I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 13 00:53:32 +14 2024 I: pbuilder-time-stamp: 1705056812 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.0-2.dsc] I: copying [./macsyfinder_2.0.orig.tar.gz] I: copying [./macsyfinder_2.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jan 16 03:18:58 2023 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.0-2.dsc: no acceptable signature found dpkg-source: info: extracting macsyfinder in macsyfinder-2.0 dpkg-source: info: unpacking macsyfinder_2.0.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying privacy dpkg-source: info: applying fix-test-parse.patch dpkg-source: info: applying do_not_test_parse_model_old_syntax.patch dpkg-source: info: applying join-threads-for-concurrency.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10842/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 12 10:53 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/10842/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/10842/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=cde044152a8449d2a6e903eabd28ca1b LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=10842 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.naUuPCwv/pbuilderrc_BS1K --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.naUuPCwv/b2 --logfile b2/build.log macsyfinder_2.0-2.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Jan 12 10:53 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/10842/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-python, python3, 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 ... 18156 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 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-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} libabsl20220623{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavif15{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1{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} libglib2.0-0{a} libgraphite2-3{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif1{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libkpathsea6{a} liblab-gamut1{a} liblapack3{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libnuma1{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} libpng16-16{a} libptexenc1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} libreadline8{a} libsm6{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libx265-199{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} libxt6{a} libyaml-0-2{a} libyuv0{a} libzzip-0-13{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} preview-latex-style{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-colorlog{a} python3-dateutil{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-tz{a} python3-urllib3{a} python3-yaml{a} python3.11{a} python3.11-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-liberation2 fonts-texgyre fonts-texgyre-math ghostscript gv javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgts-bin libjson-xs-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx mupdf okular python3-bottleneck python3-bs4 python3-gdal python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-pydot python3-pygraphviz python3-scipy python3-tables qpdfview qpdfview-ps-plugin ruby shared-mime-info tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 191 newly installed, 0 to remove and 0 not upgraded. Need to get 207 MB of archives. After unpacking 736 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 12 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 tzdata all 2023c-5+deb12u1 [296 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.11-1~deb12u2 [1423 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 38 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130+deb12u1 [104 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 docutils-common all 0.19+dfsg-6 [127 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 fontconfig i386 2.14.1-4 [450 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libcdt5 i386 2.42.2-7+b3 [40.5 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libcgraph6 i386 2.42.2-7+b3 [67.2 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libaom3 i386 3.6.0-1 [1895 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libdav1d6 i386 1.0.0-2 [316 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libabsl20220623 i386 20220623.1-1 [444 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libgav1-1 i386 0.18.0-1+b1 [307 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 librav1e0 i386 0.5.1-6 [615 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libyuv0 i386 0.0~git20230123.b2528b0-1 [108 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libavif15 i386 0.11.1-1 [101 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libde265-0 i386 1.0.11-1+deb12u1 [193 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libx265-199 i386 3.5-2+b1 [687 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libheif1 i386 1.15.1-1 [230 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libxpm4 i386 1:3.5.12-1.1+deb12u1 [50.4 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libgd3 i386 2.3.3-9 [129 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libgts-0.7-5 i386 0.7.6+darcs121130-5+b1 [162 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libltdl7 i386 2.4.7-5 [394 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libthai-data all 0.1.29-1 [176 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libdatrie1 i386 0.2.13-2+b1 [45.0 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libthai0 i386 0.1.29-1 [58.6 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libpango-1.0-0 i386 1.50.12+ds-1 [220 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 libpangoft2-1.0-0 i386 1.50.12+ds-1 [50.5 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libpangocairo-1.0-0 i386 1.50.12+ds-1 [35.4 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libpathplan4 i386 2.42.2-7+b3 [42.3 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libgvc6 i386 2.42.2-7+b3 [711 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 libgvpr2 i386 2.42.2-7+b3 [197 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 liblab-gamut1 i386 2.42.2-7+b3 [197 kB] Get: 111 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 114 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 libxmu6 i386 2:1.1.3-3 [62.5 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 libxaw7 i386 2:1.0.14-1 [209 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 graphviz i386 2.42.2-7+b3 [573 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 libdivsufsort3 i386 2.0.1-5 [49.5 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 hmmer i386 3.3.2+dfsg-1 [1172 kB] Get: 120 http://deb.debian.org/debian bookworm/main i386 tex-common all 6.18 [32.5 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 123 http://deb.debian.org/debian bookworm/main i386 libkpathsea6 i386 2022.20220321.62855-5.1+deb12u1 [155 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 libptexenc1 i386 2022.20220321.62855-5.1+deb12u1 [44.8 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 libsynctex2 i386 2022.20220321.62855-5.1+deb12u1 [62.5 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 libtexlua53-5 i386 2022.20220321.62855-5.1+deb12u1 [126 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 libteckit0 i386 2.5.11+ds1-1+b1 [282 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 libxi6 i386 2:1.8-1+b1 [86.2 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 libzzip-0-13 i386 0.13.72+dfsg.1-1.1 [60.1 kB] Get: 131 http://deb.debian.org/debian bookworm/main i386 texlive-binaries i386 2022.20220321.62855-5.1+deb12u1 [8537 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 texlive-base all 2022.20230122-3 [21.9 MB] Get: 134 http://deb.debian.org/debian bookworm/main i386 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 135 http://deb.debian.org/debian bookworm/main i386 latexmk all 1:4.79-1 [198 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libapache-pom-java all 29-2 [5276 B] Get: 137 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 145 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 149 http://deb.debian.org/debian bookworm/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB] Get: 150 http://deb.debian.org/debian bookworm/main i386 preview-latex-style all 12.2-1 [201 kB] Get: 151 http://deb.debian.org/debian bookworm/main i386 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 152 http://deb.debian.org/debian bookworm/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 153 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-4 [30.1 kB] Get: 155 http://deb.debian.org/debian bookworm/main i386 python3-babel all 2.10.3-1 [103 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 python3-certifi all 2022.9.24-1 [153 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 158 http://deb.debian.org/debian bookworm/main i386 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 159 http://deb.debian.org/debian bookworm/main i386 python3-colorama all 0.4.6-2 [36.8 kB] Get: 160 http://deb.debian.org/debian bookworm/main i386 python3-colorlog all 6.7.0-1 [26.5 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 163 http://deb.debian.org/debian bookworm/main i386 python3-roman all 3.3-3 [9880 B] Get: 164 http://deb.debian.org/debian bookworm/main i386 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 165 http://deb.debian.org/debian bookworm/main i386 python3-idna all 3.3-1 [39.4 kB] Get: 166 http://deb.debian.org/debian bookworm/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 167 http://deb.debian.org/debian bookworm/main i386 python3-markupsafe i386 2.1.2-1+b1 [13.3 kB] Get: 168 http://deb.debian.org/debian bookworm/main i386 python3-jinja2 all 3.1.2-1 [119 kB] Get: 169 http://deb.debian.org/debian bookworm/main i386 python3-networkx all 2.8.8-1 [1425 kB] Get: 170 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB] Get: 171 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB] Get: 172 http://deb.debian.org/debian bookworm/main i386 python3-pandas-lib i386 1.5.3+dfsg-2 [3382 kB] Get: 173 http://deb.debian.org/debian bookworm/main i386 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 174 http://deb.debian.org/debian bookworm/main i386 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 175 http://deb.debian.org/debian bookworm/main i386 python3-urllib3 all 1.26.12-1 [117 kB] Get: 176 http://deb.debian.org/debian bookworm/main i386 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 178 http://deb.debian.org/debian bookworm/main i386 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 179 http://deb.debian.org/debian bookworm/main i386 sphinx-common all 5.3.0-4 [653 kB] Get: 180 http://deb.debian.org/debian bookworm/main i386 python3-sphinx all 5.3.0-4 [549 kB] Get: 181 http://deb.debian.org/debian bookworm/main i386 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 182 http://deb.debian.org/debian bookworm/main i386 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 183 http://deb.debian.org/debian bookworm/main i386 python3-yaml i386 6.0-3+b2 [119 kB] Get: 184 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 185 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 186 http://deb.debian.org/debian bookworm/main i386 tex-gyre all 20180621-6 [6209 kB] Get: 187 http://deb.debian.org/debian bookworm/main i386 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 188 http://deb.debian.org/debian bookworm/main i386 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 189 http://deb.debian.org/debian bookworm/main i386 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 190 http://deb.debian.org/debian bookworm/main i386 texlive-latex-extra all 2022.20230122-4 [19.2 MB] Get: 191 http://deb.debian.org/debian bookworm/main i386 texlive-plain-generic all 2022.20230122-4 [28.9 MB] Fetched 207 MB in 14s (15.3 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 ... 18156 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18498 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package tzdata. Preparing to unpack .../002-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... 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Setting up media-types (10.0.0) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libgraphite2-3:i386 (1.3.14-1) ... Setting up libpixman-1-0:i386 (0.42.2-1) ... Setting up libaom3:i386 (3.6.0-1) ... Setting up libabsl20220623:i386 (20220623.1-1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up fonts-lato (2.0-2.1) ... Setting up libicu72:i386 (72.1-3) ... Setting up liblerc4:i386 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libdatrie1:i386 (0.2.13-2+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.5-1) ... Setting up libglib2.0-0:i386 (2.74.6-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up liblab-gamut1:i386 (2.42.2-7+b3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:i386 (1:5.44-3) ... Setting up libdeflate0:i386 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libzzip-0-13:i386 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.44-3) ... Setting up libjbig0:i386 (2.1-6.1) ... Setting up librav1e0:i386 (0.5.1-6) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 12 10:54:36 UTC 2024. Universal Time is now: Fri Jan 12 10:54:36 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgts-0.7-5:i386 (0.7.6+darcs121130-5+b1) ... Setting up libfontenc1:i386 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.11.0-2) ... 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 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libteckit0:i386 (2.5.11+ds1-1+b1) ... Setting up libpathplan4:i386 (2.42.2-7+b3) ... Setting up libapache-pom-java (29-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:i386 (1.0.8-2.1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libgav1-1:i386 (0.18.0-1+b1) ... Setting up libdav1d6:i386 (1.0.0-2) ... Setting up libltdl7:i386 (2.4.7-5) ... Setting up libkpathsea6:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libgfortran5:i386 (12.2.0-14) ... 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Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.11.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libavif15:i386 (0.11.1-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:i386 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libptexenc1:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libfreetype6:i386 (2.12.1+dfsg-5) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libx265-199:i386 (3.5-2+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libgvpr2:i386 (2.42.2-7+b3) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:i386 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up libpaper1:i386 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxpm4:i386 (1:3.5.12-1.1+deb12u1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libpango-1.0-0:i386 (1.50.12+ds-1) ... Setting up libheif1:i386 (1.15.1-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.16.0-7) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up sphinx-common (5.3.0-4) ... Setting up libgd3:i386 (2.3.3-9) ... Setting up libxt6:i386 (1:1.2.1-1.1) ... Setting up libpangoft2-1.0-0:i386 (1.50.12+ds-1) ... Setting up tex-gyre (20180621-6) ... Setting up libpangocairo-1.0-0:i386 (1.50.12+ds-1) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxmu6:i386 (2:1.1.3-3) ... Setting up libxi6:i386 (2:1.8-1+b1) ... Setting up preview-latex-style (12.2-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libxaw7:i386 (2:1.0.14-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libgvc6 (2.42.2-7+b3) ... Setting up python3-idna (3.3-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up texlive-binaries (2022.20220321.62855-5.1+deb12u1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-dateutil (2.8.2-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up texlive-base (2022.20230122-3) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up graphviz (2.42.2-7+b3) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.6-2) ... Setting up python3-colorlog (6.7.0-1) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up texlive-plain-generic (2022.20230122-4) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up texlive-latex-base (2022.20230122-3) ... Setting up texlive-latex-recommended (2022.20230122-3) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up texlive-pictures (2022.20230122-3) ... Setting up texlive-fonts-recommended (2022.20230122-3) ... Setting up python3-pandas-lib:i386 (1.5.3+dfsg-2) ... Setting up latexmk (1:4.79-1) ... Setting up texlive-latex-extra (2022.20230122-4) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Processing triggers for ca-certificates (20230311) ... 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: user script /srv/workspace/pbuilder/10842/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/10842/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/macsyfinder-2.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../macsyfinder_2.0-2_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/solution.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/database.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/profile.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/definition_parser.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/cluster.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/error.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/report.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/model_conf_parser.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/model.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/hit.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/registries.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/config.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/gene.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/system.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/search_genes.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/serialization.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/package.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/__init__.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy copying macsypy/utils.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy creating /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/macsydata.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/macsy_gembase_split.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/__init__.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/macsyconfig.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts copying macsypy/scripts/macsy_merge_results.py -> /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py test running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info creating MacSyFinder.egg-info writing MacSyFinder.egg-info/PKG-INFO writing dependency_links to MacSyFinder.egg-info/dependency_links.txt writing entry points to MacSyFinder.egg-info/entry_points.txt writing requirements to MacSyFinder.egg-info/requires.txt writing top-level names to MacSyFinder.egg-info/top_level.txt writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' reading manifest file 'MacSyFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'doc/build/html' warning: no files found matching 'doc/build/latex/macsyfinder.pdf' warning: no files found matching 'etc/macsyfinder.conf' warning: no previously-included files matching '*' found under directory 'tests/__pycache__/' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no previously-included files found matching '.coverage' warning: no previously-included files found matching 'coverage_html/' warning: no previously-included files found matching '.gitignore' warning: no previously-included files found matching '.travis.yml' warning: no previously-included files found matching '.github/' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' adding license file 'COPYING' writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' running build_ext test_Config (test_Config.TestConfig.test_Config) ... ok test_Config_args (test_Config.TestConfig.test_Config_args) ... ok test_Config_conf_file_virtualenv (test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok test_Config_default_conf_file (test_Config.TestConfig.test_Config_default_conf_file) ... ok test_Config_file_bad_values (test_Config.TestConfig.test_Config_file_bad_values) ... ok test_Config_file_n_args (test_Config.TestConfig.test_Config_file_n_args) ... ok test_bad_db_type (test_Config.TestConfig.test_bad_db_type) ... ok test_bad_models_dir (test_Config.TestConfig.test_bad_models_dir) ... ok test_bad_sequence_db (test_Config.TestConfig.test_bad_sequence_db) ... ok test_bad_topology (test_Config.TestConfig.test_bad_topology) ... ok test_bad_topology_file (test_Config.TestConfig.test_bad_topology_file) ... ok test_bad_values (test_Config.TestConfig.test_bad_values) ... ok test_cmd_config_file (test_Config.TestConfig.test_cmd_config_file) ... ok test_config_file_2_dict (test_Config.TestConfig.test_config_file_2_dict) ... ok test_e_value_search (test_Config.TestConfig.test_e_value_search) ... ok test_hit_weights (test_Config.TestConfig.test_hit_weights) ... ok test_model_conf (test_Config.TestConfig.test_model_conf) ... ok test_models_dir (test_Config.TestConfig.test_models_dir) ... ok test_no_cut_ga (test_Config.TestConfig.test_no_cut_ga) ... ok test_out_dir (test_Config.TestConfig.test_out_dir) ... ok test_previous_n_sequence_db (test_Config.TestConfig.test_previous_n_sequence_db) ... ignore sequence_db '/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta' use sequence_db from previous_run '/build/reproducible-path/macsyfinder-2.0/tests/data/data_set/results_1'. ok test_previous_wo_cfg (test_Config.TestConfig.test_previous_wo_cfg) ... ok test_project_config_file (test_Config.TestConfig.test_project_config_file) ... ok test_save (test_Config.TestConfig.test_save) ... ok test_set_log_level (test_Config.TestConfig.test_set_log_level) ... ok test_set_option (test_Config.TestConfig.test_set_option) ... ok test_str_2_tuple (test_Config.TestConfig.test_str_2_tuple) ... ok test_working_dir (test_Config.TestConfig.test_working_dir) ... ok test_NoneConfig (test_Config.TestNoneConfig.test_NoneConfig) ... ok test_bad_exchangeable_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... Models Parsing Invalid model definition 'foo/bad_exchangeable_inter_gene_max_space': inter_gene_max_space must be an integer: 1.5 ok test_bad_gene_inter_gene_max_space_2 (test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) ... Models Parsing Invalid model definition 'foo/bad_inter_gene_max_space_2': inter_gene_max_space must be an integer: 2.5 ok test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... Models Parsing Invalid model definition (/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/definitions/bad_inter_gene_max_space.xml): inter_gene_max_space must be an integer: 12.5 ok test_bad_max_nb_genes (test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... Models Parsing Invalid model definition (/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/definitions/bad_max_nb_genes.xml): max_nb_genes must be an integer: HOHOHO ok test_bad_min_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... Models Parsing model 'bad_min_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6 ok test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... Models Parsing Invalid model definition (/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/definitions/bad_min_genes_required_2.xml): min_genes_required must be an integer: 16.5 ok test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... Models Parsing model 'bad_min_mandatory_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6 ok test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... Models Parsing ok test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... Models Parsing Invalid model definition (/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/definitions/bad_min_mandatory_genes_required_4.xml): min_mandatory_genes_required must be an integer: 12.5 ok test_exchangeable_inheritance (test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... Models Parsing ok test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... Models Parsing ok test_gene_no_name (test_DefinitionParser.TestModelParser.test_gene_no_name) ... Models Parsing Invalid model definition 'foo/gene_no_name': gene without name ok test_gene_w_unkown_attr (test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... Models Parsing unable to parse model definition 'foo/gene_w_unknown_attribute' : The model definition gene_w_unknown_attribute.xml has an unknown attribute 'multi-system' for a gene. Please fix the definition. ok test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... Models Parsing ok test_invalid_homolog (test_DefinitionParser.TestModelParser.test_invalid_homolog) ... Models Parsing ok test_invalid_homolog_2 (test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... Models Parsing Invalid model definition 'foo/invalid_homolog_2': gene without name ok test_invalid_presence (test_DefinitionParser.TestModelParser.test_invalid_presence) ... Models Parsing Invalid model 'foo/fail_invalid_presence' definition: presence value must be either: 'mandatory', 'accessory', 'neutral', 'forbidden' not foo_bar ok test_loner (test_DefinitionParser.TestModelParser.test_loner) ... Models Parsing Models Parsing ok test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... Models Parsing Models Parsing ok test_min_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... Models Parsing ok test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... Models Parsing ok test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... Models Parsing model 'bad_min_mandatory_genes_required_3' is not consistent: 'min_mandatory_genes_required': 6 must be lesser or equal than the number of 'mandatory' components in the model: 5 ok test_model_w_unkown_attr (test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... Models Parsing unable to parse model definition 'foo/model_w_unknown_attribute' : The model definition model_w_unknown_attribute.xml has an unknow attribute 'multi-loci'. Please fix the definition. ok test_multi_loci_cfg (test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... Models Parsing ok test_multi_model (test_DefinitionParser.TestModelParser.test_multi_model) ... Models Parsing ok test_multi_system (test_DefinitionParser.TestModelParser.test_multi_system) ... Models Parsing ok test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... Models Parsing Invalid model definition (/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/definitions/no_inter_gene_max_space.xml): inter_gene_max_space must be defined ok test_only_one_accessory (test_DefinitionParser.TestModelParser.test_only_one_accessory) ... Models Parsing model 'only_one_accessory' is not consistent: there is only one gene in your model. So its status should be 'mandatory'. ok test_parse_model_old_syntax (test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails' test_parse_with_exchangeable (test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... Models Parsing ok test_wo_presence (test_DefinitionParser.TestModelParser.test_wo_presence) ... Models Parsing Invalid model definition 'foo/fail_wo_presence': gene 'sctN_FLG' without presence ok test_add_exchangeable (test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok test_alternate_of (test_Exchangeable.TestExchangeable.test_alternate_of) ... ok test_is_exchangeable (test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok test_loner (test_Exchangeable.TestExchangeable.test_loner) ... ok test_model (test_Exchangeable.TestExchangeable.test_model) ... ok test_multi_system (test_Exchangeable.TestExchangeable.test_multi_system) ... ok test_add_get_gene (test_GeneBank.Test.test_add_get_gene) ... ok test_contains (test_GeneBank.Test.test_contains) ... ok test_genes_fqn (test_GeneBank.Test.test_genes_fqn) ... ok test_get_uniq_object (test_GeneBank.Test.test_get_uniq_object) ... ok test_iter (test_GeneBank.Test.test_iter) ... ok test_build_force (test_Indexes.TestIndex.test_build_force) ... ok test_build_my_indexes (test_Indexes.TestIndex.test_build_my_indexes) ... unable to index the sequence dataset: /tmp/test_macsyfinder_indexes/test_base_with_errors.fa : list index out of range Traceback (most recent call last): File "/build/reproducible-path/macsyfinder-2.0/macsypy/database.py", line 192, in _build_my_indexes for seq_id, comment, length in f_iter: File "/build/reproducible-path/macsyfinder-2.0/macsypy/database.py", line 53, in fasta_iter _id = header[0] ~~~~~~^^^ IndexError: list index out of range ok test_build_no_idx (test_Indexes.TestIndex.test_build_no_idx) ... ok test_build_not_writable (test_Indexes.TestIndex.test_build_not_writable) ... The '/tmp/test_macsyfinder_indexes' dir is not writable. ok test_build_with_idx (test_Indexes.TestIndex.test_build_with_idx) ... The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building. The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building. ok test_find_my_indexes (test_Indexes.TestIndex.test_find_my_indexes) ... ok test_index_dir (test_Indexes.TestIndex.test_index_dir) ... ok test_iter (test_Indexes.TestIndex.test_iter) ... ok test_allowed_hits (test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok test_forbidden_hits (test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok test_hits (test_LikelySystem.LikelySystemTest.test_hits) ... ok test_init (test_LikelySystem.LikelySystemTest.test_init) ... ok test_str (test_LikelySystem.LikelySystemTest.test_str) ... ok test_hits (test_LikelySystem.UnlikelySystemTest.test_hits) ... ok test_init (test_LikelySystem.UnlikelySystemTest.test_init) ... ok test_reason (test_LikelySystem.UnlikelySystemTest.test_reason) ... ok test_str (test_LikelySystem.UnlikelySystemTest.test_str) ... ok test_MacsyDefaults_no_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok test_MacsyDefaults_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok test_ordered_match (test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok test_sort_hits_by_status (test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... Gene 'fliE' not found in model 'foo/model_B' ok test_unordered_match (test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok test_accessor_mutator (test_Model.TestModel.test_accessor_mutator) ... ok test_eq (test_Model.TestModel.test_eq) ... ok test_filter (test_Model.TestModel.test_filter) ... ok test_fqn (test_Model.TestModel.test_fqn) ... ok test_get_gene (test_Model.TestModel.test_get_gene) ... ok test_gt (test_Model.TestModel.test_gt) ... ok test_hash (test_Model.TestModel.test_hash) ... ok test_inter_gene_max_space (test_Model.TestModel.test_inter_gene_max_space) ... ok test_lt (test_Model.TestModel.test_lt) ... ok test_max_nb_genes (test_Model.TestModel.test_max_nb_genes) ... ok test_min_genes_required (test_Model.TestModel.test_min_genes_required) ... ok test_min_mandatory_genes_required (test_Model.TestModel.test_min_mandatory_genes_required) ... ok test_multi_loci (test_Model.TestModel.test_multi_loci) ... ok test_str (test_Model.TestModel.test_str) ... ok test_add_get_model (test_ModelBank.Test.test_add_get_model) ... ok test_contains (test_ModelBank.Test.test_contains) ... ok test_get_uniq_object (test_ModelBank.Test.test_get_uniq_object) ... ok test_iter (test_ModelBank.Test.test_iter) ... ok test_execute_hmm_protected_path (test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok test_execute_hmm_w_GA_n_nocutga (test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok test_execute_hmm_with_GA (test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping' test_execute_hmm_wo_GA (test_Profile.TestProfile.test_execute_hmm_wo_GA) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) ok test_execute_hmmer_failed (test_Profile.TestProfile.test_execute_hmmer_failed) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) an error occurred during Hmmer execution: command = "/tmp/hmmer_failed" --cpu 1 -o "/tmp/macsyfinder-20240113_00-57-16/hmmer_results/abc.search_hmm.out" -E 0.100000 "/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/profiles/abc.hmm" "/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240113_00-57-16/hmmer_results/abc.search_hmm.err ok test_execute_unknown_binary (test_Profile.TestProfile.test_execute_unknown_binary) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) an error occurred during Hmmer execution: command = "Nimportnaoik" --cpu 1 -o "/tmp/macsyfinder-20240113_00-57-16/hmmer_results/abc.search_hmm.out" -E 0.100000 "/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/profiles/abc.hmm" "/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240113_00-57-16/hmmer_results/abc.search_hmm.err ok test_ga_threshold (test_Profile.TestProfile.test_ga_threshold) ... bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''. GA score will not used for gene 'bad_GA'. bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''. GA score will not used for gene 'bad_GA'. bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'. GA score will not used for gene 'bad_GA_2'. bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'. GA score will not used for gene 'bad_GA_2'. ok test_len (test_Profile.TestProfile.test_len) ... ok test_str (test_Profile.TestProfile.test_str) ... ok test_get_profile (test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok test_get_uniq_object (test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok test_unknow_profile (test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok test_hits (test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok test_init (test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok test_str (test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok test_fill_gembase_min_max_default_topology (test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok test_fill_gembase_min_max_with_topology (test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok test_fill_ordered_replicon_min_max (test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok test_fill_topology (test_RepliconDB.Test.test_fill_topology) ... ok test_get (test_RepliconDB.Test.test_get) ... ok test_getitem (test_RepliconDB.Test.test_getitem) ... ok test_guess_if_really_gembase (test_RepliconDB.Test.test_guess_if_really_gembase) ... ok test_in (test_RepliconDB.Test.test_in) ... ok test_items (test_RepliconDB.Test.test_items) ... ok test_iteritems (test_RepliconDB.Test.test_iteritems) ... ok test_names (test_RepliconDB.Test.test_names) ... ok test_replicon_infos (test_RepliconDB.Test.test_replicon_infos) ... ok test_extract (test_Report.TestGembaseHMMReport.test_extract) ... ok test_extract_concurent (test_Report.TestGembaseHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.0/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_extract (test_Report.TestGeneralHMMReport.test_extract) ... ok test_extract_concurent (test_Report.TestGeneralHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.0/tests/test_Report.py:539: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_HMMReport (test_Report.TestHMMReport.test_HMMReport) ... ok test_best_hit (test_Report.TestHMMReport.test_best_hit) ... ok test_build_my_db (test_Report.TestHMMReport.test_build_my_db) ... ok test_fill_my_db (test_Report.TestHMMReport.test_fill_my_db) ... ok test_hit_start (test_Report.TestHMMReport.test_hit_start) ... ok test_parse_hmm_body (test_Report.TestHMMReport.test_parse_hmm_body) ... ok test_parse_hmm_header (test_Report.TestHMMReport.test_parse_hmm_header) ... ok test_save_extract (test_Report.TestHMMReport.test_save_extract) ... ok test_str (test_Report.TestHMMReport.test_str) ... ok test_extract (test_Report.TestOrderedHMMReport.test_extract) ... hit id 'NC_xxxxx_xx_056141' was not indexed, rebuild sequence 'test_base.fa' index ok test_extract_concurent (test_Report.TestOrderedHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.0/tests/test_Report.py:460: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_HitSystemTracker (test_System.SystemTest.test_HitSystemTracker) ... ok test_count (test_System.SystemTest.test_count) ... ok test_fulfilled_function (test_System.SystemTest.test_fulfilled_function) ... ok test_get_hits_encoding_multisystem (test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok test_get_loners (test_System.SystemTest.test_get_loners) ... ok test_get_multisystems (test_System.SystemTest.test_get_multisystems) ... ok test_hits (test_System.SystemTest.test_hits) ... ok test_init (test_System.SystemTest.test_init) ... ok test_is_compatible (test_System.SystemTest.test_is_compatible) ... ok test_loci_nb (test_System.SystemTest.test_loci_nb) ... ok test_loci_num (test_System.SystemTest.test_loci_num) ... ok test_multi_loci (test_System.SystemTest.test_multi_loci) ... ok test_occurrence (test_System.SystemTest.test_occurrence) ... ok test_position (test_System.SystemTest.test_position) ... ok test_score (test_System.SystemTest.test_score) ... ok test_wholeness (test_System.SystemTest.test_wholeness) ... ok test_build_clusters (test_cluster.TestBuildCluster.test_build_clusters) ... ok test_clusterize (test_cluster.TestBuildCluster.test_clusterize) ... ok test_colocates (test_cluster.TestBuildCluster.test_colocates) ... ok test_get_true_loners (test_cluster.TestBuildCluster.test_get_true_loners) ... ok test_contains (test_cluster.TestCluster.test_contains) ... ok test_fulfilled_function (test_cluster.TestCluster.test_fulfilled_function) ... ok test_init (test_cluster.TestCluster.test_init) ... Cannot build a cluster from hits coming from different replicons ok test_len (test_cluster.TestCluster.test_len) ... ok test_loner (test_cluster.TestCluster.test_loner) ... ok test_merge (test_cluster.TestCluster.test_merge) ... ok test_multi_system (test_cluster.TestCluster.test_multi_system) ... ok test_replace (test_cluster.TestCluster.test_replace) ... ok test_replicon_name (test_cluster.TestCluster.test_replicon_name) ... ok test_score (test_cluster.TestCluster.test_score) ... ok test_str (test_cluster.TestCluster.test_str) ... ok test_2_systems_not_compatible (test_functional_test.Test.test_2_systems_not_compatible) ... ok test_cfg_n_previous_run (test_functional_test.Test.test_cfg_n_previous_run) ... ok test_degenerated_systems (test_functional_test.Test.test_degenerated_systems) ... ok test_gembase (test_functional_test.Test.test_gembase) ... ok test_index_dir (test_functional_test.Test.test_index_dir) ... ok test_model_unknown (test_functional_test.Test.test_model_unknown) ... ok test_no_db_type (test_functional_test.Test.test_no_db_type) ... ok test_no_models (test_functional_test.Test.test_no_models) ... ok test_no_seq_db (test_functional_test.Test.test_no_seq_db) ... ok test_only_loners (test_functional_test.Test.test_only_loners) ... ok test_ordered_1_cluster_3_loners (test_functional_test.Test.test_ordered_1_cluster_3_loners) ... ok test_ordered_1_clusters_3_loners_w_exchangeable (test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) ... ok test_ordered_1_loner_exch_in_clust (test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... ok test_ordered_1_loner_in_clust (test_functional_test.Test.test_ordered_1_loner_in_clust) ... ok test_ordered_2_clusters_1_loner (test_functional_test.Test.test_ordered_2_clusters_1_loner) ... ok test_ordered_2_clusters_3_loners (test_functional_test.Test.test_ordered_2_clusters_3_loners) ... ok test_ordered_circular (test_functional_test.Test.test_ordered_circular) ... ok test_ordered_linear (test_functional_test.Test.test_ordered_linear) ... ok test_ordered_multi_loci (test_functional_test.Test.test_ordered_multi_loci) ... ok test_ordered_multi_model (test_functional_test.Test.test_ordered_multi_model) ... ok test_ordered_multi_system (test_functional_test.Test.test_ordered_multi_system) ... ok test_ordered_multi_system_out_system (test_functional_test.Test.test_ordered_multi_system_out_system) ... ok test_ordered_only_one_multi_model (test_functional_test.Test.test_ordered_only_one_multi_model) ... ok test_ordered_single_loci (test_functional_test.Test.test_ordered_single_loci) ... ok test_uncomplete_degenerated_systems (test_functional_test.Test.test_uncomplete_degenerated_systems) ... ok test_unordered (test_functional_test.Test.test_unordered) ... ok test_unordered_no_hits (test_functional_test.Test.test_unordered_no_hits) ... ok test_unordered_only_forbidden (test_functional_test.Test.test_unordered_only_forbidden) ... ok test_working_dir_exists (test_functional_test.Test.test_working_dir_exists) ... ok test_working_dir_exists_and_not_dir (test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok test_core_gene (test_gene.TestCoreGene.test_core_gene) ... ok test_str (test_gene.TestGeneStatus.test_str) ... ok test_add_exchangeable (test_gene.TestModelGene.test_add_exchangeable) ... ok test_alternate_of (test_gene.TestModelGene.test_alternate_of) ... ok test_core_gene (test_gene.TestModelGene.test_core_gene) test getter/setter for core_gene property ... ok test_exhangeables (test_gene.TestModelGene.test_exhangeables) ... ok test_hash (test_gene.TestModelGene.test_hash) ... ok test_init (test_gene.TestModelGene.test_init) ... ok test_inter_gene_max_space (test_gene.TestModelGene.test_inter_gene_max_space) test getter for inter_gene_max_space property ... ok test_is_Forbidden (test_gene.TestModelGene.test_is_Forbidden) test if gene belong to model mandatory genes ... ok test_is_accessory (test_gene.TestModelGene.test_is_accessory) test if gene belong to model mandatory genes ... ok test_is_exchangeable (test_gene.TestModelGene.test_is_exchangeable) ... ok test_is_mandatory (test_gene.TestModelGene.test_is_mandatory) test if gene belong to model mandatory genes ... ok test_loner (test_gene.TestModelGene.test_loner) test getter for loner property ... ok test_model (test_gene.TestModelGene.test_model) test getter/setter for model property ... ok test_multi_model (test_gene.TestModelGene.test_multi_model) test getter for multi_modelproperty ... ok test_multi_system (test_gene.TestModelGene.test_multi_system) test getter for multi_system property ... ok test_str (test_gene.TestModelGene.test_str) ... ok test_unknown_attribute (test_gene.TestModelGene.test_unknown_attribute) ... ok test_cmp (test_hit.CoreHitTest.test_cmp) ... ok test_eq (test_hit.CoreHitTest.test_eq) ... ok test_get_position (test_hit.CoreHitTest.test_get_position) ... ok test_hash (test_hit.CoreHitTest.test_hash) ... ok test_str (test_hit.CoreHitTest.test_str) ... ok test_compute_best_MSHit (test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok test_get_best_hits (test_hit.GetBestHitTest.test_get_best_hits) ... ok test_get_best_hits_4_func (test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok test_sort_multisystem_hits (test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok test_hit_weight_default (test_hit.HitWeightTest.test_hit_weight_default) ... ok test_hit_weight_not_default (test_hit.HitWeightTest.test_hit_weight_not_default) ... ok test_counterpart (test_hit.LonerMultiSystemTest.test_counterpart) ... Try to set counterpart for hit 'gspD' with non compatible hits: ['gspD', 'sctJ'] ok test_init (test_hit.LonerMultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system ok test_loner (test_hit.LonerMultiSystemTest.test_loner) ... ok test_multi_system (test_hit.LonerMultiSystemTest.test_multi_system) ... ok test_str (test_hit.LonerMultiSystemTest.test_str) ... ok test_counterpart (test_hit.LonerTest.test_counterpart) ... ok test_init (test_hit.LonerTest.test_init) ... hit_2 cannot be a loner gene_ref 'sctJ' not tag as loner ok test_len (test_hit.LonerTest.test_len) ... ok test_loner (test_hit.LonerTest.test_loner) ... ok test_multi_system (test_hit.LonerTest.test_multi_system) ... ok test_str (test_hit.LonerTest.test_str) ... ok test_delegation (test_hit.ModelHitTest.test_delegation) ... ok test_eq (test_hit.ModelHitTest.test_eq) ... ok test_hash (test_hit.ModelHitTest.test_hash) ... ok test_init (test_hit.ModelHitTest.test_init) ... ok test_loner (test_hit.ModelHitTest.test_loner) ... ok test_multi_model (test_hit.ModelHitTest.test_multi_model) ... ok test_multi_system (test_hit.ModelHitTest.test_multi_system) ... ok test_counterpart (test_hit.MultiSystemTest.test_counterpart) ... ok test_init (test_hit.MultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system ok test_len (test_hit.MultiSystemTest.test_len) ... ok test_loner (test_hit.MultiSystemTest.test_loner) ... ok test_multi_system (test_hit.MultiSystemTest.test_multi_system) ... ok test_str (test_hit.MultiSystemTest.test_str) ... ok test_functional_split (test_macsy_gembase_split.TestSplit.test_functional_split) ... /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpup7m8a07/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 (test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... /tmp/tmp1y3bug03/macsyfinder_test_split/base is not a directory ok test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... /tmp/tmp1gaoftg_/macsyfinder_test_split/base is not writable Cannot create /tmp/tmp1gaoftg_/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmp1gaoftg_/macsyfinder_test_split/base' ok test_functional_merge (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv' Merging 'best_solution.tsv' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_best_solution.tsv' Merging 'all_systems.tsv' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_all_systems.tsv' Merging 'best_solution_multisystems.tsv' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv' Merging 'best_solution_loners.tsv' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv' Merging 'rejected_candidates.tsv' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv' Merging 'all_systems.txt' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_all_systems.txt' Merging 'rejected_candidates.txt' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt' Merging 'best_solution_summary' in to '/tmp/tmppkb9kf7n/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv' /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmppkb9kf7n/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 (test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpczg9j0se/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 (test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... /tmp/tmphf2qus2p/macsyfinder_test_merge/merged_results is not a directory ok test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... /tmp/tmp0fu0wpo6/macsyfinder_test_merge/merged_results is not writable Cannot create /tmp/tmp0fu0wpo6/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmp0fu0wpo6/macsyfinder_test_merge/merged_results' ok test_functional_merge_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpompp9htw/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_merge_and_reindex_invalid_solid (test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... Cannot reindex int(GCF_000006845) + 1: invalid literal for int() with base 10: 'GCF_000006845' ok test_add_comment (test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok test_write (test_macsyconfig.TestConfigParserWithComment.test_write) ... ok test_ask (test_macsyconfig.TestMacsyconfig.test_ask) ... ok test_ask_bad_value (test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok test_ask_default_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok test_ask_use_default (test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok test_ask_value_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok test_check_bool (test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok test_check_choice (test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok test_check_dir (test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok test_check_exe (test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok test_check_file (test_macsyconfig.TestMacsyconfig.test_check_file) ... ok test_check_float (test_macsyconfig.TestMacsyconfig.test_check_float) ... ok test_check_positive_int (test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok test_check_str (test_macsyconfig.TestMacsyconfig.test_check_str) ... ok test_functional_dark_theme (test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok test_functional_file_already_exists (test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok test_parse_args (test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok test_set_base_options (test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok test_set_general_options (test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok test_set_hmmer_options (test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok test_set_path_options (test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok test_set_path_options_with_system_models_dir (test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok test_set_score_options (test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok test_set_section (test_macsyconfig.TestMacsyconfig.test_set_section) ... ok test_set_section_use_defaults (test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok test_available (test_macsydata.TestMacsydata.test_available) ... ok test_build_argparser (test_macsydata.TestMacsydata.test_build_argparser) ... ok test_check (test_macsydata.TestMacsydata.test_check) ... If everyone were like you, I'd be out of business To push the models in organization: cd /tmp/tmpelyw36r9/fake_1 Transform the models into a git repository git init . git add . git commit -m 'initial commit' add a remote repository to host the models for instance if you want to add the models to 'macsy-models' git remote add origin https://github.com/macsy-models/ git tag 0.0b2 git push origin 0.0b2 ok test_check_with_errors (test_macsydata.TestMacsydata.test_check_with_errors) ... The package 'fake_1' have no 'definitions' directory. The package 'fake_1' have no 'profiles' directory. Please fix issues above, before publishing these models. ok test_check_with_warnings (test_macsydata.TestMacsydata.test_check_with_warnings) ... The package 'fake_1' have not any LICENSE file. May be you have not right to use it. The package 'fake_1' have not any README file. macsydata says: You're only giving me a partial QA payment? I'll take it this time, but I'm not happy. I'll be really happy, if you fix warnings above, before to publish these models. ok test_cite (test_macsydata.TestMacsydata.test_cite) ... Models 'nimportnaoik' not found locally. ok test_cmd_name (test_macsydata.TestMacsydata.test_cmd_name) ... ok test_definition_all_def (test_macsydata.TestMacsydata.test_definition_all_def) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpyqppdyn5/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-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpyqppdyn5/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 (test_macsydata.TestMacsydata.test_definition_bad_def) ... Model 'fake_1/niportnaoik' not found. ok test_definition_bad_pack (test_macsydata.TestMacsydata.test_definition_bad_pack) ... Package 'nimportnaoik' not found. ok test_definition_bad_subfamily (test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... 'niportnaoik' not found in package 'fake_1'. ok test_definition_models_dir (test_macsydata.TestMacsydata.test_definition_models_dir) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpgkv4qpx3/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-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpgkv4qpx3/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 (test_macsydata.TestMacsydata.test_definition_one_def) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpgcap57qv/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-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpgcap57qv/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 (test_macsydata.TestMacsydata.test_download) ... Downloading fake_1 1.0 Successfully downloaded packaging fake_1 in /tmp/tmpcg_3383t/fake_1-1.0.tar.gz No version that satisfy requirements '>2.0' for 'fake_1'. Available versions: 1.0 Downloading fake_1 1.0 github limit error ok test_freeze (test_macsydata.TestMacsydata.test_freeze) ... ok test_help (test_macsydata.TestMacsydata.test_help) ... Models 'nimportnaoik' not found locally. ok test_info (test_macsydata.TestMacsydata.test_info) ... Models 'nimportnaoik' not found locally. ok test_install_bad_target (test_macsydata.TestMacsydata.test_install_bad_target) ... ok test_install_installed_package_corrupted (test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmppskxradt/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. fake_pack locally installed is corrupted. You can fix it by removing '/tmp/tmppskxradt/models/fake_pack'. ok test_install_local (test_macsydata.TestMacsydata.test_install_local) ... Extracting fake_pack (3.0). Installing fake_pack (3.0) in /tmp/tmpo8unsgkj/models Cleaning. The models fake_pack (3.0) have been installed successfully. ok test_install_local_already_installed (test_macsydata.TestMacsydata.test_install_local_already_installed) ... Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmp6th9s6y0/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmp6th9s6y0/models/fake_pack. To force installation use option -f --force-reinstall. ok test_install_local_already_installed_force (test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmp_7pa5y_o/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmp_7pa5y_o/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. ok test_install_remote (test_macsydata.TestMacsydata.test_install_remote) ... Downloading fake_pack (0.0b2). Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmpdcm7filt/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. ok test_install_remote_already_in_local (test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmpn_g1huuc/models/fake_pack. To force installation use option -f --force-reinstall. ok test_install_remote_already_in_local_force (test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... Downloading fake_pack (0.0b2). Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmpt1077c25/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. ok test_install_remote_lower_in_local (test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... fake_pack (0.0b2) is already installed but 1.0 version is available. To install it please run 'macsydata install --upgrade fake_pack' ok test_install_remote_permision_error (test_macsydata.TestMacsydata.test_install_remote_permision_error) ... /tmp/tmpcr7xgduf/models is not readable: [Errno 13] Permission denied: '/tmp/tmpcr7xgduf/models' : skip it. Downloading fake_pack (0.0b2). Extracting fake_pack (0.0b2). Installing fake_pack (0.0b2) in /tmp/tmpcr7xgduf/models /tmp/tmpcr7xgduf/models is not writable: [Errno 13] Permission denied: '/tmp/tmpcr7xgduf/models/fake_pack' Maybe you can use --user option to install in your HOME. ok test_install_remote_spec_not_found (test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... Could not find version that satisfied 'fake_pack>0.0b2' ok test_install_remote_upper_in_local (test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... fake_pack (0.0b2) is already installed. To downgrade to 0.0b1 use option -f --force-reinstall. ok test_install_target (test_macsydata.TestMacsydata.test_install_target) ... Extracting fake_pack (3.0). Installing fake_pack (3.0) in /tmp/tmpn1_kqoyl/target Cleaning. The models fake_pack (3.0) have been installed successfully. ok test_list (test_macsydata.TestMacsydata.test_list) ... ok test_list_outdated (test_macsydata.TestMacsydata.test_list_outdated) ... ok test_list_uptodate (test_macsydata.TestMacsydata.test_list_uptodate) ... ok test_list_verbose (test_macsydata.TestMacsydata.test_list_verbose) ... [Errno 2] No such file or directory: '/tmp/tmp7pnci9wv/models/fake_1/metadata.yml' ok test_no_subcommand (test_macsydata.TestMacsydata.test_no_subcommand) ... ok test_search_in_pack_desc (test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok test_search_in_pack_name (test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok test_search_in_pack_name_match_case (test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok test_search_reach_limit (test_macsydata.TestMacsydata.test_search_reach_limit) ... bla ok test_uninstall (test_macsydata.TestMacsydata.test_uninstall) ... models 'fake_1' in /tmp/tmp5gd7qjv_/models/fake_1 uninstalled. Models 'foo' not found locally. ok test_verbosity_to_log_level (test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok test_db_type_set_to_gembase (test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... GA bit thresholds unavailable on profile T4P_pilX. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilC. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T2SS_gspO. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilU. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilT. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilP. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_fimT. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilQ. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilO. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilD. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilV. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilB. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile MSH_mshM. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilE. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile ComM_comC. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilM. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilN. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilA. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilY. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilW. Switch to e-value threshold (-E 0.100000) Most of replicons contains only ONE sequence are you sure that '/build/reproducible-path/macsyfinder-2.0/tests/data/base/ordered_replicon_base.fasta' is a 'gembase'. ok test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok test_list_models (test_macsyfinder.TestMacsyfinder.test_list_models) ... ok test_loners_to_tsv (test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok test_multisystem_to_tsv (test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok test_parse_args (test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok test_rejected_candidates_to_tsv (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok test_rejected_candidates_to_txt (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok test_search_systems (test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok test_search_systems_unordered (test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok test_summary_best_solution (test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok test_summary_best_solution_empty (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok test_summary_best_solution_lack_models (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok test_summary_best_solution_lack_models_replicons (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok test_summary_best_solution_lack_replicon (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok test_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok test_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok test_LightHit (test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok test_build_my_db (test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok test_fill_my_db (test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok test_functional (test_macsyprofile.TestMacsyprofile.test_functional) ... ok test_functional_best_score (test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok test_functional_coverage (test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok test_functional_evalue (test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok test_functional_no_hits (test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... nimportnaoik: No such directory. ok test_functional_out_exists (test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... The file /tmp/tmprdhjl9oa already exists. Remove it or specify a new output name --out or use --force option ok test_functional_pattern (test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok test_getProfile_len (test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok test_get_gene_name (test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok test_header (test_macsyprofile.TestMacsyprofile.test_header) ... ok test_hit_start (test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok test_parse (test_macsyprofile.TestMacsyprofile.test_parse) ... ok test_parse_hmm_body (test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok test_parse_hmm_header (test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok test_pasre_args (test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok test_init_logger_default (test_macsypy.Test.test_init_logger_default) ... ok test_init_logger_logfile (test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp38mox3ia' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_init_logger_no_out (test_macsypy.Test.test_init_logger_no_out) ... ok test_logger_set_level_bad_level (test_macsypy.Test.test_logger_set_level_bad_level) ... ok test_logger_set_level_default (test_macsypy.Test.test_logger_set_level_default) ... ok test_logger_set_level_error (test_macsypy.Test.test_logger_set_level_error) ... ok test_logger_set_level_handlers (test_macsypy.Test.test_logger_set_level_handlers) ... ok test_parse (test_model_conf_parser.TestModelConfParser.test_parse) ... ok test_parse_bad_file (test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... unable to parse model configuration '/build/reproducible-path/macsyfinder-2.0/tests/data/conf_files/project.conf' : syntax error: line 2, column 0 ok test_parse_filtering (test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... cannot parse 'cut_ga' element in '/build/reproducible-path/macsyfinder-2.0/tests/data/conf_files/model_conf.xml' expect True, 1, False, 0 got : 'FOO' ok test_parse_w_bad_value (test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... The model configuration file '/build/reproducible-path/macsyfinder-2.0/tests/data/conf_files/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO' ok test_parse_w_unkown_tag (test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... unknown element 'nimportnaoik' in '/build/reproducible-path/macsyfinder-2.0/tests/data/conf_files/model_conf.xml' ignore it. ok test_parse_weights (test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok test_parse_wo_filtering (test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok test_parse_wo_weights (test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok test_init (test_package.TestLocalModelIndex.test_init) ... ok test_init (test_package.TestModelIndex.test_init) ... ok test_check (test_package.TestPackage.test_check) ... ok test_check_metadata (test_package.TestPackage.test_check_metadata) ... ok test_check_model_conf (test_package.TestPackage.test_check_model_conf) ... ok test_check_model_conf_bad_conf (test_package.TestPackage.test_check_model_conf_bad_conf) ... The model configuration file '/tmp/macsy_test_package/fake_model/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO' ok test_check_model_conf_no_conf (test_package.TestPackage.test_check_model_conf_no_conf) ... ok test_check_model_consistency (test_package.TestPackage.test_check_model_consistency) ... ok test_check_model_consistency_bad_definitions (test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok test_check_model_consistency_extra_profile (test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok test_check_model_consistency_lack_one_profile (test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok test_check_no_readme_n_no_license (test_package.TestPackage.test_check_no_readme_n_no_license) ... ok test_check_structure (test_package.TestPackage.test_check_structure) ... ok test_check_structure_bad_path (test_package.TestPackage.test_check_structure_bad_path) ... ok test_check_structure_no_def (test_package.TestPackage.test_check_structure_no_def) ... ok test_check_structure_no_license (test_package.TestPackage.test_check_structure_no_license) ... ok test_check_structure_no_metadata (test_package.TestPackage.test_check_structure_no_metadata) ... ok test_check_structure_no_profiles (test_package.TestPackage.test_check_structure_no_profiles) ... ok test_check_structure_no_readme (test_package.TestPackage.test_check_structure_no_readme) ... ok test_find_readme (test_package.TestPackage.test_find_readme) ... ok test_help (test_package.TestPackage.test_help) ... ok test_info (test_package.TestPackage.test_info) ... ok test_init (test_package.TestPackage.test_init) ... ok test_metadata (test_package.TestPackage.test_metadata) ... ok test_parse_arch_path (test_package.TestPackageFunc.test_parse_arch_path) ... ok test_download (test_package.TestRemoteModelIndex.test_download) ... ok test_get_metadata (test_package.TestRemoteModelIndex.test_get_metadata) ... ok test_init (test_package.TestRemoteModelIndex.test_init) ... ok test_list_package_vers (test_package.TestRemoteModelIndex.test_list_package_vers) ... ok test_list_packages (test_package.TestRemoteModelIndex.test_list_packages) ... ok test_remote_exists (test_package.TestRemoteModelIndex.test_remote_exists) ... ok test_unarchive (test_package.TestRemoteModelIndex.test_unarchive) ... ok test_url_json (test_package.TestRemoteModelIndex.test_url_json) ... ok test_url_json_reach_limit (test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok test_DefinitionLocationn (test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok test_add_submodel (test_registries.DefinitionLocationTest.test_add_submodel) ... ok test_all (test_registries.DefinitionLocationTest.test_all) ... ok test_eq (test_registries.DefinitionLocationTest.test_eq) ... ok test_family_name (test_registries.DefinitionLocationTest.test_family_name) ... ok test_greater (test_registries.DefinitionLocationTest.test_greater) ... ok test_hash (test_registries.DefinitionLocationTest.test_hash) ... ok test_lesser (test_registries.DefinitionLocationTest.test_lesser) ... ok test_root_name (test_registries.DefinitionLocationTest.test_root_name) ... ok test_separator (test_registries.DefinitionLocationTest.test_separator) ... ok test_split_fqn (test_registries.DefinitionLocationTest.test_split_fqn) ... ok test_str (test_registries.DefinitionLocationTest.test_str) ... ok test_ModelLocation (test_registries.ModelLocationTest.test_ModelLocation) ... ok test_get_all_definitions (test_registries.ModelLocationTest.test_get_all_definitions) ... ok test_get_definition (test_registries.ModelLocationTest.test_get_definition) ... ok test_get_definitions (test_registries.ModelLocationTest.test_get_definitions) ... ok test_get_profile (test_registries.ModelLocationTest.test_get_profile) ... ok test_get_profiles_names (test_registries.ModelLocationTest.test_get_profiles_names) ... ok test_str (test_registries.ModelLocationTest.test_str) ... ok test_version (test_registries.ModelLocationTest.test_version) ... ok test_version_no_metadata (test_registries.ModelLocationTest.test_version_no_metadata) ... The models package 'simple' is not versioned contact the package manager to fix it. ok test_add_get (test_registries.ModelRegistryTest.test_add_get) ... ok test_models (test_registries.ModelRegistryTest.test_models) ... ok test_scan_models_dir (test_registries.ModelRegistryTest.test_scan_models_dir) ... ok test_str (test_registries.ModelRegistryTest.test_str) ... ok test_join_def_path (test_registries.RegitriesUtilsTest.test_join_def_path) ... ok test_split_def_name (test_registries.RegitriesUtilsTest.test_split_def_name) ... ok test_search (test_search_genes.TestSearchGenes.test_search) ... ok test_search_fail (test_search_genes.TestSearchGenes.test_search_fail) ... ok test_search_recover (test_search_genes.TestSearchGenes.test_search_recover) ... ok test_LikelySystemSerializer_txt (test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok test_RejectedClusters_tsv (test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok test_SolutionSerializer_tsv (test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok test_SpecialHitSerializer_tsv (test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok test_SystemSerializer_str (test_serialization.SerializationTest.test_SystemSerializer_str) ... ok test_SystemSerializer_tsv (test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok test_combine_clusters (test_solution.SolutionExplorerTest.test_combine_clusters) ... ok test_combine_multisystems (test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok test_find_best_solution (test_solution.SolutionExplorerTest.test_find_best_solution) ... ok test_average_wholeness (test_solution.SolutionTest.test_average_wholeness) ... ok test_gt (test_solution.SolutionTest.test_gt) ... ok test_hits_number (test_solution.SolutionTest.test_hits_number) ... ok test_hits_positions (test_solution.SolutionTest.test_hits_positions) ... ok test_iteration (test_solution.SolutionTest.test_iteration) ... ok test_lt (test_solution.SolutionTest.test_lt) ... ok test_score (test_solution.SolutionTest.test_score) ... ok test_sorting (test_solution.SolutionTest.test_sorting) ... ok test_systems (test_solution.SolutionTest.test_systems) ... ok test_get_def_to_detect (test_utils.TestUtils.test_get_def_to_detect) ... ok test_get_replicon_names (test_utils.TestUtils.test_get_replicon_names) ... ok test_threads_available (test_utils.TestUtils.test_threads_available) ... ok ---------------------------------------------------------------------- Ran 486 tests in 27.447s OK (skipped=2) create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/macsyfinder/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running install_lib creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11 creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/solution.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/database.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/macsyfinder.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/macsy_gembase_split.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/macsyprofile.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/__init__.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/macsyconfig.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/scripts/macsy_merge_results.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/profile.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/definition_parser.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/cluster.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/error.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/report.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/model_conf_parser.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/model.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/hit.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/registries.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/config.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/gene.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/system.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/search_genes.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/serialization.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/package.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/__init__.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0/.pybuild/cpython3_3.11/build/macsypy/utils.py -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/solution.py to solution.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/database.py to database.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsyfinder.py to macsyfinder.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsydata.py to macsydata.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsy_gembase_split.py to macsy_gembase_split.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsyprofile.py to macsyprofile.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsyconfig.py to macsyconfig.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsy_merge_results.py to macsy_merge_results.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/profile.py to profile.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/definition_parser.py to definition_parser.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/cluster.py to cluster.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/error.py to error.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/report.py to report.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/model_conf_parser.py to model_conf_parser.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/model.py to model.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/hit.py to hit.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/registries.py to registries.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/config.py to config.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/gene.py to gene.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/system.py to system.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/search_genes.py to search_genes.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/serialization.py to serialization.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/package.py to package.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/utils.py to utils.cpython-311.pyc running install_data creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/share creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/share/macsyfinder creating /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/share/macsyfinder/models copying data/models/README -> /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/share/macsyfinder/models running install_egg_info running 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 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 found matching 'tests/__init__.pyc' warning: no previously-included files found matching '.coverage' warning: no previously-included files found matching 'coverage_html/' warning: no previously-included files found matching '.gitignore' warning: no previously-included files found matching '.travis.yml' warning: no previously-included files found matching '.github/' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' adding license file 'COPYING' writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' Copying MacSyFinder.egg-info to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/lib/python3.11/dist-packages/MacSyFinder-2.0.egg-info Skipping SOURCES.txt running install_scripts Installing macsyconfig script to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/bin Installing macsydata script to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/bin Installing macsyfinder script to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/bin Installing macsymerge script to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/bin Installing macsyprofile script to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/bin Installing macsysplit script to /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/usr/bin I: pybuild pybuild:333: cp -a /build/reproducible-path/macsyfinder-2.0/debian/etc /build/reproducible-path/macsyfinder-2.0/debian/macsyfinder/etc && cd /build/reproducible-path/macsyfinder-2.0/doc && make html latexpdf make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.0/doc' Running Sphinx v5.3.0 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 42 source files that are out of date updating environment: [new config] 42 added, 0 changed, 0 removed reading sources... 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Running Sphinx v5.3.0 making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found processing macsyfinder.tex... index user_guide/index user_guide/new_v2 user_guide/installation user_guide/quickstart user_guide/input user_guide/gembase_convention user_guide/outputs user_guide/big_data user_guide/model_definition user_guide/functioning user_guide/FAQ modeler_guide/index modeler_guide/package modeler_guide/modeling modeler_guide/helper_tools modeler_guide/publish_package modeler_guide/gallery modeler_guide/models_V1ToV2 modeler_guide/FAQ_modeler developer_guide/index developer_guide/overview developer_guide/api/index developer_guide/api/config developer_guide/api/model_conf_parser developer_guide/api/registries developer_guide/api/definition_parser developer_guide/api/model developer_guide/api/gene developer_guide/api/profile developer_guide/api/hit developer_guide/api/cluster developer_guide/api/system developer_guide/api/report developer_guide/api/search_genes developer_guide/api/solution developer_guide/api/serialization developer_guide/api/database developer_guide/api/error developer_guide/api/utils developer_guide/api/package developer_guide/api/scripts resolving references... /build/reproducible-path/macsyfinder-2.0/doc/source/user_guide/functioning.rst:109: WARNING: undefined label: 'rejected_candidates_file' done writing... done copying images... 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Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). make[2]: Entering directory '/build/reproducible-path/macsyfinder-2.0/doc/build/latex' latexmk -pdf -dvi- -ps- 'macsyfinder.tex' Rc files read: /etc/LatexMk latexmkrc Latexmk: This is Latexmk, John Collins, 7 Jan. 2023. Version 4.79. No existing .aux file, so I'll make a simple one, and require run of *latex. Latexmk: applying rule 'pdflatex'... 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[8] Underfull \hbox (badness 6412) in paragraph at lines 704--707 []\T1/qtm/m/n/10 On a ^^Pmetage-nomic^^Q (un-ordered) dataset for ex-am-ple: \T 1/txtt/m/n/10 macsyfinder [][]db[]type unordered Underfull \hbox (badness 10000) in paragraph at lines 715--717 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 727--729 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [9] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 5417) in paragraph at lines 1537--1539 []\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 [20] [21] Underfull \vbox (badness 10000) detected at line 1750 Underfull \vbox (badness 10000) detected at line 1750 [22] [23] [24] [25] [26] [27] Underfull \vbox (badness 10000) detected at line 2067 Underfull \vbox (badness 10000) detected at line 2067 [28] [29] [30] [31] Overfull \vbox (1.97241pt too high) detected at line 2252 [32] [33] Overfull \vbox (0.7195pt too high) detected at line 2422 [34] Underfull \vbox (badness 10000) detected at line 2422 Underfull \vbox (badness 10000) detected at line 2422 [35] [36] [37] [38] Overfull \vbox (1.97241pt too high) detected at line 2608 [39] [40] [41 <./graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.pdf>] [42] [43] [44] [45] [46] [47] [48] [49 <./msf_functionning_step1.pdf>] [50 <./m sf_functionning_step2.pdf>] [51] [52 <./msf_functionning_step3.pdf> <./msf_func tionning_step4.pdf pdfTeX warning: pdflatex (file ./msf_functionning_step4.pdf): PDF inclusion: mu ltiple pdfs with page group included in a single page >] [53 <./msf_functionning_step5.pdf>] [54] Underfull \hbox (badness 10000) in paragraph at lines 3619--3621 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3627--3629 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3635--3637 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3643--3645 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3654--3656 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir [55] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 3697. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 3742. [56] [57] [58] Chapter 2. [59 <./logo_macsymodels.png>] [60] [61] [62] [63] [64] [65 <./MSF_modelling.pdf >] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4344. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 43 58. Package wrapfig Warning: Collision between wrapping environments on input line 4364. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4364. Package wrapfig Warning: Collision between wrapping environments on input line 4386. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4386. [66 <./loner.pdf>] Package wrapfig Warning: Stationary wrapfigure forced to float on input line 44 00. 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[][]\T1/txtt/m/sl/10 macsypy.solution. [90] [91] [92] [93] Underfull \hbox (badness 6775) in paragraph at lines 6440--6442 \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 [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 6987--6990 []\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 [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 10090--10090 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10090--10090 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10090--10090 [][][]\T1/txtt/m/sl/10 macsypy.hit. 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[126] [127] [128] [129] [130] Underfull \hbox (badness 10000) in paragraph at lines 11578--11580 []\T1/qtm/m/n/10 true_loners: a dict { str func-tion: :class:macsypy.hit.Loner | [131] [132 <./inheritance-1f1a9535b4e521a58745655f7fde6169b803487d.pdf> <./inhe ritance-d38d58199ba0af98a545498012fba27f43247208.pdf pdfTeX warning: pdflatex (file ./inheritance-d38d58199ba0af98a545498012fba27f43 247208.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [133] [134] [135] [136] [137] [138] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 \T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (//< /usr/share/texmf/fonts/type1/public/tex-gyre/qtmr.pfb> Output written on macsyfinder.pdf (193 pages, 2536098 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' Latexmk: All targets () are up-to-date make[2]: Leaving directory '/build/reproducible-path/macsyfinder-2.0/doc/build/latex' make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.0/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-2.0' 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-2.0' 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_2.0-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../macsyfinder_2.0-2_i386.buildinfo dpkg-genchanges --build=binary -O../macsyfinder_2.0-2_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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/10842/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/10842/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/10842 and its subdirectories I: Current time: Sat Jan 13 00:59:01 +14 2024 I: pbuilder-time-stamp: 1705057141