I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 9 02:28:27 +14 2025 I: pbuilder-time-stamp: 1739017707 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [macsyfinder_2.0~rc1-3.dsc] I: copying [./macsyfinder_2.0~rc1.orig.tar.gz] I: copying [./macsyfinder_2.0~rc1-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.1ILtdJjK/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 11 11:17:20 2021 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./macsyfinder_2.0~rc1-3.dsc dpkg-source: info: extracting macsyfinder in macsyfinder-2.0~rc1 dpkg-source: info: unpacking macsyfinder_2.0~rc1.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.0~rc1-3.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 allow_setuptools dpkg-source: info: applying debian_path dpkg-source: info: applying privacy I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/865629/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. 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 Feb 8 12:28 /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/865629/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/865629/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=36245c2080434474b1c2c607b223f9d8 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=865629 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.JdHnQIzC/pbuilderrc_GHcS --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JdHnQIzC/b2 --logfile b2/build.log macsyfinder_2.0~rc1-3.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 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 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 9 Feb 8 12:28 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 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 5898 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 8049 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/865629/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-sphinx, python3-networkx, python3-yaml, python3-colorlog, python3-sphinx-rtd-theme, texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17743 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-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme 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. 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} libann0{a} libapache-pom-java{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libice6{a} libicu67{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libkpathsea6{a} liblab-gamut1{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{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} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsm6{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libyaml-0-2{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-colorlog{a} python3-decorator{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-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{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} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} t1utils{a} tex-common{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} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: atril curl dvisvgm evince fonts-liberation ghostscript gv javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgts-bin libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx mupdf okular python3-gdal python3-matplotlib python3-numpy python3-pil python3-pydot python3-pygraphviz python3-scipy qpdfview qpdfview-ps-plugin ruby shared-mime-info tex-gyre tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 172 newly installed, 0 to remove and 0 not upgraded. Need to get 166 MB of archives. After unpacking 558 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 tex-common all 6.16 [53.7 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 fonts-lmodern all 2.004.5-6.1 [4540 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libann0 amd64 1.1.2+doc-7 [25.3 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libcdt5 amd64 2.42.2-5 [62.2 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libcgraph6 amd64 2.42.2-5 [85.5 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u1 [772 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1.1~deb11u1 [49.6 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4+b1 [158 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libpathplan4 amd64 2.42.2-5 [64.3 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libgvc6 amd64 2.42.2-5 [695 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libgvpr2 amd64 2.42.2-5 [212 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 liblab-gamut1 amd64 2.42.2-5 [221 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libxaw7 amd64 2:1.0.13-1.1 [202 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 graphviz amd64 2.42.2-5 [632 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libkpathsea6 amd64 2020.20200327.54578-7+deb11u1 [172 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libptexenc1 amd64 2020.20200327.54578-7+deb11u1 [64.7 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libsynctex2 amd64 2020.20200327.54578-7+deb11u1 [83.4 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libtexlua53 amd64 2020.20200327.54578-7+deb11u1 [131 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libtexluajit2 amd64 2020.20200327.54578-7+deb11u1 [267 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libteckit0 amd64 2.5.10+ds1-3 [329 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libzzip-0-13 amd64 0.13.62-3.3+deb11u1 [55.9 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 texlive-binaries amd64 2020.20200327.54578-7+deb11u1 [10.1 MB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 texlive-base all 2020.20210202-3 [20.8 MB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-base all 2020.20210202-3 [1120 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 latexmk all 1:4.70b-0.2 [407 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 preview-latex-style all 12.2-1 [201 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 python3-certifi all 2020.6.20-1 [151 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 python3-colorlog all 4.7.2-1 [25.6 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 python3-roman all 2.0.0-5 [9064 B] Get: 149 http://deb.debian.org/debian bullseye/main amd64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 python3-idna all 2.10-1 [37.4 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get: 152 http://deb.debian.org/debian bullseye/main amd64 python3-markupsafe amd64 1.1.1-1+b3 [15.2 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 python3-packaging all 20.9-2 [33.5 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx all 3.4.3-2 [545 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 sphinx-rtd-theme-common all 0.5.1+dfsg-1 [995 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 python3-sphinx-rtd-theme all 0.5.1+dfsg-1 [20.9 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 texlive-fonts-recommended all 2020.20210202-3 [5002 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-recommended all 2020.20210202-3 [14.5 MB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 texlive-pictures all 2020.20210202-3 [6743 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-extra all 2020.20210202-3 [13.7 MB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 texlive-plain-generic all 2020.20210202-3 [27.0 MB] Fetched 166 MB in 2s (91.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Preparing to unpack .../8-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18636 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package tzdata. Preparing to unpack .../2-tzdata_2021a-1+deb11u10_all.deb ... Unpacking tzdata (2021a-1+deb11u10) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../3-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../6-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../7-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... 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Setting up media-types (4.0.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up fonts-lato (2.0-2.1) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libdatrie1:amd64 (0.2.13-1) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libtexlua53:amd64 (2020.20200327.54578-7+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libtexluajit2:amd64 (2020.20200327.54578-7+deb11u1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up liblab-gamut1:amd64 (2.42.2-5) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up libzzip-0-13:amd64 (0.13.62-3.3+deb11u1) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 8 12:29:05 UTC 2025. Universal Time is now: Sat Feb 8 12:29:05 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-4+b1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up libteckit0:amd64 (2.5.10+ds1-3) ... Setting up libpathplan4:amd64 (2.42.2-5) ... Setting up libapache-pom-java (18-1) ... Setting up libann0 (1.1.2+doc-7) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libfribidi0:amd64 (1.0.8-2+deb11u1) ... Setting up t1utils (1.41-4) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libltdl7:amd64 (2.4.6-15) ... Setting up libkpathsea6:amd64 (2020.20200327.54578-7+deb11u1) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up fonts-lmodern (2.004.5-6.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up sgml-base (1.30) ... Setting up libcdt5:amd64 (2.42.2-5) ... Setting up libcgraph6:amd64 (2.42.2-5) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (0.5.1+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:amd64 (2020.20200327.54578-7+deb11u1) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libptexenc1:amd64 (2020.20200327.54578-7+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libgvpr2:amd64 (2.42.2-5) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libxpm4:amd64 (1:3.5.12-1.1~deb11u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up tex-common (6.16) ... update-language: texlive-base not installed and configured, doing nothing! Setting up sphinx-common (3.4.3-2) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up preview-latex-style (12.2-1) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libxaw7:amd64 (2:1.0.13-1.1) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up python3-idna (2.10-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up texlive-binaries (2020.20200327.54578-7+deb11u1) ... 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 libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up texlive-base (2020.20210202-3) ... 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 libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorlog (4.7.2-1) ... Setting up python3-alabaster (0.7.8-1.1) ... Setting up texlive-plain-generic (2020.20210202-3) ... Setting up python3-yaml (5.3.1-5) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up texlive-latex-base (2020.20210202-3) ... Setting up texlive-latex-recommended (2020.20210202-3) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up libgvc6 (2.42.2-5) ... Setting up texlive-pictures (2020.20210202-3) ... Setting up texlive-fonts-recommended (2020.20210202-3) ... Setting up graphviz (2.42.2-5) ... Setting up latexmk (1:4.70b-0.2) ... Setting up texlive-latex-extra (2020.20210202-3) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.4.3-2) ... Setting up python3-sphinx-rtd-theme (0.5.1+dfsg-1) ... Processing triggers for ca-certificates (20210119) ... 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 (6.16) ... 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/865629/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/865629/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/macsyfinder-2.0~rc1/ && 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~rc1-3_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.0~rc1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' 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:232: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/utils.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/system.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/solution.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/serialization.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/search_genes.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/report.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/registries.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/profile.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/package.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/model.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/hit.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/gene.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/error.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/definition_parser.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/database.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/config.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/cluster.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/__init__.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy creating /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsydata.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/__init__.py -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts dh_auto_test -O--buildsystem=pybuild I: pybuild base:232: python3.9 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 previously-included files matching '*' found under directory 'tests/__pycache__' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' writing manifest file 'macsyfinder.egg-info/SOURCES.txt' running build_ext test_Config (test_Config.TestConfig) ... ok test_Config_args (test_Config.TestConfig) ... ok test_Config_default_conf_file (test_Config.TestConfig) ... ok test_Config_file (test_Config.TestConfig) ... ok test_Config_file_bad_values (test_Config.TestConfig) ... ok test_Config_file_n_args (test_Config.TestConfig) ... ok test_bad_db_type (test_Config.TestConfig) ... ok test_bad_models_dir (test_Config.TestConfig) ... ok test_bad_sequence_db (test_Config.TestConfig) ... ok test_bad_topology (test_Config.TestConfig) ... ok test_bad_topology_file (test_Config.TestConfig) ... ok test_bad_values (test_Config.TestConfig) ... ok test_config_file_2_dict (test_Config.TestConfig) ... ok test_e_value_search (test_Config.TestConfig) ... ok test_hit_weights (test_Config.TestConfig) ... ok test_no_cut_ga (test_Config.TestConfig) ... ok test_out_dir (test_Config.TestConfig) ... ok test_previous_n_sequence_db (test_Config.TestConfig) ... ok test_previous_wo_cfg (test_Config.TestConfig) ... ok test_save (test_Config.TestConfig) ... ok test_str_2_tuple (test_Config.TestConfig) ... ok test_working_dir (test_Config.TestConfig) ... ok test_bad_gene_inter_gene_max_space_2 (test_DefinitionParser.TestModelParser) ... ok test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... ok test_bad_max_nb_genes (test_DefinitionParser.TestModelParser) ... ok test_bad_min_genes_required (test_DefinitionParser.TestModelParser) ... ok test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser) ... ok test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser) ... ok test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser) ... ok test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser) ... ok test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... ok test_gene_no_name (test_DefinitionParser.TestModelParser) ... ok test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser) ... ok test_invalid_homolog (test_DefinitionParser.TestModelParser) ... ok test_invalid_homolog_2 (test_DefinitionParser.TestModelParser) ... ok test_invalid_presence (test_DefinitionParser.TestModelParser) ... ok test_loner (test_DefinitionParser.TestModelParser) ... ok test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser) ... ok test_min_genes_required_cfg (test_DefinitionParser.TestModelParser) ... ok test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser) ... ok test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser) ... ok test_multi_loci_cfg (test_DefinitionParser.TestModelParser) ... ok test_multi_system (test_DefinitionParser.TestModelParser) ... ok test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... ok test_parse_model_old_syntax (test_DefinitionParser.TestModelParser) ... ok test_parse_with_exchangeable (test_DefinitionParser.TestModelParser) ... ok test_wo_presence (test_DefinitionParser.TestModelParser) ... ok test_add_exchangeable (test_Exchangeable.TestExchangeable) ... ok test_alternate_of (test_Exchangeable.TestExchangeable) ... ok test_is_exchangeable (test_Exchangeable.TestExchangeable) ... ok test_loner (test_Exchangeable.TestExchangeable) ... ok test_model (test_Exchangeable.TestExchangeable) ... ok test_multi_system (test_Exchangeable.TestExchangeable) ... ok test_core_gene (test_Gene.TestCoreGene) ... ok test_str (test_Gene.TestGeneStatus) ... ok test_add_exchangeable (test_Gene.TestModelGene) ... ok test_alternate_of (test_Gene.TestModelGene) ... ok test_exhangeables (test_Gene.TestModelGene) ... ok test_hash (test_Gene.TestModelGene) ... ok test_init (test_Gene.TestModelGene) ... ok test_inter_gene_max_space (test_Gene.TestModelGene) test getter for inter_gene_max_space property ... ok test_is_Forbidden (test_Gene.TestModelGene) test if gene belong to model mandatory genes ... ok test_is_accessory (test_Gene.TestModelGene) test if gene belong to model mandatory genes ... ok test_is_exchangeable (test_Gene.TestModelGene) ... ok test_is_mandatory (test_Gene.TestModelGene) test if gene belong to model mandatory genes ... ok test_loner (test_Gene.TestModelGene) test getter for loner property ... ok test_model (test_Gene.TestModelGene) test getter/setter for model property ... ok test_multi_system (test_Gene.TestModelGene) test getter for multi_system property ... ok test_str (test_Gene.TestModelGene) ... ok test_unknown_attribute (test_Gene.TestModelGene) ... ok test_add_get_gene (test_GeneBank.Test) ... ok test_contains (test_GeneBank.Test) ... ok test_get_uniq_object (test_GeneBank.Test) ... ok test_iter (test_GeneBank.Test) ... ok test_build_force (test_Indexes.Test) ... ok test_build_my_indexes (test_Indexes.Test) ... ok test_build_no_idx (test_Indexes.Test) ... ok test_build_not_writable (test_Indexes.Test) ... ok test_build_with_idx (test_Indexes.Test) ... ok test_find_my_indexes (test_Indexes.Test) ... ok test_allowed_hits (test_LikelySystem.LikelySystemTest) ... ok test_forbidden_hits (test_LikelySystem.LikelySystemTest) ... ok test_hits (test_LikelySystem.LikelySystemTest) ... ok test_init (test_LikelySystem.LikelySystemTest) ... ok test_str (test_LikelySystem.LikelySystemTest) ... ok test_hits (test_LikelySystem.UnlikelySystemTest) ... ok test_init (test_LikelySystem.UnlikelySystemTest) ... ok test_reason (test_LikelySystem.UnlikelySystemTest) ... ok test_str (test_LikelySystem.UnlikelySystemTest) ... ok test_MacsyDefaults (test_MacsyDefaults.TestMacsyDefaults) ... ok test_MacsyDefaults_with_MACSY_DATA (test_MacsyDefaults.TestMacsyDefaults) ... ok test_ordered_match (test_MatchMaker.MatchMakerTest) ... ok test_sort_hits_by_status (test_MatchMaker.MatchMakerTest) ... ok test_unordered_match (test_MatchMaker.MatchMakerTest) ... ok test_accessor_mutator (test_Model.TestModel) ... ok test_eq (test_Model.TestModel) ... ok test_filter (test_Model.TestModel) ... ok test_fqn (test_Model.TestModel) ... ok test_get_gene (test_Model.TestModel) ... ok test_gt (test_Model.TestModel) ... ok test_hash (test_Model.TestModel) ... ok test_inter_gene_max_space (test_Model.TestModel) ... ok test_lt (test_Model.TestModel) ... ok test_max_nb_genes (test_Model.TestModel) ... ok test_min_genes_required (test_Model.TestModel) ... ok test_min_mandatory_genes_required (test_Model.TestModel) ... ok test_multi_loci (test_Model.TestModel) ... ok test_str (test_Model.TestModel) ... ok test_add_get_model (test_ModelBank.Test) ... ok test_contains (test_ModelBank.Test) ... ok test_get_uniq_object (test_ModelBank.Test) ... ok test_iter (test_ModelBank.Test) ... ok test_execute (test_Profile.TestProfile) ... skipped 'For some reason this fails to find hmmer_results - skipping' test_execute_hmmer_failed (test_Profile.TestProfile) ... ok test_execute_unknown_binary (test_Profile.TestProfile) ... ok test_ga_threshold (test_Profile.TestProfile) ... ok test_len (test_Profile.TestProfile) ... ok test_str (test_Profile.TestProfile) ... ok test_get_profile (test_ProfileFactory.TestProfileFactory) ... ok test_get_uniq_object (test_ProfileFactory.TestProfileFactory) ... ok test_unknow_profile (test_ProfileFactory.TestProfileFactory) ... ok test_hits (test_RejectedClusters.TestRejectedCluster) ... ok test_init (test_RejectedClusters.TestRejectedCluster) ... ok test_str (test_RejectedClusters.TestRejectedCluster) ... ok test_fill_gembase_min_max_default_topology (test_RepliconDB.Test) ... ok test_fill_gembase_min_max_with_topology (test_RepliconDB.Test) ... ok test_fill_ordered_replicon_min_max (test_RepliconDB.Test) ... ok test_fill_topology (test_RepliconDB.Test) ... ok test_get (test_RepliconDB.Test) ... ok test_getitem (test_RepliconDB.Test) ... ok test_in (test_RepliconDB.Test) ... ok test_items (test_RepliconDB.Test) ... ok test_iteritems (test_RepliconDB.Test) ... ok test_replicon_infos (test_RepliconDB.Test) ... ok test_extract (test_Report.TestGembaseHMMReport) ... ok test_extract_concurent (test_Report.TestGembaseHMMReport) ... ok test_extract (test_Report.TestGeneralHMMReport) ... ok test_extract_concurent (test_Report.TestGeneralHMMReport) ... ok test_HMMReport (test_Report.TestHMMReport) ... ok test_best_hit (test_Report.TestHMMReport) ... ok test_build_my_db (test_Report.TestHMMReport) ... ok test_fill_my_db (test_Report.TestHMMReport) ... ok test_hit_start (test_Report.TestHMMReport) ... ok test_parse_hmm_body (test_Report.TestHMMReport) ... ok test_parse_hmm_header (test_Report.TestHMMReport) ... ok test_save_extract (test_Report.TestHMMReport) ... ok test_str (test_Report.TestHMMReport) ... ok test_extract (test_Report.TestOrderedHMMReport) ... ok test_extract_concurent (test_Report.TestOrderedHMMReport) ... ok test_ClusteSystemTracker (test_System.SystemTest) ... ok test_HitSystemTracker (test_System.SystemTest) ... ok test_count (test_System.SystemTest) ... ok test_hits (test_System.SystemTest) ... ok test_init (test_System.SystemTest) ... ok test_is_compatible (test_System.SystemTest) ... ok test_loci (test_System.SystemTest) ... ok test_multi_loci (test_System.SystemTest) ... ok test_occurrence (test_System.SystemTest) ... ok test_position (test_System.SystemTest) ... ok test_score (test_System.SystemTest) ... ok test_wholeness (test_System.SystemTest) ... ok test_build_clusters (test_cluster.TestBuildCluster) ... ok test_contains (test_cluster.TestCluster) ... ok test_fulfilled_function (test_cluster.TestCluster) ... ok test_init (test_cluster.TestCluster) ... ok test_len (test_cluster.TestCluster) ... ok test_loner (test_cluster.TestCluster) ... ok test_merge (test_cluster.TestCluster) ... ok test_replicon_name (test_cluster.TestCluster) ... ok test_score (test_cluster.TestCluster) ... ok test_str (test_cluster.TestCluster) ... ok test_filter_loners (test_cluster.TestHitFunc) ... ok test_get_loners (test_cluster.TestHitFunc) ... ok test_gembase (test_functional_test.Test) ... ok test_model_unknown (test_functional_test.Test) ... ok test_no_db_type (test_functional_test.Test) ... ok test_no_models (test_functional_test.Test) ... ok test_no_seq_db (test_functional_test.Test) ... ok test_only_loners (test_functional_test.Test) ... ok test_ordered_circular (test_functional_test.Test) ... ok test_ordered_linear (test_functional_test.Test) ... ok test_ordered_multi_loci (test_functional_test.Test) ... ok test_ordered_multi_system (test_functional_test.Test) ... ok test_ordered_multi_system_loner_in_clust (test_functional_test.Test) ... ok test_ordered_single_loci (test_functional_test.Test) ... ok test_unordered (test_functional_test.Test) ... ok test_working_dir_exists (test_functional_test.Test) ... ok test_working_dir_exists_and_not_dir (test_functional_test.Test) ... ok test_get_best_hits (test_hit.GetBestHitTest) ... ok test_cmp (test_hit.HitTest) ... ok test_eq (test_hit.HitTest) ... ok test_get_position (test_hit.HitTest) ... ok test_hash (test_hit.HitTest) ... ok test_str (test_hit.HitTest) ... ok test_hit_weight_default (test_hit.HitWeightTest) ... ok test_hit_weight_not_default (test_hit.HitWeightTest) ... ok test_delegation (test_hit.ValidHitTest) ... ok test_eq (test_hit.ValidHitTest) ... ok test_hash (test_hit.ValidHitTest) ... ok test_init (test_hit.ValidHitTest) ... ok test_available (test_macsydata.TestMacsydata) ... ok test_build_argparser (test_macsydata.TestMacsydata) ... ok test_check (test_macsydata.TestMacsydata) ... ok test_check_with_errors (test_macsydata.TestMacsydata) ... ok test_check_with_warnings (test_macsydata.TestMacsydata) ... ok test_cite (test_macsydata.TestMacsydata) ... ok test_cmd_name (test_macsydata.TestMacsydata) ... ok test_download (test_macsydata.TestMacsydata) ... ok test_freeze (test_macsydata.TestMacsydata) ... ok test_info (test_macsydata.TestMacsydata) ... ok test_install_installed_package_corrupted (test_macsydata.TestMacsydata) ... ok test_install_local (test_macsydata.TestMacsydata) ... ok test_install_local_already_installed (test_macsydata.TestMacsydata) ... ok test_install_local_already_installed_force (test_macsydata.TestMacsydata) ... ok test_install_remote (test_macsydata.TestMacsydata) ... ok test_install_remote_already_in_local (test_macsydata.TestMacsydata) ... ok test_install_remote_already_in_local_force (test_macsydata.TestMacsydata) ... ok test_install_remote_lower_in_local (test_macsydata.TestMacsydata) ... ok test_install_remote_permision_error (test_macsydata.TestMacsydata) ... ok test_install_remote_spec_not_found (test_macsydata.TestMacsydata) ... ok test_install_remote_upper_in_local (test_macsydata.TestMacsydata) ... ok test_list (test_macsydata.TestMacsydata) ... ok test_list_outdated (test_macsydata.TestMacsydata) ... ok test_list_uptodate (test_macsydata.TestMacsydata) ... ok test_list_verbose (test_macsydata.TestMacsydata) ... ok test_search_in_pack_desc (test_macsydata.TestMacsydata) ... ok test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata) ... ok test_search_in_pack_name (test_macsydata.TestMacsydata) ... ok test_search_in_pack_name_match_case (test_macsydata.TestMacsydata) ... ok test_search_reach_limit (test_macsydata.TestMacsydata) ... ok test_uninstall (test_macsydata.TestMacsydata) ... ok test_verbosity_to_log_level (test_macsydata.TestMacsydata) ... ok test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_list_models (test_macsyfinder.TestMacsyfinder) ... ok test_parse_args (test_macsyfinder.TestMacsyfinder) ... ok test_rejected_clst_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_search_systems (test_macsyfinder.TestMacsyfinder) ... ok test_search_systems_model_unknown (test_macsyfinder.TestMacsyfinder) ... ok test_search_systems_unordered (test_macsyfinder.TestMacsyfinder) ... ok test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok test_systems_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok test_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_init (test_package.TestLocalModelIndex) ... ok test_init (test_package.TestModelIndex) ... ok test_check (test_package.TestPackage) ... ok test_check_metadata (test_package.TestPackage) ... ok test_check_no_readme_n_no_license (test_package.TestPackage) ... ok test_check_structure (test_package.TestPackage) ... ok test_check_structure_bad_path (test_package.TestPackage) ... ok test_check_structure_no_def (test_package.TestPackage) ... ok test_check_structure_no_license (test_package.TestPackage) ... ok test_check_structure_no_metadata (test_package.TestPackage) ... ok test_check_structure_no_profiles (test_package.TestPackage) ... ok test_check_structure_no_readme (test_package.TestPackage) ... ok test_find_readme (test_package.TestPackage) ... ok test_help (test_package.TestPackage) ... ok test_info (test_package.TestPackage) ... ok test_init (test_package.TestPackage) ... ok test_metadata (test_package.TestPackage) ... ok test_parse_arch_path (test_package.TestPackageFunc) ... ok test_download (test_package.TestRemoteModelIndex) ... ok test_get_metadata (test_package.TestRemoteModelIndex) ... ok test_init (test_package.TestRemoteModelIndex) ... ok test_list_package_vers (test_package.TestRemoteModelIndex) ... ok test_list_packages (test_package.TestRemoteModelIndex) ... ok test_remote_exists (test_package.TestRemoteModelIndex) ... ok test_unarchive (test_package.TestRemoteModelIndex) ... ok test_url_json (test_package.TestRemoteModelIndex) ... ok test_url_json_reach_limit (test_package.TestRemoteModelIndex) ... ok test_DefinitionLocationn (test_registries.DefinitionLocationTest) ... ok test_add_submodel (test_registries.DefinitionLocationTest) ... ok test_all (test_registries.DefinitionLocationTest) ... ok test_eq (test_registries.DefinitionLocationTest) ... ok test_family_name (test_registries.DefinitionLocationTest) ... ok test_greater (test_registries.DefinitionLocationTest) ... ok test_hash (test_registries.DefinitionLocationTest) ... ok test_lesser (test_registries.DefinitionLocationTest) ... ok test_root_name (test_registries.DefinitionLocationTest) ... ok test_separator (test_registries.DefinitionLocationTest) ... ok test_split_fqn (test_registries.DefinitionLocationTest) ... ok test_str (test_registries.DefinitionLocationTest) ... ok test_ModelLocation (test_registries.ModelLocationTest) ... ok test_get_all_definitions (test_registries.ModelLocationTest) ... ok test_get_definition (test_registries.ModelLocationTest) ... ok test_get_definitions (test_registries.ModelLocationTest) ... ok test_get_profile (test_registries.ModelLocationTest) ... ok test_str (test_registries.ModelLocationTest) ... ok test_add_get (test_registries.ModelRegistryTest) ... ok test_models (test_registries.ModelRegistryTest) ... ok test_scan_models_dir (test_registries.ModelRegistryTest) ... ok test_str (test_registries.ModelRegistryTest) ... ok test_join_def_path (test_registries.RegitriesUtilsTest) ... ok test_split_def_name (test_registries.RegitriesUtilsTest) ... ok test_search (test_search_genes.TestSearchGenes) ... ok test_search_recover (test_search_genes.TestSearchGenes) ... ok test_LikelySystemSerializer_txt (test_serialization.SerializationTest) ... ok test_SolutionSerializer_tsv (test_serialization.SerializationTest) ... ok test_SystemSerializer_str (test_serialization.SerializationTest) ... ok test_SystemSerializer_tsv (test_serialization.SerializationTest) ... ok test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest) ... ok test_find_best_solution (test_solution.SolutionExplorerTest) ... ok test_get_def_to_detect (test_utils.TestUtils) ... ok ---------------------------------------------------------------------- Ran 304 tests in 14.588s OK (skipped=1) create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root '/build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder' running install running build running build_py running install_lib moving /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/__init__.py.tmp -> /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/__init__.py creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9 creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/__init__.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts/__init__.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts/macsydata.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/scripts/macsyfinder.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/cluster.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/config.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/database.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/definition_parser.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/error.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/gene.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/hit.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/model.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/package.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/profile.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/registries.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/report.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/search_genes.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/serialization.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/solution.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/system.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/reproducible-path/macsyfinder-2.0~rc1/.pybuild/cpython3_3.9/build/macsypy/utils.py -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsydata.py to macsydata.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsyfinder.py to macsyfinder.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/cluster.py to cluster.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/config.py to config.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/database.py to database.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/definition_parser.py to definition_parser.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/error.py to error.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/gene.py to gene.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/hit.py to hit.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/model.py to model.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/package.py to package.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/profile.py to profile.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/registries.py to registries.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/report.py to report.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/search_genes.py to search_genes.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/serialization.py to serialization.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/solution.py to solution.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/system.py to system.cpython-39.pyc byte-compiling /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/utils.py to utils.cpython-39.pyc running install_data creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/results.macsyfinder.json -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/datatest_gembase.topology -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/datatest_gembase.fasta -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/models copying data/models/readme -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/models creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/psae.001.c01.13.prt -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/prru_psae.001.c01.fasta -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/prru.001.c01.11.prt -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/esco.030.p01.12.prt -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/data_replicons_topology_Prokaryotes_0213.dat -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/share/macsyfinder/data/base creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/etc creating /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/etc/macsyfinder copying etc/macsyfinder.conf -> /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/etc/macsyfinder 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 previously-included files matching '*' found under directory 'tests/__pycache__' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' writing manifest file 'macsyfinder.egg-info/SOURCES.txt' Copying macsyfinder.egg-info to /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsyfinder-2.0rc1.egg-info Skipping SOURCES.txt running install_scripts Installing macsydata script to /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/bin Installing macsyfinder script to /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/bin I: pybuild pybuild:310: mv /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/usr/etc /build/reproducible-path/macsyfinder-2.0~rc1/debian/macsyfinder/etc && cd /build/reproducible-path/macsyfinder-2.0~rc1/doc && make html latexpdf make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.0~rc1/doc' Running Sphinx v3.4.3 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 30 source files that are out of date updating environment: [new config] 30 added, 0 changed, 0 removed reading sources... [ 3%] developer_guide/api/cluster reading sources... [ 6%] developer_guide/api/config reading sources... [ 10%] developer_guide/api/database reading sources... [ 13%] developer_guide/api/definition_parser reading sources... [ 16%] developer_guide/api/error reading sources... [ 20%] developer_guide/api/gene reading sources... [ 23%] developer_guide/api/hit reading sources... [ 26%] developer_guide/api/index reading sources... [ 30%] developer_guide/api/model reading sources... [ 33%] developer_guide/api/package reading sources... [ 36%] developer_guide/api/profile reading sources... [ 40%] developer_guide/api/registries reading sources... [ 43%] developer_guide/api/report reading sources... [ 46%] developer_guide/api/search_genes reading sources... [ 50%] developer_guide/api/serialization reading sources... [ 53%] developer_guide/api/solution reading sources... [ 56%] developer_guide/api/system reading sources... [ 60%] developer_guide/api/utils reading sources... [ 63%] developer_guide/index reading sources... [ 66%] developer_guide/overview reading sources... [ 70%] index reading sources... [ 73%] user_guide/functioning reading sources... [ 76%] user_guide/gembase_convention reading sources... [ 80%] user_guide/index reading sources... [ 83%] user_guide/input reading sources... [ 86%] user_guide/installation reading sources... [ 90%] user_guide/model_definition reading sources... [ 93%] user_guide/new_v2 reading sources... [ 96%] user_guide/outputs reading sources... [100%] user_guide/quickstart /build/reproducible-path/macsyfinder-2.0~rc1/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 3%] developer_guide/api/cluster writing output... [ 6%] developer_guide/api/config writing output... [ 10%] developer_guide/api/database writing output... [ 13%] developer_guide/api/definition_parser writing output... [ 16%] developer_guide/api/error writing output... [ 20%] developer_guide/api/gene writing output... [ 23%] developer_guide/api/hit writing output... [ 26%] developer_guide/api/index writing output... [ 30%] developer_guide/api/model writing output... [ 33%] developer_guide/api/package writing output... [ 36%] developer_guide/api/profile writing output... [ 40%] developer_guide/api/registries writing output... [ 43%] developer_guide/api/report writing output... [ 46%] developer_guide/api/search_genes writing output... [ 50%] developer_guide/api/serialization writing output... [ 53%] developer_guide/api/solution writing output... [ 56%] developer_guide/api/system writing output... [ 60%] developer_guide/api/utils writing output... [ 63%] developer_guide/index writing output... [ 66%] developer_guide/overview writing output... [ 70%] index writing output... [ 73%] user_guide/functioning writing output... [ 76%] user_guide/gembase_convention writing output... [ 80%] user_guide/index writing output... [ 83%] user_guide/input writing output... [ 86%] user_guide/installation writing output... [ 90%] user_guide/model_definition writing output... [ 93%] user_guide/new_v2 writing output... [ 96%] user_guide/outputs writing output... [100%] user_guide/quickstart generating indices... genindex py-modindex done highlighting module code... [ 5%] collections highlighting module code... [ 10%] macsypy.cluster highlighting module code... [ 15%] macsypy.config highlighting module code... [ 21%] macsypy.database highlighting module code... [ 26%] macsypy.definition_parser highlighting module code... [ 31%] macsypy.error highlighting module code... [ 36%] macsypy.gene highlighting module code... [ 42%] macsypy.hit highlighting module code... [ 47%] macsypy.model highlighting module code... [ 52%] macsypy.package highlighting module code... [ 57%] macsypy.profile highlighting module code... [ 63%] macsypy.registries highlighting module code... [ 68%] macsypy.report highlighting module code... [ 73%] macsypy.search_genes highlighting module code... [ 78%] macsypy.serialization highlighting module code... [ 84%] macsypy.solution highlighting module code... [ 89%] macsypy.system highlighting module code... [ 94%] macsypy.utils highlighting module code... [100%] namedtuple_RepliconInfo writing additional pages... search done copying images... [ 10%] _static/gene_obj_interaction.svg copying images... [ 20%] _static/macsyfinder_classes.svg copying images... [ 30%] _static/figure_main-2.svg copying images... [ 40%] _static/msf_functionning_step1.svg copying images... [ 50%] _static/msf_functionning_step2.svg copying images... [ 60%] _static/msf_functionning_step3.svg copying images... [ 70%] _static/msf_functionning_step4.svg copying images... [ 80%] _static/msf_functionning_step5.svg copying images... [ 90%] _static/MSF_modelling.svg copying images... [100%] user_guide/../_static/under_construction.gif copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in build/html. Running Sphinx v3.4.3 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/model_definition user_guide/functioning developer_guide/index developer_guide/overview developer_guide/api/index developer_guide/api/config 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 resolving references... done writing... done copying images... [ 10%] _static/figure_main-2.png copying images... [ 20%] user_guide/../_static/under_construction.jpeg copying images... [ 30%] _static/MSF_modelling.pdf copying images... [ 40%] _static/msf_functionning_step1.pdf copying images... [ 50%] _static/msf_functionning_step2.pdf copying images... [ 60%] _static/msf_functionning_step3.pdf copying images... [ 70%] _static/msf_functionning_step4.pdf copying images... [ 80%] _static/msf_functionning_step5.pdf copying images... [ 90%] _static/macsyfinder_classes.pdf copying images... [100%] _static/gene_obj_interaction.pdf copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in build/latex. 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~rc1/doc/build/latex' latexmk -pdf -dvi- -ps- 'macsyfinder.tex' Rc files read: /etc/LatexMk ./latexmkrc Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b. Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-01-09> xparse <2020-03-03> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2020/04/10 v1.4m Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.7182818 (TeX Live 2020/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. 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Output written on tctt0900.600gf (128 characters, 17564 bytes). Transcript written on tctt0900.log. mktexpk: /build/reproducible-path/macsyfinder-2.0~rc1/debian/.debhelper/generated/_source/home/.texlive2020/texmf-var/fonts/pk/ljfour/jknappen/ec/tctt0900.600pk: successfully generated. Output written on macsyfinder.pdf (97 pages, 1311831 bytes). Transcript written on macsyfinder.log. Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Missing input file: 'macsyfinder.ind' from line 'No file macsyfinder.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'macsyfinder.pdf' Latexmk: List of undefined refs and citations: Reference `developer_guide/api/cluster:module-macsypy.cluster' on page 93 undefined on input line 7876 Reference `developer_guide/api/config:module-macsypy.config' on page 93 undefined on input line 7877 Reference `developer_guide/api/database:module-macsypy.database' on page 93 undefined on input line 7878 Reference `developer_guide/api/definition_parser:module-macsypy.definition_parser' on page 93 undefined on input line 7879 Reference `developer_guide/api/error:module-macsypy.error' on page 93 undefined on input line 7880 Reference `developer_guide/api/hit:module-macsypy.hit' on page 93 undefined on input line 7881 Reference `developer_guide/api/package:module-macsypy.package' on page 93 undefined on input line 7882 Reference `developer_guide/api/registries:module-macsypy.registries' on page 93 undefined on input line 7883 Reference `developer_guide/api/search_genes:module-macsypy.search_genes' on page 93 undefined on input line 7884 Reference `developer_guide/api/serialization:module-macsypy.serialization' on page 93 undefined on input line 7885 Reference `developer_guide/api/solution:module-macsypy.solution' on page 93 undefined on input line 7886 Reference `developer_guide/api/system:module-macsypy.system' on page 93 undefined on input line 7887 Reference `developer_guide/api/utils:module-macsypy.utils' on page 93 undefined on input line 7888 Rule 'makeindex macsyfinder.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'macsyfinder.idx' ------------ Run number 1 of rule 'makeindex macsyfinder.idx' ------------ ------------ Running 'makeindex -s python.ist -o "macsyfinder.ind" "macsyfinder.idx"' ------------ Latexmk: Examining 'macsyfinder.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex macsyfinder.idx'... 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[3] [4] [5] [6] [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 667--669 \T1/pcr/m/n/10 --sequence-db metagenome.fasta --models-dir my-models --models Underfull \hbox (badness 10000) in paragraph at lines 675--676 []\T1/pcr/m/n/10 macsyfinder --db-type ordered-replicon --sequence-db mygenome. fasta [11 <./under_construction.jpeg>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \vbox (badness 1874) detected at line 815 [13] Overfull \vbox (13.68166pt too high) detected at line 861 [14] Overfull \vbox (13.68166pt too high) detected at line 913 [15] [16] [17] Overfull \vbox (0.97772pt too high) detected at line 1222 [18] [19] [20] [21] Underfull \vbox (badness 10000) detected at line 1485 Overfull \vbox (16.52583pt too high) detected at line 1485 [22] [23] [24] [25] Underfull \vbox (badness 2351) detected at line 1758 Overfull \vbox (20.53116pt too high) detected at line 1758 [26] Overfull \vbox (13.98015pt too high) detected at line 1800 [27] [28] [29] [30] [31] [32 <./MSF_modelling.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 2066--2067 []\T1/ptm/b/n/10 inter_gene_max_space\T1/ptm/m/n/10 : an \T1/ptm/m/it/10 in-te- ger \T1/ptm/m/n/10 that de-fines gene-wise value of sys-tem's ^^Pin- Overfull \vbox (1.72583pt too high) detected at line 2111 [33] [34] [35] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. 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[76] [77] [78] [79] [80] [81] [82] Overfull \hbox (27.20956pt too wide) in paragraph at lines 6995--6998 []\T1/ptm/m/n/10 replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_l oci\tsys_wholeness\tsys_score Overfull \hbox (44.58925pt too wide) in paragraph at lines 6995--6998 \T1/ptm/m/n/10 \tsys_occ\thit_gene_ref.alternate_of\thit_status\thit_seq_len\th it_i_eval\thit_score\thit_profile_cov [83] Underfull \hbox (badness 10000) in paragraph at lines 7214--7215 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by the con- Underfull \hbox (badness 10000) in paragraph at lines 7228--7230 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by con- [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 []\T1/pcr/b/n/10 models \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 list of tuple with the following structure: Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 \T1/pcr/m/sl/10 [(\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 model_1\TS1/pcr/m/sl/10 '\T 1/pcr/m/sl/10 , (\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 def1, def2, ..)), (\TS1/pcr/ m/sl/10 '\T1/pcr/m/sl/10 model_2\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , (\TS1/pcr/m /sl/10 '\T1/pcr/m/sl/10 def1\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , ..)), [86] [87] [88] [89] [90] Chapter 3. [91] [92] [93] (./macsyfinder.ind [94] Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.databa se.RepliconDB Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.model. ModelBank Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 __eq__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries.D efinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 __getitem__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.databas e.RepliconDB Underfull \hbox (badness 10000) in paragraph at lines 21--22 []\T1/pcr/m/n/10 __getitem__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.model.M odelBank Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 __getitem__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registr ies.ModelRegistry Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 __gt__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries.D efinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/pcr/m/n/10 __hash__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .DefinitionLocation Overfull \hbox (8.23074pt too wide) in paragraph at lines 43--45 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.definition _parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 53--55 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Ab stractModelIndex Underfull \hbox (badness 10000) in paragraph at lines 55--56 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Lo calModelIndex Underfull \hbox (badness 10000) in paragraph at lines 57--58 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Re moteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 60--62 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .DefinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 62--63 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .ModelLocation Underfull \hbox (badness 10000) in paragraph at lines 63--64 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .ModelRegistry Overfull \hbox (10.36pt too wide) in paragraph at lines 65--67 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.serializat ion.TsvSolutionSerializer Underfull \hbox (badness 10000) in paragraph at lines 67--68 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Abs tractSetOfHits Underfull \hbox (badness 10000) in paragraph at lines 68--69 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Abs tractUnordered Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Clu sterSystemTracker Underfull \hbox (badness 10000) in paragraph at lines 71--72 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Hit SystemTracker [95] Underfull \hbox (badness 10000) in paragraph at lines 73--74 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Ord eredMatchMaker Underfull \hbox (badness 10000) in paragraph at lines 74--75 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Rej ectedClusters Underfull \hbox (badness 10000) in paragraph at lines 84--86 []\T1/pcr/m/n/10 __lt__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries.D efinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 87--89 []\T1/pcr/m/n/10 __new__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database.Re pliconInfo static Underfull \hbox (badness 10000) in paragraph at lines 89--91 []\T1/pcr/m/n/10 __new__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Abs tractModelIndex Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/pcr/m/n/10 __str__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries. 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HMMReport Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/pcr/m/n/10 _fill_ordered_min_max() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 _find_readme() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.packag e.Package Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 _get_model_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 170--172 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 173--174 []\T1/pcr/m/n/10 _load_metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.pack age.Package Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 _make() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database.Repl iconInfo class Underfull \hbox (badness 10000) in paragraph at lines 175--177 []\T1/pcr/m/n/10 _parse_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 175--177 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 177--179 []\T1/pcr/m/n/10 _parse_genes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 177--179 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 179--180 []\T1/pcr/m/n/10 _parse_hmm_body() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.rep ort.HMMReport Underfull \hbox (badness 10000) in paragraph at lines 180--181 []\T1/pcr/m/n/10 _parse_hmm_header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 181--182 []\T1/pcr/m/n/10 _profile_features() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.p rofile.Profile Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\T1/pcr/m/n/10 _scan_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 185--187 []\T1/pcr/m/n/10 _scan_profiles() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 188--190 []\T1/pcr/m/n/10 _set_inter_gene_max_space() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 ma c- Underfull \hbox (badness 10000) in paragraph at lines 190--191 []\T1/pcr/m/n/10 _set_max_nb_genes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.c onfig.Config Underfull \hbox (badness 10000) in paragraph at lines 191--193 []\T1/pcr/m/n/10 _set_min_genes_required() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 193--195 []\T1/pcr/m/n/10 _set_min_mandatory_genes_required() Underfull \hbox (badness 10000) in paragraph at lines 196--197 []\T1/pcr/m/n/10 _set_models_dir() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.con fig.Config Underfull \hbox (badness 10000) in paragraph at lines 197--198 []\T1/pcr/m/n/10 _set_multi_loci() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.con fig.Config Underfull \hbox (badness 10000) in paragraph at lines 198--200 []\T1/pcr/m/n/10 _set_replicon_topology() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 200--201 []\T1/pcr/m/n/10 _set_sequence_db() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.co nfig.Config Underfull \hbox (badness 10000) in paragraph at lines 201--202 []\T1/pcr/m/n/10 _set_topology_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. config.Config Underfull \hbox (badness 10000) in paragraph at lines 203--204 []\T1/pcr/m/n/10 _url_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.R emoteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 210--212 []\T1/pcr/m/n/10 accessory_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 210--212 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 214--215 []\T1/pcr/m/n/10 add_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.ge ne.ModelGene Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 add_subdefinition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 217--219 \T1/ptm/m/it/10 sypy.registries.DefinitionLocation method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 allowed_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 219--221 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 221--222 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.E xchangeable Underfull \hbox (badness 10000) in paragraph at lines 222--223 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/pcr/m/n/10 check_consistency() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 233--235 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser [97] Underfull \hbox (badness 10000) in paragraph at lines 250--251 []\T1/pcr/m/n/10 DefinitionParser \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in mac- Underfull \hbox (badness 10000) in paragraph at lines 252--253 []\T1/pcr/m/n/10 download() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Re moteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 260--261 []\T1/pcr/m/n/10 extract() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.report.Gemb aseHMMReport Underfull \hbox (badness 10000) in paragraph at lines 261--262 []\T1/pcr/m/n/10 extract() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.report.Gene ralHMMReport Underfull \hbox (badness 10000) in paragraph at lines 263--264 []\T1/pcr/m/n/10 extract() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.report.Orde redHMMReport Underfull \hbox (badness 10000) in paragraph at lines 271--272 []\T1/pcr/m/n/10 find_best_solutions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le mac- Underfull \hbox (badness 10000) in paragraph at lines 272--273 []\T1/pcr/m/n/10 find_my_indexes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.dat abase.Indexes Underfull \hbox (badness 10000) in paragraph at lines 273--275 []\T1/pcr/m/n/10 forbidden_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 273--275 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 275--276 []\T1/pcr/m/n/10 fulfilled_function() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. cluster.Cluster Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 get_all_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/pcr/m/n/10 get_definition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 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[3] [4] [5] [6] [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 667--669 \T1/pcr/m/n/10 --sequence-db metagenome.fasta --models-dir my-models --models Underfull \hbox (badness 10000) in paragraph at lines 675--676 []\T1/pcr/m/n/10 macsyfinder --db-type ordered-replicon --sequence-db mygenome. fasta [11 <./under_construction.jpeg>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \vbox (badness 1874) detected at line 815 [13] Overfull \vbox (13.68166pt too high) detected at line 861 [14] Overfull \vbox (13.68166pt too high) detected at line 913 [15] [16] [17] Overfull \vbox (0.97772pt too high) detected at line 1222 [18] [19] [20] [21] Underfull \vbox (badness 10000) detected at line 1485 Overfull \vbox (16.52583pt too high) detected at line 1485 [22] [23] [24] [25] Underfull \vbox (badness 2351) detected at line 1758 Overfull \vbox (20.53116pt too high) detected at line 1758 [26] Overfull \vbox (13.98015pt too high) detected at line 1800 [27] [28] [29] [30] [31] [32 <./MSF_modelling.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 2066--2067 []\T1/ptm/b/n/10 inter_gene_max_space\T1/ptm/m/n/10 : an \T1/ptm/m/it/10 in-te- ger \T1/ptm/m/n/10 that de-fines gene-wise value of sys-tem's ^^Pin- Overfull \vbox (1.72583pt too high) detected at line 2111 [33] [34] [35] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. 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[58] [59] Underfull \hbox (badness 10000) in paragraph at lines 4336--4336 []\T1/ptm/m/it/10 fqn\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_gene_max_space\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 min_mandatory_genes_required=None\T1/ptm/m/n/10 , [60] [61] [62] [63] Underfull \hbox (badness 10000) in paragraph at lines 4798--4798 []\T1/ptm/m/it/10 gene\T1/ptm/m/n/10 , \T1/ptm/m/it/10 model\T1/ptm/m/n/10 , \T 1/ptm/m/it/10 loner=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 multi_system=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 in- [64] [65] [66] [67] [68] [69 <./gene_obj_interaction.pdf>] [70] [71] [72] [73 <./inheritance-8ba7a954ca815e13e62e2f63ee3be443ea836ee9.pdf>] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6303--6305 [][][]\T1/pcr/m/sl/10 macsypy.system.System[][] \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 macsypy.cluster. [76] [77] [78] [79] [80] [81] [82] Overfull \hbox (27.20956pt too wide) in paragraph at lines 6995--6998 []\T1/ptm/m/n/10 replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_l oci\tsys_wholeness\tsys_score Overfull \hbox (44.58925pt too wide) in paragraph at lines 6995--6998 \T1/ptm/m/n/10 \tsys_occ\thit_gene_ref.alternate_of\thit_status\thit_seq_len\th it_i_eval\thit_score\thit_profile_cov [83] Underfull \hbox (badness 10000) in paragraph at lines 7214--7215 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by the con- Underfull \hbox (badness 10000) in paragraph at lines 7228--7230 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by con- [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 []\T1/pcr/b/n/10 models \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 list of tuple with the following structure: Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 \T1/pcr/m/sl/10 [(\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 model_1\TS1/pcr/m/sl/10 '\T 1/pcr/m/sl/10 , (\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 def1, def2, ..)), (\TS1/pcr/ m/sl/10 '\T1/pcr/m/sl/10 model_2\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , (\TS1/pcr/m /sl/10 '\T1/pcr/m/sl/10 def1\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , ..)), [86] [87] [88] [89] [90] Chapter 3. [91] [92] [93] (./macsyfinder.ind [94] Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.databa se.RepliconDB Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.model. 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HMMReport Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/pcr/m/n/10 _fill_ordered_min_max() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 _find_readme() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.packag e.Package Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 _get_model_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 170--172 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 173--174 []\T1/pcr/m/n/10 _load_metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.pack age.Package Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 _make() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database.Repl iconInfo class Underfull \hbox (badness 10000) in paragraph at lines 175--177 []\T1/pcr/m/n/10 _parse_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 175--177 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 177--179 []\T1/pcr/m/n/10 _parse_genes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 177--179 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 179--180 []\T1/pcr/m/n/10 _parse_hmm_body() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.rep ort.HMMReport Underfull \hbox (badness 10000) in paragraph at lines 180--181 []\T1/pcr/m/n/10 _parse_hmm_header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 181--182 []\T1/pcr/m/n/10 _profile_features() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.p rofile.Profile Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\T1/pcr/m/n/10 _scan_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox 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\hbox (badness 10000) in paragraph at lines 198--200 []\T1/pcr/m/n/10 _set_replicon_topology() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 200--201 []\T1/pcr/m/n/10 _set_sequence_db() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.co nfig.Config Underfull \hbox (badness 10000) in paragraph at lines 201--202 []\T1/pcr/m/n/10 _set_topology_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. config.Config Underfull \hbox (badness 10000) in paragraph at lines 203--204 []\T1/pcr/m/n/10 _url_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.R emoteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 210--212 []\T1/pcr/m/n/10 accessory_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 210--212 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 214--215 []\T1/pcr/m/n/10 add_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.ge ne.ModelGene Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 add_subdefinition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 217--219 \T1/ptm/m/it/10 sypy.registries.DefinitionLocation method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 allowed_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 219--221 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 221--222 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.E xchangeable Underfull \hbox (badness 10000) in paragraph at lines 222--223 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/pcr/m/n/10 check_consistency() 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[]\T1/pcr/m/n/10 find_best_solutions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le mac- Underfull \hbox (badness 10000) in paragraph at lines 272--273 []\T1/pcr/m/n/10 find_my_indexes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.dat abase.Indexes Underfull \hbox (badness 10000) in paragraph at lines 273--275 []\T1/pcr/m/n/10 forbidden_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 273--275 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 275--276 []\T1/pcr/m/n/10 fulfilled_function() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. cluster.Cluster Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 get_all_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/pcr/m/n/10 get_definition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 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paragraph at lines 323--324 []\T1/pcr/m/n/10 is_accessory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene [98] Underfull \hbox (badness 10000) in paragraph at lines 325--326 []\T1/pcr/m/n/10 is_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gen e.Exchangeable Underfull \hbox (badness 10000) in paragraph at lines 326--327 []\T1/pcr/m/n/10 is_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gen e.ModelGene Underfull \hbox (badness 10000) in paragraph at lines 327--328 []\T1/pcr/m/n/10 is_forbidden() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 328--329 []\T1/pcr/m/n/10 is_mandatory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 330--331 []\T1/pcr/m/n/10 iteritems() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database. 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Transcript written on macsyfinder.log. Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Log file says output to 'macsyfinder.pdf' Latexmk: Examining 'macsyfinder.log' === TeX engine is 'pdfTeX' Latexmk: All targets (macsyfinder.pdf) are up-to-date make[2]: Leaving directory '/build/reproducible-path/macsyfinder-2.0~rc1/doc/build/latex' make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.0~rc1/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~rc1' 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~rc1' 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~rc1-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../macsyfinder_2.0~rc1-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/865629/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/865629/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/865629 and its subdirectories I: Current time: Sun Feb 9 02:30:57 +14 2025 I: pbuilder-time-stamp: 1739017857