gyre (20180621-6) ... Setting up libpangocairo-1.0-0:i386 (1.54.0+ds-2) ... Setting up libxmu6:i386 (2:1.1.3-3+b2) ... Setting up libpython3.12-stdlib:i386 (3.12.6-1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libxaw7:i386 (2:1.0.14-1+b2) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... 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 texlive-base (2024.20240829-2) ... 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 libpython3-stdlib:i386 (3.12.5-1) ... Setting up texlive-plain-generic (2024.20240829-1) ... Setting up python3 (3.12.5-1) ... Setting up python3-zipp (3.20.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up python3-wheel (0.44.0-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up python3-pyproject-hooks (1.1.0-2) ... Setting up texlive-latex-base (2024.20240829-2) ... Setting up python3-certifi (2024.6.2-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Setting up python3-idna (3.6-2.1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-toml (0.10.2-1) ... Setting up texlive-pictures (2024.20240829-2) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up texlive-fonts-recommended (2024.20240829-2) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-build (1.2.1-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-colorlog (6.8.2-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.3.2-2) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up latexmk (1:4.85-1) ... Setting up python3-yaml (6.0.2-1) ... Setting up texlive-latex-extra (2024.20240829-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up python3-pkg-resources (73.0.1-1) ... Setting up python3-setuptools (73.0.1-1) ... 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-networkx (3.2.1-4) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up dh-python (6.20240824) ... Setting up pybuild-plugin-pyproject (6.20240824) ... Setting up python3-pandas-lib:i386 (2.2.2+dfsg-4+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up libheif-plugin-dav1d:i386 (1.18.1-2) ... Setting up libheif-plugin-libde265:i386 (1.18.1-2) ... Setting up libheif1:i386 (1.18.1-2) ... Setting up libgd3:i386 (2.3.3-12) ... Setting up libgvc6 (2.42.4-2) ... Setting up graphviz (2.42.4-2) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-3) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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-2.1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../macsyfinder_2.1.4-1_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.1.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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 python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12 * Building wheel... /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/macsypy copying macsypy/search_genes.py -> build/lib/macsypy copying macsypy/package.py -> build/lib/macsypy copying macsypy/gene.py -> build/lib/macsypy copying macsypy/config.py -> build/lib/macsypy copying macsypy/utils.py -> build/lib/macsypy copying macsypy/registries.py -> build/lib/macsypy copying macsypy/error.py -> build/lib/macsypy copying macsypy/definition_parser.py -> build/lib/macsypy copying macsypy/metadata.py -> build/lib/macsypy copying macsypy/cluster.py -> build/lib/macsypy copying macsypy/profile.py -> build/lib/macsypy copying macsypy/hit.py -> build/lib/macsypy copying macsypy/licenses.py -> build/lib/macsypy copying macsypy/report.py -> build/lib/macsypy copying macsypy/model.py -> build/lib/macsypy copying macsypy/__init__.py -> build/lib/macsypy copying macsypy/model_conf_parser.py -> build/lib/macsypy copying macsypy/serialization.py -> build/lib/macsypy copying macsypy/database.py -> build/lib/macsypy copying macsypy/system.py -> build/lib/macsypy copying macsypy/solution.py -> build/lib/macsypy creating build/lib/macsypy/scripts copying macsypy/scripts/macsy_merge_results.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyconfig.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsydata.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsy_gembase_split.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> build/lib/macsypy/scripts copying macsypy/scripts/__init__.py -> build/lib/macsypy/scripts creating build/lib/macsypy/data copying macsypy/data/pre-push -> build/lib/macsypy/data installing to build/bdist.linux-i686/wheel running install running install_lib creating build/bdist.linux-i686 creating build/bdist.linux-i686/wheel creating build/bdist.linux-i686/wheel/macsypy copying build/lib/macsypy/search_genes.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/package.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/gene.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/config.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/utils.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/registries.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/error.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/definition_parser.py -> build/bdist.linux-i686/wheel/./macsypy creating build/bdist.linux-i686/wheel/macsypy/data copying build/lib/macsypy/data/pre-push -> build/bdist.linux-i686/wheel/./macsypy/data copying build/lib/macsypy/metadata.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/cluster.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/profile.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/hit.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/licenses.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/report.py -> build/bdist.linux-i686/wheel/./macsypy creating build/bdist.linux-i686/wheel/macsypy/scripts copying build/lib/macsypy/scripts/macsy_merge_results.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyconfig.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsydata.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyfinder.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsy_gembase_split.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyprofile.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/__init__.py -> build/bdist.linux-i686/wheel/./macsypy/scripts copying build/lib/macsypy/model.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/__init__.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/model_conf_parser.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/serialization.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/database.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/system.py -> build/bdist.linux-i686/wheel/./macsypy copying build/lib/macsypy/solution.py -> build/bdist.linux-i686/wheel/./macsypy running install_data creating build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.data creating build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.data/data creating build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.data/data/share creating build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.data/data/share/macsyfinder creating build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.data/data/share/macsyfinder/models copying data/models/README -> build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.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 'CITATION.cff' adding license file 'COPYING' writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' Copying MacSyFinder.egg-info to build/bdist.linux-i686/wheel/./MacSyFinder-2.1.4.egg-info running install_scripts creating build/bdist.linux-i686/wheel/MacSyFinder-2.1.4.dist-info/WHEEL creating '/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/.tmp-nt6_lhd1/MacSyFinder-2.1.4-py3-none-any.whl' and adding 'build/bdist.linux-i686/wheel' to it adding 'MacSyFinder-2.1.4.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/metadata.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/data/pre-push' 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-2.1.4.dist-info/COPYING' adding 'MacSyFinder-2.1.4.dist-info/METADATA' adding 'MacSyFinder-2.1.4.dist-info/WHEEL' adding 'MacSyFinder-2.1.4.dist-info/entry_points.txt' adding 'MacSyFinder-2.1.4.dist-info/top_level.txt' adding 'MacSyFinder-2.1.4.dist-info/RECORD' removing build/bdist.linux-i686/wheel Successfully built MacSyFinder-2.1.4-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:56: UserWarning: GitPython is not installed, `macsydata init` is disabled () To turn this feature ON: - install git - then run `python -m pip install macsyfinder[model]` in your activated environment. warnings.warn("GitPython is not installed, `macsydata init` is disabled ()\n" 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) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if filtering_node: 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) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:59: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if weights_node: 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-2.1.4/.pybuild/cpython3_3.12/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-2.1.4/.pybuild/cpython3_3.12/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-2.1.4/.pybuild/cpython3_3.12/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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if filtering_node: /usr/lib/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: 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/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpcex1g8hb/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/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpg60llagw/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/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpcn5dfijr/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/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpq9zr4hv4/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-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp8lde2aj3/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-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp8lde2aj3/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-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpuixbh4hn/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-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpuixbh4hn/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-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpt7g3_iqy/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-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpt7g3_iqy/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_dir_exists_look_pack (tests.test_macsydata.TestMacsydata.test_init_dir_exists_look_pack) ... skipped 'GitPython is not installed' test_init_dir_exists_not_pack (tests.test_macsydata.TestMacsydata.test_init_dir_exists_not_pack) ... skipped 'GitPython is not installed' test_init_empty_dir_exists (tests.test_macsydata.TestMacsydata.test_init_empty_dir_exists) ... skipped 'GitPython is not installed' test_init_existing_file (tests.test_macsydata.TestMacsydata.test_init_existing_file) ... ok test_init_existing_pack (tests.test_macsydata.TestMacsydata.test_init_existing_pack) ... skipped 'GitPython is not installed' test_init_package_complete (tests.test_macsydata.TestMacsydata.test_init_package_complete) ... skipped 'GitPython is not installed' test_init_package_minimal (tests.test_macsydata.TestMacsydata.test_init_package_minimal) ... skipped 'GitPython is not installed' 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) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/package.py:110: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. tar.extractall(path, members, numeric_owner=numeric_owner) 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_old_conf (tests.test_macsyprofile.TestMacsyprofile.test_functional_old_conf) ... 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/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp68835que' 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_cite (tests.test_metadata.TestMetadata.test_cite) ... ok test_copyright (tests.test_metadata.TestMetadata.test_copyright) ... ok test_doc (tests.test_metadata.TestMetadata.test_doc) ... ok test_init (tests.test_metadata.TestMetadata.test_init) ... ok test_license (tests.test_metadata.TestMetadata.test_license) ... ok test_load (tests.test_metadata.TestMetadata.test_load) ... ok test_maintainer (tests.test_metadata.TestMetadata.test_maintainer) ... ok test_save (tests.test_metadata.TestMetadata.test_save) ... ok test_short_desc (tests.test_metadata.TestMetadata.test_short_desc) ... ok test_vers (tests.test_metadata.TestMetadata.test_vers) ... ok test_parse (tests.test_model_conf_parser.TestModelConfParser.test_parse) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:59: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if weights_node: /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if filtering_node: 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_repos_url (tests.test_package.TestLocalModelIndex.test_repos_url) ... ok test_init (tests.test_package.TestModelIndex.test_init) ... ok test_check (tests.test_package.TestPackage.test_check) ... ok test_check_bad_metadata (tests.test_package.TestPackage.test_check_bad_metadata) ... ok test_check_metadata (tests.test_package.TestPackage.test_check_metadata) ... ok test_check_metadata_no_cite (tests.test_package.TestPackage.test_check_metadata_no_cite) ... ok test_check_metadata_no_copyright (tests.test_package.TestPackage.test_check_metadata_no_copyright) ... ok test_check_metadata_no_desc (tests.test_package.TestPackage.test_check_metadata_no_desc) ... ok test_check_metadata_no_doc (tests.test_package.TestPackage.test_check_metadata_no_doc) ... ok test_check_metadata_no_email (tests.test_package.TestPackage.test_check_metadata_no_email) ... ok test_check_metadata_no_license (tests.test_package.TestPackage.test_check_metadata_no_license) ... ok test_check_metadata_no_maintainer (tests.test_package.TestPackage.test_check_metadata_no_maintainer) ... ok test_check_metadata_no_name (tests.test_package.TestPackage.test_check_metadata_no_name) ... ok test_check_metadata_no_vers (tests.test_package.TestPackage.test_check_metadata_no_vers) ... ok test_check_metadata_with_vers (tests.test_package.TestPackage.test_check_metadata_with_vers) ... 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_poor_quality_metadata (tests.test_package.TestPackage.test_check_poor_quality_metadata) ... 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_info_no_citation (tests.test_package.TestPackage.test_info_no_citation) ... ok test_info_no_doc (tests.test_package.TestPackage.test_info_no_doc) ... ok test_info_no_license (tests.test_package.TestPackage.test_info_no_license) ... 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_repos_url (tests.test_package.TestRemoteModelIndex.test_repos_url) ... ok test_unarchive (tests.test_package.TestRemoteModelIndex.test_unarchive) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/package.py:110: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. tar.extractall(path, members, numeric_owner=numeric_owner) 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_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 540 tests in 21.828s OK (skipped=8) 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 python3.12 to destdir I: pybuild pybuild:334: cp -a /build/reproducible-path/macsyfinder-2.1.4/debian/etc /build/reproducible-path/macsyfinder-2.1.4/debian/macsyfinder/etc && cd /build/reproducible-path/macsyfinder-2.1.4/doc && make html latexpdf make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.1.4/doc' Running Sphinx v7.4.7 loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 44 source files that are out of date updating environment: [new config] 44 added, 0 changed, 0 removed reading sources... [ 2%] developer_guide/api/cluster reading sources... [ 5%] developer_guide/api/config reading sources... [ 7%] developer_guide/api/database reading sources... [ 9%] developer_guide/api/definition_parser reading sources... [ 11%] developer_guide/api/error reading sources... [ 14%] developer_guide/api/gene reading sources... [ 16%] developer_guide/api/hit reading sources... [ 18%] developer_guide/api/index reading sources... [ 20%] developer_guide/api/model reading sources... [ 23%] developer_guide/api/model_conf_parser reading sources... [ 25%] developer_guide/api/package reading sources... [ 27%] developer_guide/api/profile reading sources... [ 30%] developer_guide/api/registries reading sources... [ 32%] developer_guide/api/report reading sources... [ 34%] developer_guide/api/scripts /build/reproducible-path/macsyfinder-2.1.4/macsypy/scripts/macsydata.py:56: UserWarning: GitPython is not installed, `macsydata init` is disabled () To turn this feature ON: - install git - then run `python -m pip install macsyfinder[model]` in your activated environment. warnings.warn("GitPython is not installed, `macsydata init` is disabled ()\n" reading sources... [ 36%] developer_guide/api/search_genes reading sources... [ 39%] developer_guide/api/serialization reading sources... [ 41%] developer_guide/api/solution reading sources... [ 43%] developer_guide/api/system reading sources... [ 45%] developer_guide/api/utils reading sources... [ 48%] developer_guide/index reading sources... [ 50%] developer_guide/installation reading sources... [ 52%] developer_guide/overview reading sources... [ 55%] index reading sources... [ 57%] modeler_guide/FAQ_modeler reading sources... [ 59%] modeler_guide/gallery reading sources... 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[100%] user_guide/quickstart /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:8: ERROR: Unexpected indentation. /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:10: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:11: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:12: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/gene.py:docstring of macsypy.gene.ModelGene.multi_model:3: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: ERROR: Unexpected indentation. /build/reproducible-path/macsyfinder-2.1.4/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:4: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/system.py:docstring of macsypy.system.MatchMaker.present_genes:4: WARNING: Block quote 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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[11] [12] Underfull \hbox (badness 10000) in paragraph at lines 948--950 []\T1/txtt/m/n/10 macsyfinder [][]db[]type unordered [][]sequence[]db unordered _genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 959--961 []\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 971--973 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [13] Overfull \hbox (57.99365pt too wide) in paragraph at lines 1035--1039 []\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 1045--1048 []\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 1045--1048 [][]\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- [14] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \vbox (2.56042pt too high) detected at line 1174 [15] [16] Underfull \vbox (badness 1226) detected at line 1267 [17] [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 5417) in paragraph at lines 1876--1878 []\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 [25] [26] Underfull \vbox (badness 10000) detected at line 2089 Underfull \vbox (badness 10000) detected at line 2089 [27] [28] [29] [30] [31] Underfull \vbox (badness 1226) detected at line 2406 [32] Underfull \vbox (badness 10000) detected at line 2406 Underfull \vbox (badness 10000) detected at line 2406 [33] [34] [35] [36] Overfull \vbox (1.17242pt too high) detected at line 2591 [37] Overfull \vbox (0.91234pt too high) detected at line 2638 [38] Overfull \vbox (1.73233pt too high) detected at line 2761 [39] Underfull \vbox (badness 10000) detected at line 2761 Underfull \vbox (badness 10000) detected at line 2761 [40] [41] [42] [43] Underfull \vbox (badness 10000) detected at line 2936 Underfull \vbox (badness 10000) detected at line 2936 [44] Overfull \vbox (1.17242pt too high) detected at line 2989 [45] [46] 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 [47 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz-bb320 290fa50a2c64c42d68cab416461f9843641.pdf pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag e >] [48] [49] [50] [51] [52] [53] [54] [55] [56 <./msf_functionning_step1.pdf>] [57 <./msf_functionning_step2.pdf>] [58] [59 <./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 >] [60 <./msf_functionning_step5.pdf>] [61] Underfull \hbox (badness 10000) in paragraph at lines 4063--4065 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4071--4073 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4079--4081 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4087--4089 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4098--4100 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir [62] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4176. [63] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4221. [64] [65] [66] Chapter 2. [67 <./logo_macsymodels.png>] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4393. [68] [69] [70] [71] [72] [73] [74] [75 <./MSF_modelling.pdf>] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5045. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 58. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 61. Package wrapfig Warning: Collision between wrapping environments on input line 5067. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5067. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 79. [76 <./loner.pdf>] Package wrapfig Warning: Collision between wrapping environments on input line 5091. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5091. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 04. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 07. Overfull \vbox (19.57245pt too high) detected at line 5188 [77 <./multi_system.pdf>] [78] [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5531--5536 \T1/txtt/m/n/10 models in conf file XXX. May be these results have been generat ed with an old version [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 5661--5663 [][][]$\T1/qtm/m/n/10 https : / / the-[]hitchhikers-[]guide-[]to-[]packaging . readthedocs . io / en / latest / speci^^\cation . html # [85] [86] [87] [88] [89 <./T1SS_example.pdf>] [90] Overfull \vbox (0.97131pt too high) detected at line 6075 [91 <./T3SS_example.pdf>] [92] [93] [94] Underfull \vbox (badness 1226) detected at line 6332 [95] [96] [97 <./multi_model.pdf>] [98] Chapter 3. [99] [100] [101] pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [102 <./macsyfinder_classes.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 6812--6817 []\T1/qtm/m/n/10 Among all this po-ten-tial sys-tems, MSF com-pute the best com -bi-na-tion. [][]\T1/txtt/m/sl/10 macsypy.solution. [103] [104] [105] [106] [107] Underfull \hbox (badness 6775) in paragraph at lines 7341--7343 \T1/txtt/bx/n/10 options \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dictionary with opt ion name as keys and values as values\T1/qtm/m/n/10 ) ^^U [108] [109] [110] Underfull \hbox (badness 10000) in paragraph at lines 7868--7871 []\T1/txtt/bx/n/10 allowed_elements \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dict wit h options name as keys and function to [111] [112] [113] [114] [115] [116] [117] [118] [119{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. pdfTeX warning: pdflatex (file ./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f958 9da157.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed pdfTeX warning: pdflatex (file ./gene_obj_interaction.pdf): PDF inclusion: foun d PDF version <1.7>, but at most version <1.5> allowed LaTeX Warning: Float too large for page by 127.0251pt on input line 10847. [131 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>] [132 <./gene_obj_interaction.pdf>] [133] [134] [135] [136] [137] [138] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 12315--12317 []\T1/qtm/m/n/10 true_loners: a dict { str func-tion: :class:macsypy.hit.Loner | pdfTeX warning: pdflatex (file ./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c662 2aab72.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [142] pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [143 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf> <./inheritanc e-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [144] [145] [146] [147] [148] [149] [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 13670--13672 \T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (// Output written on macsyfinder.pdf (206 pages, 2645045 bytes). 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-2.1.4/doc/build/latex' make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.4/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-2.1.4' 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-2.1.4' 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_2.1.4-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../macsyfinder_2.1.4-1_i386.buildinfo dpkg-genchanges --build=binary -O../macsyfinder_2.1.4-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/16556 and its subdirectories I: Current time: Sat Oct 11 01:51:36 -12 2025 I: pbuilder-time-stamp: 1760190696 Sun Sep 8 07:28:42 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net. Sun Sep 8 07:28:42 UTC 2024 I: Preparing to do remote build '2' on infom07-i386.debian.net. Sun Sep 8 07:32:33 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. Sun Sep 8 07:32:34 UTC 2024 I: macsyfinder_2.1.4-1_i386.changes: Format: 1.8 Date: Sat, 07 Sep 2024 16:18:00 +0200 Source: macsyfinder Binary: macsyfinder Architecture: i386 Version: 2.1.4-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: macsyfinder - detection of macromolecular systems in protein datasets Closes: 1048586 1079747 Changes: macsyfinder (2.1.4-1) unstable; urgency=medium . * Team upload. * New upstream version * Refreshed patches. Dropped fix-test-parse.patch as that is no longer needed. * Add patch to make a test more flexible. * d/clean: also remove doc/build/ Closes: #1048586 * Switch to autopkgtest-pkg-pybuild. Closes: #1079747 Checksums-Sha1: b029cdf913b4c44328cb033de609e32cfe171fdb 10615 macsyfinder_2.1.4-1_i386.buildinfo 390a8b36abfaffb768b140d197a80e6dc3519636 14538592 macsyfinder_2.1.4-1_i386.deb Checksums-Sha256: f76833df07dfb275e87884c7132137f8dda52c0965f54a582774a75250b57640 10615 macsyfinder_2.1.4-1_i386.buildinfo be933748208049a48ca90445be538a19c7c683eedd4c8ebe62ca2c7b3f7da2b8 14538592 macsyfinder_2.1.4-1_i386.deb Files: ce4e7460ffe0f87d8e29e0ab73177c67 10615 science optional macsyfinder_2.1.4-1_i386.buildinfo 42f08655e59c6ead2da9190980330ded 14538592 science optional macsyfinder_2.1.4-1_i386.deb Sun Sep 8 07:32:36 UTC 2024 I: diffoscope 277 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_14-40295.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zmfZpgds/macsyfinder_2.1.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zmfZpgds/macsyfinder_2.1.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zmfZpgds/macsyfinder_2.1.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zmfZpgds/b1/macsyfinder_2.1.4-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.zmfZpgds/b2/macsyfinder_2.1.4-1_i386.changes ## close_archive (total time: 0.000s) 0.000s 4 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 24.008s) 12.346s 11 calls dumppdf 9.308s 7 calls diff 1.626s 6 calls xz 0.528s 11 calls pdftotext 0.069s 2 calls gzip 0.064s 1 call cmp 0.064s 1 call cmp (external) 0.003s 36 calls cmp (internal) ## compare_files (cumulative) (total time: 998.389s) 167.702s 1 call abc.DotChangesFile 167.633s 1 call abc.DebFile 167.454s 2 calls abc.XzFile 165.661s 1 call abc.DebDataTarFile 164.967s 1 call abc.GzipFile 164.875s 1 call abc.PdfFile 0.081s 1 call abc.TarFile 0.015s 1 call abc.Md5sumsFile ## container_extract (total time: 2.112s) 1.627s 6 calls diffoscope.comparators.xz.XzContainer 0.315s 546 calls diffoscope.comparators.deb.DebTarContainer 0.094s 8 calls diffoscope.comparators.deb.DebContainer 0.070s 2 calls diffoscope.comparators.gzip.GzipContainer 0.007s 12 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.018s) 0.018s 13 calls linediff ## has_same_content_as (total time: 0.070s) 0.064s 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.GzipFile 0.000s 1 call abc.PdfFile ## main (total time: 169.352s) 169.253s 2 calls outputs 0.099s 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: 0.935s) 0.927s 1 call html 0.004s 1 call text 0.004s 1 call json ## recognizes (total time: 0.453s) 0.192s 12 calls diffoscope.comparators.binary.FilesystemFile 0.148s 776 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.057s 54 calls diffoscope.comparators.debian.DebControlMember 0.056s 364 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 0.247s) 0.247s 40 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 2min 49.894s CPU time consumed: 2min 51.903s Sun Sep 8 07:35:26 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sun Sep 8 07:35:26 UTC 2024 E: macsyfinder failed to build reproducibly in unstable on i386. Sun Sep 8 07:35:28 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Sep 8 07:35:28 UTC 2024 I: Submitting 12K b1/macsyfinder_2.1.4-1_i386.buildinfo.asc Sun Sep 8 07:35:29 UTC 2024 I: Submitting 12K b2/macsyfinder_2.1.4-1_i386.buildinfo.asc Sun Sep 8 07:35:30 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Sep 8 07:35:30 UTC 2024 I: Done submitting .buildinfo files. Sun Sep 8 07:35:30 UTC 2024 I: Removing signed macsyfinder_2.1.4-1_i386.buildinfo.asc files: removed './b1/macsyfinder_2.1.4-1_i386.buildinfo.asc' removed './b2/macsyfinder_2.1.4-1_i386.buildinfo.asc'