I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 2 09:33:31 +14 2026 I: pbuilder-time-stamp: 1767296011 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [macsyfinder_2.1.4-1.dsc] I: copying [./macsyfinder_2.1.4.orig.tar.gz] I: copying [./macsyfinder_2.1.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 7 20:31:40 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.1.4-1.dsc: no acceptable signature found dpkg-source: info: extracting macsyfinder in macsyfinder-2.1.4 dpkg-source: info: unpacking macsyfinder_2.1.4.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.1.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying adjust_test dpkg-source: info: applying privacy dpkg-source: info: applying do_not_test_parse_model_old_syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4023626/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 1 19:33 /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/4023626/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4023626/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=d3c4ec9c0e2e4b7c95ea0d0afb7b8427 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=4023626 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.2fNFm1zr/pbuilderrc_84ep --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2fNFm1zr/b2 --logfile b2/build.log macsyfinder_2.1.4-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4023626/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3, pybuild-plugin-pyproject, python3-setuptools, python3-sphinx, python3-networkx, python3-yaml, python3-colorlog, python3-colorama, python3-pandas, python3-sphinx-rtd-theme, tex-gyre, texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-colorlog; however: Package python3-colorlog is not installed. pbuilder-satisfydepends-dummy depends on python3-colorama; however: Package python3-colorama is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-plain-generic; however: Package texlive-plain-generic is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on latexmk; however: Package latexmk is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lmodern{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} hmmer{a} intltool-debian{a} latexmk{a} libabsl20230802{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack3{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libnsl2{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsvtav1enc2{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyaml-0-2{a} libyuv0{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} preview-latex-style{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-colorama{a} python3-colorlog{a} python3-dateutil{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pygments{a} python3-pyproject-hooks{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-plain-generic{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apvlv atril curl default-jre dvisvgm evince fonts-liberation fonts-texgyre fonts-texgyre-math ghostscript gv javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx mupdf okular python3-bottleneck python3-bs4 python3-gdal python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-pydot python3-pygraphviz python3-scipy python3-tables qpdfview qpdfview-ps-plugin ruby shared-mime-info tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 221 newly installed, 0 to remove and 0 not upgraded. Need to get 226 MB of archives. After unpacking 870 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-2+b1 [39.4 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-2+b1 [61.3 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.11.0-1 [1690 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-2+b2 [493 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-7+b2 [653 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.2.1+dfsg-2 [1463 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1898.20241125-1 [136 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.3-1 [11.2 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.3-1 [14.9 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.3-1 [419 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b2 [53.2 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [210 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [51.8 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [33.5 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-2+b1 [41.4 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-2+b1 [628 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-2+b1 [182 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-2+b1 [198 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b3 [55.6 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-2+b1 [574 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 hmmer arm64 3.4+dfsg-2+b1 [977 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B] Get: 146 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5 [153 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5 [47.9 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5 [60.3 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5 [106 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5 [7358 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 159 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 latexmk all 1:4.85-1 [501 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 162 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-9 [361 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b2 [49.3 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.45.1-1 [56.7 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.2-1 [36.0 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20241024 [11.4 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-colorlog all 6.9.0-1 [27.5 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 212 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b1 [148 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 220 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Get: 221 http://deb.debian.org/debian unstable/main arm64 texlive-plain-generic all 2024.20241115-1 [28.6 MB] Fetched 226 MB in 1s (254 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20433 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21495 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../016-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../017-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../018-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../019-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../020-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../021-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../022-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../023-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../026-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../034-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../035-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../036-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../037-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../038-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../039-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../040-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../041-python3-pkg-resources_75.2.0-1_all.deb ... Unpacking python3-pkg-resources (75.2.0-1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../042-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../043-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../044-python3-setuptools_75.2.0-1_all.deb ... Unpacking python3-setuptools (75.2.0-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../045-dh-python_6.20241024_all.deb ... Unpacking dh-python (6.20241024) ... Selecting previously unselected package xml-core. Preparing to unpack .../046-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package docutils-common. Preparing to unpack .../047-docutils-common_0.21.2+dfsg-2_all.deb ... Unpacking docutils-common (0.21.2+dfsg-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../048-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../049-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../050-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../051-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../052-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../053-fontconfig-config_2.15.0-1.1+b1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../054-libfontconfig1_2.15.0-1.1+b1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../055-fontconfig_2.15.0-1.1+b1_arm64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../056-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../057-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package libann0. Preparing to unpack .../058-libann0_1.1.2+doc-9+b2_arm64.deb ... Unpacking libann0 (1.1.2+doc-9+b2) ... Selecting previously unselected package libcdt5:arm64. Preparing to unpack .../059-libcdt5_2.42.4-2+b1_arm64.deb ... Unpacking libcdt5:arm64 (2.42.4-2+b1) ... Selecting previously unselected package libcgraph6:arm64. Preparing to unpack .../060-libcgraph6_2.42.4-2+b1_arm64.deb ... Unpacking libcgraph6:arm64 (2.42.4-2+b1) ... Selecting previously unselected package libaom3:arm64. Preparing to unpack .../061-libaom3_3.11.0-1_arm64.deb ... Unpacking libaom3:arm64 (3.11.0-1) ... Selecting previously unselected package libdav1d7:arm64. Preparing to unpack .../062-libdav1d7_1.5.0-1+b1_arm64.deb ... Unpacking libdav1d7:arm64 (1.5.0-1+b1) ... Selecting previously unselected package libabsl20230802:arm64. Preparing to unpack .../063-libabsl20230802_20230802.1-4_arm64.deb ... Unpacking libabsl20230802:arm64 (20230802.1-4) ... Selecting previously unselected package libgav1-1:arm64. Preparing to unpack .../064-libgav1-1_0.19.0-2+b2_arm64.deb ... Unpacking libgav1-1:arm64 (0.19.0-2+b2) ... Selecting previously unselected package librav1e0.7:arm64. Preparing to unpack .../065-librav1e0.7_0.7.1-7+b2_arm64.deb ... Unpacking librav1e0.7:arm64 (0.7.1-7+b2) ... Selecting previously unselected package libsvtav1enc2:arm64. Preparing to unpack .../066-libsvtav1enc2_2.2.1+dfsg-2_arm64.deb ... Unpacking libsvtav1enc2:arm64 (2.2.1+dfsg-2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../067-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libyuv0:arm64. Preparing to unpack .../068-libyuv0_0.0.1898.20241125-1_arm64.deb ... Unpacking libyuv0:arm64 (0.0.1898.20241125-1) ... Selecting previously unselected package libavif16:arm64. Preparing to unpack .../069-libavif16_1.1.1-1_arm64.deb ... Unpacking libavif16:arm64 (1.1.1-1) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../070-libsharpyuv0_1.4.0-0.1+b1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Selecting previously unselected package libheif-plugin-dav1d:arm64. Preparing to unpack .../071-libheif-plugin-dav1d_1.19.3-1_arm64.deb ... Unpacking libheif-plugin-dav1d:arm64 (1.19.3-1) ... Selecting previously unselected package libde265-0:arm64. Preparing to unpack .../072-libde265-0_1.0.15-1+b2_arm64.deb ... Unpacking libde265-0:arm64 (1.0.15-1+b2) ... Selecting previously unselected package libheif-plugin-libde265:arm64. Preparing to unpack .../073-libheif-plugin-libde265_1.19.3-1_arm64.deb ... Unpacking libheif-plugin-libde265:arm64 (1.19.3-1) ... Selecting previously unselected package libheif1:arm64. Preparing to unpack .../074-libheif1_1.19.3-1_arm64.deb ... Unpacking libheif1:arm64 (1.19.3-1) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../075-libimagequant0_2.18.0-1+b2_arm64.deb ... Unpacking libimagequant0:arm64 (2.18.0-1+b2) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../076-libfribidi0_1.0.15-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.15-1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../077-libglib2.0-0t64_2.82.2-3_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.2-3) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../078-libgraphite2-3_1.3.14-2+b1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../079-libharfbuzz0b_10.0.1-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... Selecting previously unselected package libraqm0:arm64. Preparing to unpack .../080-libraqm0_0.10.1-1+b2_arm64.deb ... Unpacking libraqm0:arm64 (0.10.1-1+b2) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../081-libdeflate0_1.22-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.22-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../082-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../083-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../084-libwebp7_1.4.0-0.1+b1_arm64.deb ... Unpacking libwebp7:arm64 (1.4.0-0.1+b1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../085-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../086-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../087-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../088-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../089-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../090-libx11-6_2%3a1.8.10-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.10-2) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../091-libxpm4_1%3a3.5.17-1+b2_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.17-1+b2) ... Selecting previously unselected package libgd3:arm64. Preparing to unpack .../092-libgd3_2.3.3-12+b1_arm64.deb ... Unpacking libgd3:arm64 (2.3.3-12+b1) ... Selecting previously unselected package libgts-0.7-5t64:arm64. Preparing to unpack .../093-libgts-0.7-5t64_0.7.6+darcs121130-5.2+b1_arm64.deb ... Unpacking libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../094-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../095-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../096-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../097-libxext6_2%3a1.3.4-1+b2_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../098-libxrender1_1%3a0.9.10-1.1+b2_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b2) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../099-libcairo2_1.18.2-2_arm64.deb ... Unpacking libcairo2:arm64 (1.18.2-2) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../100-libltdl7_2.4.7-8_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-8) ... Selecting previously unselected package libthai-data. Preparing to unpack .../101-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../102-libdatrie1_0.2.13-3+b1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../103-libthai0_0.1.29-2+b1_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../104-libpango-1.0-0_1.54.0+ds-3_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.54.0+ds-3) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../105-libpangoft2-1.0-0_1.54.0+ds-3_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../106-libpangocairo-1.0-0_1.54.0+ds-3_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ... Selecting previously unselected package libpathplan4:arm64. Preparing to unpack .../107-libpathplan4_2.42.4-2+b1_arm64.deb ... Unpacking libpathplan4:arm64 (2.42.4-2+b1) ... Selecting previously unselected package libgvc6. Preparing to unpack .../108-libgvc6_2.42.4-2+b1_arm64.deb ... Unpacking libgvc6 (2.42.4-2+b1) ... Selecting previously unselected package libgvpr2:arm64. Preparing to unpack .../109-libgvpr2_2.42.4-2+b1_arm64.deb ... Unpacking libgvpr2:arm64 (2.42.4-2+b1) ... Selecting previously unselected package liblab-gamut1:arm64. Preparing to unpack .../110-liblab-gamut1_2.42.4-2+b1_arm64.deb ... Unpacking liblab-gamut1:arm64 (2.42.4-2+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../111-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../112-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../113-libsm6_2%3a1.2.4-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.4-1) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../114-libxt6t64_1%3a1.2.1-1.2+b1_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b1) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../115-libxmu6_2%3a1.1.3-3+b3_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.3-3+b3) ... Selecting previously unselected package libxaw7:arm64. Preparing to unpack .../116-libxaw7_2%3a1.0.16-1_arm64.deb ... Unpacking libxaw7:arm64 (2:1.0.16-1) ... Selecting previously unselected package graphviz. Preparing to unpack .../117-graphviz_2.42.4-2+b1_arm64.deb ... Unpacking graphviz (2.42.4-2+b1) ... Selecting previously unselected package libdivsufsort3:arm64. Preparing to unpack .../118-libdivsufsort3_2.0.1-6+b1_arm64.deb ... Unpacking libdivsufsort3:arm64 (2.0.1-6+b1) ... Selecting previously unselected package hmmer. Preparing to unpack .../119-hmmer_3.4+dfsg-2+b1_arm64.deb ... Unpacking hmmer (3.4+dfsg-2+b1) ... Selecting previously unselected package tex-common. Preparing to unpack .../120-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package libpaper1:arm64. Preparing to unpack .../121-libpaper1_1.1.29+b2_arm64.deb ... Unpacking libpaper1:arm64 (1.1.29+b2) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../122-libpaper-utils_1.1.29+b2_arm64.deb ... Unpacking libpaper-utils (1.1.29+b2) ... Selecting previously unselected package libkpathsea6:arm64. Preparing to unpack .../123-libkpathsea6_2024.20240313.70630+ds-5_arm64.deb ... Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-5) ... Selecting previously unselected package libptexenc1:arm64. Preparing to unpack .../124-libptexenc1_2024.20240313.70630+ds-5_arm64.deb ... Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-5) ... Selecting previously unselected package libsynctex2:arm64. Preparing to unpack .../125-libsynctex2_2024.20240313.70630+ds-5_arm64.deb ... Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-5) ... Selecting previously unselected package libtexlua53-5:arm64. Preparing to unpack .../126-libtexlua53-5_2024.20240313.70630+ds-5_arm64.deb ... Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-5) ... Selecting previously unselected package t1utils. Preparing to unpack .../127-t1utils_1.41-4+b1_arm64.deb ... Unpacking t1utils (1.41-4+b1) ... Selecting previously unselected package libmpfi0:arm64. Preparing to unpack .../128-libmpfi0_1.5.4+ds-4_arm64.deb ... Unpacking libmpfi0:arm64 (1.5.4+ds-4) ... Selecting previously unselected package libpotrace0:arm64. Preparing to unpack .../129-libpotrace0_1.16-2+b2_arm64.deb ... Unpacking libpotrace0:arm64 (1.16-2+b2) ... Selecting previously unselected package libteckit0:arm64. Preparing to unpack .../130-libteckit0_2.5.12+ds1-1+b1_arm64.deb ... Unpacking libteckit0:arm64 (2.5.12+ds1-1+b1) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../131-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libzzip-0-13t64:arm64. Preparing to unpack .../132-libzzip-0-13t64_0.13.72+dfsg.1-1.3_arm64.deb ... Unpacking libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../133-texlive-binaries_2024.20240313.70630+ds-5_arm64.deb ... Unpacking texlive-binaries (2024.20240313.70630+ds-5) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../134-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package texlive-base. Preparing to unpack .../135-texlive-base_2024.20241115-1_all.deb ... Unpacking texlive-base (2024.20241115-1) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../136-texlive-latex-base_2024.20241115-1_all.deb ... Unpacking texlive-latex-base (2024.20241115-1) ... Selecting previously unselected package latexmk. Preparing to unpack .../137-latexmk_1%3a4.85-1_all.deb ... Unpacking latexmk (1:4.85-1) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../138-libapache-pom-java_33-2_all.deb ... Unpacking libapache-pom-java (33-2) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../139-libblas3_3.12.0-4_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-4) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../140-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../141-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libfontbox-java. Preparing to unpack .../142-libfontbox-java_1%3a1.8.16-5_all.deb ... Unpacking libfontbox-java (1:1.8.16-5) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../143-libfontenc1_1%3a1.1.8-1+b1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../144-libgfortran5_14.2.0-9_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-9) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../145-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../146-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../147-libjs-sphinxdoc_7.4.7-4_all.deb ... Unpacking libjs-sphinxdoc (7.4.7-4) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../148-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../149-liblapack3_3.12.0-4_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-4) ... Selecting previously unselected package libpdfbox-java. Preparing to unpack .../150-libpdfbox-java_1%3a1.8.16-5_all.deb ... Unpacking libpdfbox-java (1:1.8.16-5) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../151-libyaml-0-2_0.2.5-1+b2_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b2) ... Selecting previously unselected package preview-latex-style. Preparing to unpack .../152-preview-latex-style_13.2-1_all.deb ... Unpacking preview-latex-style (13.2-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../153-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-pyproject-hooks. Preparing to unpack .../154-python3-pyproject-hooks_1.2.0-1_all.deb ... Unpacking python3-pyproject-hooks (1.2.0-1) ... Selecting previously unselected package python3-toml. Preparing to unpack .../155-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../156-python3-wheel_0.45.1-1_all.deb ... Unpacking python3-wheel (0.45.1-1) ... Selecting previously unselected package python3-build. Preparing to unpack .../157-python3-build_1.2.2-1_all.deb ... Unpacking python3-build (1.2.2-1) ... Selecting previously unselected package python3-installer. Preparing to unpack .../158-python3-installer_0.7.0+dfsg1-3_all.deb ... Unpacking python3-installer (0.7.0+dfsg1-3) ... Selecting previously unselected package pybuild-plugin-pyproject. Preparing to unpack .../159-pybuild-plugin-pyproject_6.20241024_all.deb ... Unpacking pybuild-plugin-pyproject (6.20241024) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../160-python-babel-localedata_2.16.0-1_all.deb ... Unpacking python-babel-localedata (2.16.0-1) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../161-python3-alabaster_0.7.16-0.1_all.deb ... Unpacking python3-alabaster (0.7.16-0.1) ... Selecting previously unselected package python3-babel. Preparing to unpack .../162-python3-babel_2.16.0-1_all.deb ... Unpacking python3-babel (2.16.0-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../163-python3-certifi_2024.8.30+dfsg-1_all.deb ... Unpacking python3-certifi (2024.8.30+dfsg-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../164-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../165-python3-charset-normalizer_3.4.0-1+b1_arm64.deb ... Unpacking python3-charset-normalizer (3.4.0-1+b1) ... Selecting previously unselected package python3-colorama. Preparing to unpack .../166-python3-colorama_0.4.6-4_all.deb ... Unpacking python3-colorama (0.4.6-4) ... Selecting previously unselected package python3-colorlog. Preparing to unpack .../167-python3-colorlog_6.9.0-1_all.deb ... Unpacking python3-colorlog (6.9.0-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../168-python3-dateutil_2.9.0-3_all.deb ... Unpacking python3-dateutil (2.9.0-3) ... Selecting previously unselected package python3-defusedxml. Preparing to unpack .../169-python3-defusedxml_0.7.1-2_all.deb ... Unpacking python3-defusedxml (0.7.1-2) ... Selecting previously unselected package python3-roman. Preparing to unpack .../170-python3-roman_4.2-1_all.deb ... Unpacking python3-roman (4.2-1) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../171-python3-docutils_0.21.2+dfsg-2_all.deb ... Unpacking python3-docutils (0.21.2+dfsg-2) ... Selecting previously unselected package python3-idna. Preparing to unpack .../172-python3-idna_3.8-2_all.deb ... Unpacking python3-idna (3.8-2) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../173-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../174-python3-markupsafe_2.1.5-1+b3_arm64.deb ... Unpacking python3-markupsafe (2.1.5-1+b3) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../175-python3-jinja2_3.1.3-1_all.deb ... Unpacking python3-jinja2 (3.1.3-1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../176-python3-networkx_3.2.1-5_all.deb ... Unpacking python3-networkx (3.2.1-5) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../177-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... Unpacking python3-numpy (1:1.26.4+ds-12) ... Selecting previously unselected package python3-tz. Preparing to unpack .../178-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../179-python3-pandas-lib_2.2.3+dfsg-5+b1_arm64.deb ... Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../180-python3-pandas_2.2.3+dfsg-5_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-5) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../181-python3-pygments_2.18.0+dfsg-1_all.deb ... Unpacking python3-pygments (2.18.0+dfsg-1) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../182-python3-urllib3_2.0.7-2_all.deb ... Unpacking python3-urllib3 (2.0.7-2) ... Selecting previously unselected package python3-requests. Preparing to unpack .../183-python3-requests_2.32.3+dfsg-1_all.deb ... Unpacking python3-requests (2.32.3+dfsg-1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../184-python3-snowballstemmer_2.2.0-4_all.deb ... Unpacking python3-snowballstemmer (2.2.0-4) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../185-sphinx-common_7.4.7-4_all.deb ... Unpacking sphinx-common (7.4.7-4) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../186-python3-sphinx_7.4.7-4_all.deb ... Unpacking python3-sphinx (7.4.7-4) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../187-sphinx-rtd-theme-common_3.0.2+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-1) ... Selecting previously unselected package python3-sphinxcontrib.jquery. Preparing to unpack .../188-python3-sphinxcontrib.jquery_4.1-5_all.deb ... Unpacking python3-sphinxcontrib.jquery (4.1-5) ... Selecting previously unselected package python3-sphinx-rtd-theme. Preparing to unpack .../189-python3-sphinx-rtd-theme_3.0.2+dfsg-1_all.deb ... Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-1) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../190-python3-yaml_6.0.2-1+b1_arm64.deb ... Unpacking python3-yaml (6.0.2-1+b1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../191-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../192-xfonts-utils_1%3a7.7+7_arm64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package tex-gyre. Preparing to unpack .../193-tex-gyre_20180621-6_all.deb ... Unpacking tex-gyre (20180621-6) ... Selecting previously unselected package texlive-fonts-recommended. Preparing to unpack .../194-texlive-fonts-recommended_2024.20241115-1_all.deb ... Unpacking texlive-fonts-recommended (2024.20241115-1) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../195-texlive-latex-recommended_2024.20241115-1_all.deb ... Unpacking texlive-latex-recommended (2024.20241115-1) ... Selecting previously unselected package texlive-pictures. Preparing to unpack .../196-texlive-pictures_2024.20241115-1_all.deb ... Unpacking texlive-pictures (2024.20241115-1) ... Selecting previously unselected package texlive-latex-extra. Preparing to unpack .../197-texlive-latex-extra_2024.20241115-1_all.deb ... Unpacking texlive-latex-extra (2024.20241115-1) ... Selecting previously unselected package texlive-plain-generic. Preparing to unpack .../198-texlive-plain-generic_2024.20241115-1_all.deb ... Unpacking texlive-plain-generic (2024.20241115-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libaom3:arm64 (3.11.0-1) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libfontbox-java (1:1.8.16-5) ... Setting up liblab-gamut1:arm64 (2.42.4-2+b1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jan 1 19:34:10 UTC 2026. Universal Time is now: Thu Jan 1 19:34:10 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:arm64 (2.2.1+dfsg-2) ... Setting up libteckit0:arm64 (2.5.12+ds1-1+b1) ... Setting up libpathplan4:arm64 (2.42.4-2+b1) ... Setting up libapache-pom-java (33-2) ... Setting up libann0 (1.1.2+doc-9+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up t1utils (1.41-4+b1) ... Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-5) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:arm64 (1.5.4+ds-4) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libltdl7:arm64 (2.4.7-8) ... Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-5) ... Setting up libgfortran5:arm64 (14.2.0-9) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:arm64 (1.5.0-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up librav1e0.7:arm64 (0.7.1-7+b2) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:arm64 (20230802.1-4) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up sgml-base (1.31) ... Setting up libcdt5:arm64 (2.42.4-2+b1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libcgraph6:arm64 (2.42.4-2+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:arm64 (1.0.15-1+b2) ... Setting up libdivsufsort3:arm64 (2.0.1-6+b1) ... Setting up openssl (3.3.2-2) ... Setting up libyuv0:arm64 (0.0.1898.20241125-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (1.16-2+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxpm4:arm64 (1:3.5.17-1+b2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libgav1-1:arm64 (0.19.0-2+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:arm64 (2.42.4-2+b1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up hmmer (3.4+dfsg-2+b1) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libpaper1:arm64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libavif16:arm64 (1.1.1-1) ... Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ... Setting up tex-gyre (20180621-6) ... Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ... Setting up libxmu6:arm64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20241115-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up texlive-plain-generic (2024.20241115-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up python3-wheel (0.45.1-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pyproject-hooks (1.2.0-1) ... Setting up texlive-latex-base (2024.20241115-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up texlive-latex-recommended (2024.20241115-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-toml (0.10.2-1) ... Setting up texlive-pictures (2024.20241115-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up texlive-fonts-recommended (2024.20241115-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-build (1.2.2-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-colorlog (6.9.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up latexmk (1:4.85-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up texlive-latex-extra (2024.20241115-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-networkx (3.2.1-5) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Setting up pybuild-plugin-pyproject (6.20241024) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up libheif-plugin-dav1d:arm64 (1.19.3-1) ... Setting up libheif-plugin-libde265:arm64 (1.19.3-1) ... Setting up libheif1:arm64 (1.19.3-1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up graphviz (2.42.4-2+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/4023626/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/4023626/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/macsyfinder-2.1.4/ && 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_2.1.4-1_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.1.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12 * Building wheel... /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running bdist_wheel running build running build_py creating build/lib/macsypy copying macsypy/utils.py -> build/lib/macsypy copying macsypy/system.py -> build/lib/macsypy copying macsypy/solution.py -> build/lib/macsypy copying macsypy/serialization.py -> build/lib/macsypy copying macsypy/search_genes.py -> build/lib/macsypy copying macsypy/report.py -> build/lib/macsypy copying macsypy/registries.py -> build/lib/macsypy copying macsypy/profile.py -> build/lib/macsypy copying macsypy/package.py -> build/lib/macsypy copying macsypy/model_conf_parser.py -> build/lib/macsypy copying macsypy/model.py -> build/lib/macsypy copying macsypy/metadata.py -> build/lib/macsypy copying macsypy/licenses.py -> build/lib/macsypy copying macsypy/hit.py -> build/lib/macsypy copying macsypy/gene.py -> build/lib/macsypy copying macsypy/error.py -> build/lib/macsypy copying macsypy/definition_parser.py -> build/lib/macsypy copying macsypy/database.py -> build/lib/macsypy copying macsypy/config.py -> build/lib/macsypy copying macsypy/cluster.py -> build/lib/macsypy copying macsypy/__init__.py -> build/lib/macsypy creating build/lib/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsydata.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyconfig.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsy_merge_results.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsy_gembase_split.py -> build/lib/macsypy/scripts copying macsypy/scripts/__init__.py -> build/lib/macsypy/scripts creating build/lib/macsypy/data copying macsypy/data/pre-push -> build/lib/macsypy/data installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/macsypy creating build/bdist.linux-aarch64/wheel/macsypy/data copying build/lib/macsypy/data/pre-push -> build/bdist.linux-aarch64/wheel/./macsypy/data creating build/bdist.linux-aarch64/wheel/macsypy/scripts copying build/lib/macsypy/scripts/__init__.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsy_gembase_split.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsy_merge_results.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyconfig.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsydata.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyfinder.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyprofile.py -> build/bdist.linux-aarch64/wheel/./macsypy/scripts copying build/lib/macsypy/__init__.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/cluster.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/config.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/database.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/definition_parser.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/error.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/gene.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/hit.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/licenses.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/metadata.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/model.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/model_conf_parser.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/package.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/profile.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/registries.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/report.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/search_genes.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/serialization.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/solution.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/system.py -> build/bdist.linux-aarch64/wheel/./macsypy copying build/lib/macsypy/utils.py -> build/bdist.linux-aarch64/wheel/./macsypy running install_data creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.4.data/data creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.4.data/data/share/macsyfinder/models copying data/models/README -> build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.4.data/data/share/macsyfinder/models running install_egg_info running egg_info creating MacSyFinder.egg-info writing MacSyFinder.egg-info/PKG-INFO writing dependency_links to MacSyFinder.egg-info/dependency_links.txt writing entry points to MacSyFinder.egg-info/entry_points.txt writing requirements to MacSyFinder.egg-info/requires.txt writing top-level names to MacSyFinder.egg-info/top_level.txt writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' reading manifest file 'MacSyFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'doc/build/html' warning: no files found matching 'doc/build/latex/macsyfinder.pdf' warning: no files found matching 'etc/macsyfinder.conf' warning: no previously-included files matching '*' found under directory 'tests/__pycache__' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no previously-included files found matching '.coverage' warning: no previously-included files found matching 'coverage_html' warning: no previously-included files found matching '.gitignore' warning: no previously-included files found matching '.travis.yml' warning: no previously-included files found matching '.github' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'CITATION.cff' adding license file 'COPYING' writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' Copying MacSyFinder.egg-info to build/bdist.linux-aarch64/wheel/./MacSyFinder-2.1.4.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/MacSyFinder-2.1.4.dist-info/WHEEL creating '/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/.tmp-5di9twds/MacSyFinder-2.1.4-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'MacSyFinder-2.1.4.data/data/share/macsyfinder/models/README' adding 'macsypy/__init__.py' adding 'macsypy/cluster.py' adding 'macsypy/config.py' adding 'macsypy/database.py' adding 'macsypy/definition_parser.py' adding 'macsypy/error.py' adding 'macsypy/gene.py' adding 'macsypy/hit.py' adding 'macsypy/licenses.py' adding 'macsypy/metadata.py' adding 'macsypy/model.py' adding 'macsypy/model_conf_parser.py' adding 'macsypy/package.py' adding 'macsypy/profile.py' adding 'macsypy/registries.py' adding 'macsypy/report.py' adding 'macsypy/search_genes.py' adding 'macsypy/serialization.py' adding 'macsypy/solution.py' adding 'macsypy/system.py' adding 'macsypy/utils.py' adding 'macsypy/data/pre-push' adding 'macsypy/scripts/__init__.py' adding 'macsypy/scripts/macsy_gembase_split.py' adding 'macsypy/scripts/macsy_merge_results.py' adding 'macsypy/scripts/macsyconfig.py' adding 'macsypy/scripts/macsydata.py' adding 'macsypy/scripts/macsyfinder.py' adding 'macsypy/scripts/macsyprofile.py' adding 'MacSyFinder-2.1.4.dist-info/COPYING' adding 'MacSyFinder-2.1.4.dist-info/METADATA' adding 'MacSyFinder-2.1.4.dist-info/WHEEL' adding 'MacSyFinder-2.1.4.dist-info/entry_points.txt' adding 'MacSyFinder-2.1.4.dist-info/top_level.txt' adding 'MacSyFinder-2.1.4.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Successfully built MacSyFinder-2.1.4-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover -v /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:56: UserWarning: GitPython is not installed, `macsydata init` is disabled () To turn this feature ON: - install git - then run `python -m pip install macsyfinder[model]` in your activated environment. warnings.warn("GitPython is not installed, `macsydata init` is disabled ()\n" test_Config (tests.test_Config.TestConfig.test_Config) ... ok test_Config_args (tests.test_Config.TestConfig.test_Config_args) ... ok test_Config_conf_file_virtualenv (tests.test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok test_Config_default_conf_file (tests.test_Config.TestConfig.test_Config_default_conf_file) ... ok test_Config_file_bad_values (tests.test_Config.TestConfig.test_Config_file_bad_values) ... ok test_Config_file_n_args (tests.test_Config.TestConfig.test_Config_file_n_args) ... ok test_bad_db_type (tests.test_Config.TestConfig.test_bad_db_type) ... ok test_bad_models_dir (tests.test_Config.TestConfig.test_bad_models_dir) ... ok test_bad_sequence_db (tests.test_Config.TestConfig.test_bad_sequence_db) ... ok test_bad_topology (tests.test_Config.TestConfig.test_bad_topology) ... ok test_bad_topology_file (tests.test_Config.TestConfig.test_bad_topology_file) ... ok test_bad_values (tests.test_Config.TestConfig.test_bad_values) ... ok test_cmd_config_file (tests.test_Config.TestConfig.test_cmd_config_file) ... ok test_config_file_2_dict (tests.test_Config.TestConfig.test_config_file_2_dict) ... ok test_cut_ga (tests.test_Config.TestConfig.test_cut_ga) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if filtering_node: ok test_e_value_search (tests.test_Config.TestConfig.test_e_value_search) ... ok test_hit_weights (tests.test_Config.TestConfig.test_hit_weights) ... ok test_hmmsearch (tests.test_Config.TestConfig.test_hmmsearch) ... ok test_hmmsearch_set_by_user (tests.test_Config.TestConfig.test_hmmsearch_set_by_user) ... ok test_model_conf (tests.test_Config.TestConfig.test_model_conf) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:59: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if weights_node: ok test_models_dir (tests.test_Config.TestConfig.test_models_dir) ... ok test_no_hmmsearch (tests.test_Config.TestConfig.test_no_hmmsearch) ... ok test_out_dir (tests.test_Config.TestConfig.test_out_dir) ... ok test_previous_n_sequence_db (tests.test_Config.TestConfig.test_previous_n_sequence_db) ... ok test_previous_wo_cfg (tests.test_Config.TestConfig.test_previous_wo_cfg) ... ok test_project_config_file (tests.test_Config.TestConfig.test_project_config_file) ... ok test_save (tests.test_Config.TestConfig.test_save) ... ok test_set_log_level (tests.test_Config.TestConfig.test_set_log_level) ... ok test_set_option (tests.test_Config.TestConfig.test_set_option) ... ok test_str_2_tuple (tests.test_Config.TestConfig.test_str_2_tuple) ... ok test_working_dir (tests.test_Config.TestConfig.test_working_dir) ... ok test_NoneConfig (tests.test_Config.TestNoneConfig.test_NoneConfig) ... ok test_bad_exchangeable_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... ok test_bad_gene_inter_gene_max_space_2 (tests.test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) ... ok test_bad_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... ok test_bad_max_nb_genes (tests.test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... ok test_bad_min_genes_required (tests.test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... ok test_bad_min_genes_required_2 (tests.test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... ok test_bad_min_mandatory_genes_required (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... ok test_bad_min_mandatory_genes_required_2 (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... ok test_bad_min_mandatory_genes_required_4 (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... ok test_exchangeable_inheritance (tests.test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... ok test_gene_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... ok test_gene_no_name (tests.test_DefinitionParser.TestModelParser.test_gene_no_name) ... ok test_gene_w_unkown_attr (tests.test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... ok test_inter_gene_max_space_cfg (tests.test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... ok test_invalid_homolog (tests.test_DefinitionParser.TestModelParser.test_invalid_homolog) ... ok test_invalid_homolog_2 (tests.test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... ok test_invalid_presence (tests.test_DefinitionParser.TestModelParser.test_invalid_presence) ... ok test_loner (tests.test_DefinitionParser.TestModelParser.test_loner) ... ok test_max_nb_genes_cfg (tests.test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... ok test_min_genes_required_cfg (tests.test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... ok test_min_mandatory_genes_required_cfg (tests.test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... ok test_min_mandatory_genes_required_lesser_than_mandatory_genes (tests.test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... ok test_model_w_unkown_attr (tests.test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... ok test_multi_loci_cfg (tests.test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... ok test_multi_model (tests.test_DefinitionParser.TestModelParser.test_multi_model) ... ok test_multi_system (tests.test_DefinitionParser.TestModelParser.test_multi_system) ... ok test_no_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... ok test_only_one_accessory (tests.test_DefinitionParser.TestModelParser.test_only_one_accessory) ... ok test_parse_model_old_syntax (tests.test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails' test_parse_with_exchangeable (tests.test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... ok test_wo_presence (tests.test_DefinitionParser.TestModelParser.test_wo_presence) ... ok test_add_exchangeable (tests.test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok test_alternate_of (tests.test_Exchangeable.TestExchangeable.test_alternate_of) ... ok test_is_exchangeable (tests.test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok test_loner (tests.test_Exchangeable.TestExchangeable.test_loner) ... ok test_model (tests.test_Exchangeable.TestExchangeable.test_model) ... ok test_multi_system (tests.test_Exchangeable.TestExchangeable.test_multi_system) ... ok test_add_get_gene (tests.test_GeneBank.Test.test_add_get_gene) ... ok test_contains (tests.test_GeneBank.Test.test_contains) ... ok test_genes_fqn (tests.test_GeneBank.Test.test_genes_fqn) ... ok test_get_uniq_object (tests.test_GeneBank.Test.test_get_uniq_object) ... ok test_iter (tests.test_GeneBank.Test.test_iter) ... ok test_fasta_iter (tests.test_Indexes.TestFastaIter.test_fasta_iter) ... ok test_fasta_iter_bad_fasta (tests.test_Indexes.TestFastaIter.test_fasta_iter_bad_fasta) ... ok test_build_force (tests.test_Indexes.TestIndex.test_build_force) ... ok test_build_idx_gzip_seq (tests.test_Indexes.TestIndex.test_build_idx_gzip_seq) ... ok test_build_idx_older_than_fasta (tests.test_Indexes.TestIndex.test_build_idx_older_than_fasta) ... ok test_build_idx_point_wrong_fasta (tests.test_Indexes.TestIndex.test_build_idx_point_wrong_fasta) ... ok test_build_my_indexes (tests.test_Indexes.TestIndex.test_build_my_indexes) ... ok test_build_no_idx (tests.test_Indexes.TestIndex.test_build_no_idx) ... ok test_build_not_writable (tests.test_Indexes.TestIndex.test_build_not_writable) ... ok test_build_with_idx (tests.test_Indexes.TestIndex.test_build_with_idx) ... ok test_empty_fasta (tests.test_Indexes.TestIndex.test_empty_fasta) ... ok test_find_my_indexes (tests.test_Indexes.TestIndex.test_find_my_indexes) ... ok test_index_dir (tests.test_Indexes.TestIndex.test_index_dir) ... ok test_iter (tests.test_Indexes.TestIndex.test_iter) ... ok test_allowed_hits (tests.test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok test_forbidden_hits (tests.test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok test_hits (tests.test_LikelySystem.LikelySystemTest.test_hits) ... ok test_init (tests.test_LikelySystem.LikelySystemTest.test_init) ... ok test_str (tests.test_LikelySystem.LikelySystemTest.test_str) ... ok test_hits (tests.test_LikelySystem.UnlikelySystemTest.test_hits) ... ok test_init (tests.test_LikelySystem.UnlikelySystemTest.test_init) ... ok test_reason (tests.test_LikelySystem.UnlikelySystemTest.test_reason) ... ok test_str (tests.test_LikelySystem.UnlikelySystemTest.test_str) ... ok test_MacsyDefaults_no_virtual_env (tests.test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok test_MacsyDefaults_virtual_env (tests.test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok test_ordered_match (tests.test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok test_sort_hits_by_status (tests.test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... ok test_unordered_match (tests.test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok test_accessor_mutator (tests.test_Model.TestModel.test_accessor_mutator) ... ok test_eq (tests.test_Model.TestModel.test_eq) ... ok test_filter (tests.test_Model.TestModel.test_filter) ... ok test_fqn (tests.test_Model.TestModel.test_fqn) ... ok test_get_gene (tests.test_Model.TestModel.test_get_gene) ... ok test_gt (tests.test_Model.TestModel.test_gt) ... ok test_hash (tests.test_Model.TestModel.test_hash) ... ok test_inter_gene_max_space (tests.test_Model.TestModel.test_inter_gene_max_space) ... ok test_lt (tests.test_Model.TestModel.test_lt) ... ok test_max_nb_genes (tests.test_Model.TestModel.test_max_nb_genes) ... ok test_min_genes_required (tests.test_Model.TestModel.test_min_genes_required) ... ok test_min_mandatory_genes_required (tests.test_Model.TestModel.test_min_mandatory_genes_required) ... ok test_multi_loci (tests.test_Model.TestModel.test_multi_loci) ... ok test_str (tests.test_Model.TestModel.test_str) ... ok test_add_get_model (tests.test_ModelBank.Test.test_add_get_model) ... ok test_contains (tests.test_ModelBank.Test.test_contains) ... ok test_get_uniq_object (tests.test_ModelBank.Test.test_get_uniq_object) ... ok test_iter (tests.test_ModelBank.Test.test_iter) ... ok test_execute_hmm_protected_path (tests.test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok test_execute_hmm_w_GA_n_nocutga (tests.test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok test_execute_hmm_with_GA (tests.test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping' test_execute_hmm_wo_GA (tests.test_Profile.TestProfile.test_execute_hmm_wo_GA) ... ok test_execute_hmmer_failed (tests.test_Profile.TestProfile.test_execute_hmmer_failed) ... ok test_execute_unknown_binary (tests.test_Profile.TestProfile.test_execute_unknown_binary) ... ok test_ga_threshold (tests.test_Profile.TestProfile.test_ga_threshold) ... ok test_len (tests.test_Profile.TestProfile.test_len) ... ok test_str (tests.test_Profile.TestProfile.test_str) ... ok test_get_profile (tests.test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok test_get_uniq_object (tests.test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok test_unknow_profile (tests.test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok test_hits (tests.test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok test_init (tests.test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok test_str (tests.test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok test_fill_gembase_min_max_default_topology (tests.test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok test_fill_gembase_min_max_with_topology (tests.test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok test_fill_ordered_replicon_min_max (tests.test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok test_fill_topology (tests.test_RepliconDB.Test.test_fill_topology) ... ok test_get (tests.test_RepliconDB.Test.test_get) ... ok test_getitem (tests.test_RepliconDB.Test.test_getitem) ... ok test_guess_if_really_gembase (tests.test_RepliconDB.Test.test_guess_if_really_gembase) ... ok test_in (tests.test_RepliconDB.Test.test_in) ... ok test_items (tests.test_RepliconDB.Test.test_items) ... ok test_iteritems (tests.test_RepliconDB.Test.test_iteritems) ... ok test_names (tests.test_RepliconDB.Test.test_names) ... ok test_replicon_infos (tests.test_RepliconDB.Test.test_replicon_infos) ... ok test_extract (tests.test_Report.TestGembaseHMMReport.test_extract) ... ok test_extract_concurent (tests.test_Report.TestGembaseHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_extract (tests.test_Report.TestGeneralHMMReport.test_extract) ... ok test_extract_concurent (tests.test_Report.TestGeneralHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/tests/test_Report.py:541: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_HMMReport (tests.test_Report.TestHMMReport.test_HMMReport) ... ok test_best_hit (tests.test_Report.TestHMMReport.test_best_hit) ... ok test_build_my_db (tests.test_Report.TestHMMReport.test_build_my_db) ... ok test_fill_my_db (tests.test_Report.TestHMMReport.test_fill_my_db) ... ok test_hit_start (tests.test_Report.TestHMMReport.test_hit_start) ... ok test_parse_hmm_body (tests.test_Report.TestHMMReport.test_parse_hmm_body) ... ok test_parse_hmm_header (tests.test_Report.TestHMMReport.test_parse_hmm_header) ... ok test_save_extract (tests.test_Report.TestHMMReport.test_save_extract) ... ok test_str (tests.test_Report.TestHMMReport.test_str) ... ok test_extract (tests.test_Report.TestOrderedHMMReport.test_extract) ... ok test_extract_concurent (tests.test_Report.TestOrderedHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/tests/test_Report.py:461: DeprecationWarning: currentThread() is deprecated, use current_thread() instead main_thread = threading.currentThread() ok test_HitSystemTracker (tests.test_System.SystemTest.test_HitSystemTracker) ... ok test_count (tests.test_System.SystemTest.test_count) ... ok test_fulfilled_function (tests.test_System.SystemTest.test_fulfilled_function) ... ok test_get_hits_encoding_multisystem (tests.test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok test_get_loners (tests.test_System.SystemTest.test_get_loners) ... ok test_get_multisystems (tests.test_System.SystemTest.test_get_multisystems) ... ok test_hits (tests.test_System.SystemTest.test_hits) ... ok test_init (tests.test_System.SystemTest.test_init) ... ok test_is_compatible (tests.test_System.SystemTest.test_is_compatible) ... ok test_loci_nb (tests.test_System.SystemTest.test_loci_nb) ... ok test_loci_num (tests.test_System.SystemTest.test_loci_num) ... ok test_multi_loci (tests.test_System.SystemTest.test_multi_loci) ... ok test_occurrence (tests.test_System.SystemTest.test_occurrence) ... ok test_position (tests.test_System.SystemTest.test_position) ... ok test_score (tests.test_System.SystemTest.test_score) ... ok test_wholeness (tests.test_System.SystemTest.test_wholeness) ... ok test_build_clusters (tests.test_cluster.TestBuildCluster.test_build_clusters) ... ok test_clusterize (tests.test_cluster.TestBuildCluster.test_clusterize) ... ok test_colocates (tests.test_cluster.TestBuildCluster.test_colocates) ... ok test_get_true_loners (tests.test_cluster.TestBuildCluster.test_get_true_loners) ... ok test_contains (tests.test_cluster.TestCluster.test_contains) ... ok test_fulfilled_function (tests.test_cluster.TestCluster.test_fulfilled_function) ... ok test_init (tests.test_cluster.TestCluster.test_init) ... ok test_len (tests.test_cluster.TestCluster.test_len) ... ok test_loner (tests.test_cluster.TestCluster.test_loner) ... ok test_merge (tests.test_cluster.TestCluster.test_merge) ... ok test_multi_system (tests.test_cluster.TestCluster.test_multi_system) ... ok test_replace (tests.test_cluster.TestCluster.test_replace) ... ok test_replicon_name (tests.test_cluster.TestCluster.test_replicon_name) ... ok test_score (tests.test_cluster.TestCluster.test_score) ... ok test_str (tests.test_cluster.TestCluster.test_str) ... ok test_2_systems_not_compatible (tests.test_functional_test.Test.test_2_systems_not_compatible) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_cfg_n_previous_run (tests.test_functional_test.Test.test_cfg_n_previous_run) ... ok test_degenerated_systems (tests.test_functional_test.Test.test_degenerated_systems) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_force (tests.test_functional_test.Test.test_force) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_functional_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_gembase (tests.test_functional_test.Test.test_gembase) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if filtering_node: /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_gzip (tests.test_functional_test.Test.test_gzip) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gzip/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_index_dir (tests.test_functional_test.Test.test_index_dir) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_model_unknown (tests.test_functional_test.Test.test_model_unknown) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_db_type (tests.test_functional_test.Test.test_no_db_type) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_models (tests.test_functional_test.Test.test_no_models) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_seq_db (tests.test_functional_test.Test.test_no_seq_db) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_no_sequence (tests.test_functional_test.Test.test_no_sequence) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_no_sequence/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_only_loners (tests.test_functional_test.Test.test_only_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_cluster_3_loners (tests.test_functional_test.Test.test_ordered_1_cluster_3_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_cluster_and_clusters_of_loners (tests.test_functional_test.Test.test_ordered_1_cluster_and_clusters_of_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_and_clusters_of_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_clusters_3_loners_w_exchangeable (tests.test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_loner_exch_in_clust (tests.test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_1_loner_in_clust (tests.test_functional_test.Test.test_ordered_1_loner_in_clust) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_2_clusters_1_loner (tests.test_functional_test.Test.test_ordered_2_clusters_1_loner) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_2_clusters_3_loners (tests.test_functional_test.Test.test_ordered_2_clusters_3_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_circular (tests.test_functional_test.Test.test_ordered_circular) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_linear (tests.test_functional_test.Test.test_ordered_linear) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_loci (tests.test_functional_test.Test.test_ordered_multi_loci) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_model (tests.test_functional_test.Test.test_ordered_multi_model) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_system (tests.test_functional_test.Test.test_ordered_multi_system) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_multi_system_out_system (tests.test_functional_test.Test.test_ordered_multi_system_out_system) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_only_one_multi_model (tests.test_functional_test.Test.test_ordered_only_one_multi_model) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_ordered_single_loci (tests.test_functional_test.Test.test_ordered_single_loci) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_timeout (tests.test_functional_test.Test.test_timeout) ... ok test_uncomplete_degenerated_systems (tests.test_functional_test.Test.test_uncomplete_degenerated_systems) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_unordered (tests.test_functional_test.Test.test_unordered) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_unordered_no_hits (tests.test_functional_test.Test.test_unordered_no_hits) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_unordered_only_forbidden (tests.test_functional_test.Test.test_unordered_only_forbidden) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_working_dir_exists (tests.test_functional_test.Test.test_working_dir_exists) ... ok test_working_dir_exists_and_not_dir (tests.test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok test_core_gene (tests.test_gene.TestCoreGene.test_core_gene) ... ok test_str (tests.test_gene.TestGeneStatus.test_str) ... ok test_add_exchangeable (tests.test_gene.TestModelGene.test_add_exchangeable) ... ok test_alternate_of (tests.test_gene.TestModelGene.test_alternate_of) ... ok test_core_gene (tests.test_gene.TestModelGene.test_core_gene) test getter/setter for core_gene property ... ok test_exhangeables (tests.test_gene.TestModelGene.test_exhangeables) ... ok test_hash (tests.test_gene.TestModelGene.test_hash) ... ok test_init (tests.test_gene.TestModelGene.test_init) ... ok test_inter_gene_max_space (tests.test_gene.TestModelGene.test_inter_gene_max_space) test getter for inter_gene_max_space property ... ok test_is_Forbidden (tests.test_gene.TestModelGene.test_is_Forbidden) test if gene belong to model mandatory genes ... ok test_is_accessory (tests.test_gene.TestModelGene.test_is_accessory) test if gene belong to model mandatory genes ... ok test_is_exchangeable (tests.test_gene.TestModelGene.test_is_exchangeable) ... ok test_is_mandatory (tests.test_gene.TestModelGene.test_is_mandatory) test if gene belong to model mandatory genes ... ok test_loner (tests.test_gene.TestModelGene.test_loner) test getter for loner property ... ok test_model (tests.test_gene.TestModelGene.test_model) test getter/setter for model property ... ok test_multi_model (tests.test_gene.TestModelGene.test_multi_model) test getter for multi_modelproperty ... ok test_multi_system (tests.test_gene.TestModelGene.test_multi_system) test getter for multi_system property ... ok test_str (tests.test_gene.TestModelGene.test_str) ... ok test_unknown_attribute (tests.test_gene.TestModelGene.test_unknown_attribute) ... ok test_cmp (tests.test_hit.CoreHitTest.test_cmp) ... ok test_eq (tests.test_hit.CoreHitTest.test_eq) ... ok test_get_position (tests.test_hit.CoreHitTest.test_get_position) ... ok test_hash (tests.test_hit.CoreHitTest.test_hash) ... ok test_str (tests.test_hit.CoreHitTest.test_str) ... ok test_compute_best_MSHit (tests.test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok test_get_best_hits (tests.test_hit.GetBestHitTest.test_get_best_hits) ... ok test_get_best_hits_4_func (tests.test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok test_sort_multisystem_hits (tests.test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok test_hit_weight_default (tests.test_hit.HitWeightTest.test_hit_weight_default) ... ok test_hit_weight_not_default (tests.test_hit.HitWeightTest.test_hit_weight_not_default) ... ok test_counterpart (tests.test_hit.LonerMultiSystemTest.test_counterpart) ... ok test_init (tests.test_hit.LonerMultiSystemTest.test_init) ... ok test_loner (tests.test_hit.LonerMultiSystemTest.test_loner) ... ok test_multi_system (tests.test_hit.LonerMultiSystemTest.test_multi_system) ... ok test_str (tests.test_hit.LonerMultiSystemTest.test_str) ... ok test_counterpart (tests.test_hit.LonerTest.test_counterpart) ... ok test_init (tests.test_hit.LonerTest.test_init) ... ok test_len (tests.test_hit.LonerTest.test_len) ... ok test_loner (tests.test_hit.LonerTest.test_loner) ... ok test_multi_system (tests.test_hit.LonerTest.test_multi_system) ... ok test_str (tests.test_hit.LonerTest.test_str) ... ok test_delegation (tests.test_hit.ModelHitTest.test_delegation) ... ok test_eq (tests.test_hit.ModelHitTest.test_eq) ... ok test_hash (tests.test_hit.ModelHitTest.test_hash) ... ok test_init (tests.test_hit.ModelHitTest.test_init) ... ok test_loner (tests.test_hit.ModelHitTest.test_loner) ... ok test_multi_model (tests.test_hit.ModelHitTest.test_multi_model) ... ok test_multi_system (tests.test_hit.ModelHitTest.test_multi_system) ... ok test_counterpart (tests.test_hit.MultiSystemTest.test_counterpart) ... ok test_init (tests.test_hit.MultiSystemTest.test_init) ... ok test_len (tests.test_hit.MultiSystemTest.test_len) ... ok test_loner (tests.test_hit.MultiSystemTest.test_loner) ... ok test_multi_system (tests.test_hit.MultiSystemTest.test_multi_system) ... ok test_str (tests.test_hit.MultiSystemTest.test_str) ... ok test_functional_split (tests.test_macsy_gembase_split.TestSplit.test_functional_split) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpskh72t91/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_functional_split_out_error (tests.test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... ok test_functional_split_out_not_writable (tests.test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... ok test_functional_merge (tests.test_macsy_merge_results.TestMerge.test_functional_merge) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmppa3_5hgx/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_functional_merge_one_results_empty (tests.test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpp_i_jq9h/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_functional_merge_out_error (tests.test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... ok test_functional_merge_out_not_writable (tests.test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... ok test_functional_merge_results_empty (tests.test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpjt2d_f_0/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_get_warning (tests.test_macsy_merge_results.TestMerge.test_get_warning) ... ok test_merge_and_reindex_invalid_solid (tests.test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... ok test_add_comment (tests.test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok test_write (tests.test_macsyconfig.TestConfigParserWithComment.test_write) ... ok test_ask (tests.test_macsyconfig.TestMacsyconfig.test_ask) ... ok test_ask_bad_value (tests.test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok test_ask_default_is_sequence (tests.test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok test_ask_use_default (tests.test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok test_ask_value_is_sequence (tests.test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok test_check_bool (tests.test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok test_check_choice (tests.test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok test_check_dir (tests.test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok test_check_exe (tests.test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok test_check_file (tests.test_macsyconfig.TestMacsyconfig.test_check_file) ... ok test_check_float (tests.test_macsyconfig.TestMacsyconfig.test_check_float) ... ok test_check_positive_int (tests.test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok test_check_str (tests.test_macsyconfig.TestMacsyconfig.test_check_str) ... ok test_functional_dark_theme (tests.test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok test_functional_file_already_exists (tests.test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok test_parse_args (tests.test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok test_set_base_options (tests.test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok test_set_general_options (tests.test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok test_set_hmmer_options (tests.test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok test_set_path_options (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok test_set_path_options_with_system_models_dir (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok test_set_score_options (tests.test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok test_set_section (tests.test_macsyconfig.TestMacsyconfig.test_set_section) ... ok test_set_section_use_defaults (tests.test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok test_available (tests.test_macsydata.TestMacsydata.test_available) ... ok test_build_argparser (tests.test_macsydata.TestMacsydata.test_build_argparser) ... ok test_check (tests.test_macsydata.TestMacsydata.test_check) ... ok test_check_with_errors (tests.test_macsydata.TestMacsydata.test_check_with_errors) ... ok test_check_with_warnings (tests.test_macsydata.TestMacsydata.test_check_with_warnings) ... ok test_cite (tests.test_macsydata.TestMacsydata.test_cite) ... ok test_cmd_name (tests.test_macsydata.TestMacsydata.test_cmd_name) ... ok test_definition_all_def (tests.test_macsydata.TestMacsydata.test_definition_all_def) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbm0ikmep/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbm0ikmep/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_definition_bad_def (tests.test_macsydata.TestMacsydata.test_definition_bad_def) ... ok test_definition_bad_pack (tests.test_macsydata.TestMacsydata.test_definition_bad_pack) ... ok test_definition_bad_subfamily (tests.test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... ok test_definition_models_dir (tests.test_macsydata.TestMacsydata.test_definition_models_dir) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmplrn8_h5p/model_dir/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmplrn8_h5p/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_definition_one_def (tests.test_macsydata.TestMacsydata.test_definition_one_def) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpc9pjq7iy/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpc9pjq7iy/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_download (tests.test_macsydata.TestMacsydata.test_download) ... ok test_freeze (tests.test_macsydata.TestMacsydata.test_freeze) ... ok test_help (tests.test_macsydata.TestMacsydata.test_help) ... ok test_info (tests.test_macsydata.TestMacsydata.test_info) ... ok test_init_dir_exists_look_pack (tests.test_macsydata.TestMacsydata.test_init_dir_exists_look_pack) ... skipped 'GitPython is not installed' test_init_dir_exists_not_pack (tests.test_macsydata.TestMacsydata.test_init_dir_exists_not_pack) ... skipped 'GitPython is not installed' test_init_empty_dir_exists (tests.test_macsydata.TestMacsydata.test_init_empty_dir_exists) ... skipped 'GitPython is not installed' test_init_existing_file (tests.test_macsydata.TestMacsydata.test_init_existing_file) ... ok test_init_existing_pack (tests.test_macsydata.TestMacsydata.test_init_existing_pack) ... skipped 'GitPython is not installed' test_init_package_complete (tests.test_macsydata.TestMacsydata.test_init_package_complete) ... skipped 'GitPython is not installed' test_init_package_minimal (tests.test_macsydata.TestMacsydata.test_init_package_minimal) ... skipped 'GitPython is not installed' test_install_bad_target (tests.test_macsydata.TestMacsydata.test_install_bad_target) ... ok test_install_installed_package_corrupted (tests.test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/package.py:110: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. tar.extractall(path, members, numeric_owner=numeric_owner) ok test_install_local (tests.test_macsydata.TestMacsydata.test_install_local) ... ok test_install_local_already_installed (tests.test_macsydata.TestMacsydata.test_install_local_already_installed) ... ok test_install_local_already_installed_force (tests.test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... ok test_install_remote (tests.test_macsydata.TestMacsydata.test_install_remote) ... ok test_install_remote_already_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... ok test_install_remote_already_in_local_force (tests.test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... ok test_install_remote_lower_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... ok test_install_remote_permision_error (tests.test_macsydata.TestMacsydata.test_install_remote_permision_error) ... ok test_install_remote_spec_not_found (tests.test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... ok test_install_remote_upper_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... ok test_install_target (tests.test_macsydata.TestMacsydata.test_install_target) ... ok test_list (tests.test_macsydata.TestMacsydata.test_list) ... ok test_list_long (tests.test_macsydata.TestMacsydata.test_list_long) ... ok test_list_outdated (tests.test_macsydata.TestMacsydata.test_list_outdated) ... ok test_list_uptodate (tests.test_macsydata.TestMacsydata.test_list_uptodate) ... ok test_list_verbose (tests.test_macsydata.TestMacsydata.test_list_verbose) ... ok test_no_subcommand (tests.test_macsydata.TestMacsydata.test_no_subcommand) ... ok test_search_in_pack_desc (tests.test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok test_search_in_pack_desc_match_case (tests.test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok test_search_in_pack_name (tests.test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok test_search_in_pack_name_match_case (tests.test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok test_search_reach_limit (tests.test_macsydata.TestMacsydata.test_search_reach_limit) ... ok test_uninstall (tests.test_macsydata.TestMacsydata.test_uninstall) ... ok test_verbosity_to_log_level (tests.test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok test_likely_systems_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok test_likely_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok test_loners_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok test_multisystem_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok test_rejected_candidates_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok test_rejected_candidates_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok test_solutions_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok test_summary_best_solution (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok test_summary_best_solution_empty (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok test_summary_best_solution_lack_models (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok test_summary_best_solution_lack_models_replicons (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok test_summary_best_solution_lack_replicon (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok test_systems_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok test_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok test_unnlikely_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok test_LightHit (tests.test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok test_build_my_db (tests.test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok test_fill_my_db (tests.test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok test_functional (tests.test_macsyprofile.TestMacsyprofile.test_functional) ... ok test_functional_best_score (tests.test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok test_functional_coverage (tests.test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok test_functional_evalue (tests.test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok test_functional_no_hits (tests.test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok test_functional_no_previous_run (tests.test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... ok test_functional_old_conf (tests.test_macsyprofile.TestMacsyprofile.test_functional_old_conf) ... ok test_functional_out_exists (tests.test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... ok test_functional_pattern (tests.test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok test_getProfile_len (tests.test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok test_get_gene_name (tests.test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok test_header (tests.test_macsyprofile.TestMacsyprofile.test_header) ... ok test_hit_start (tests.test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok test_parse (tests.test_macsyprofile.TestMacsyprofile.test_parse) ... ok test_parse_hmm_body (tests.test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok test_parse_hmm_header (tests.test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok test_pasre_args (tests.test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok test_verbosity_to_log_level (tests.test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok test_init_logger_default (tests.test_macsypy.Test.test_init_logger_default) ... ok test_init_logger_logfile (tests.test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpuq2iecb_' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_init_logger_no_out (tests.test_macsypy.Test.test_init_logger_no_out) ... ok test_logger_set_level_bad_level (tests.test_macsypy.Test.test_logger_set_level_bad_level) ... ok test_logger_set_level_default (tests.test_macsypy.Test.test_logger_set_level_default) ... ok test_logger_set_level_error (tests.test_macsypy.Test.test_logger_set_level_error) ... ok test_logger_set_level_handlers (tests.test_macsypy.Test.test_logger_set_level_handlers) ... ok test_cite (tests.test_metadata.TestMetadata.test_cite) ... ok test_copyright (tests.test_metadata.TestMetadata.test_copyright) ... ok test_doc (tests.test_metadata.TestMetadata.test_doc) ... ok test_init (tests.test_metadata.TestMetadata.test_init) ... ok test_license (tests.test_metadata.TestMetadata.test_license) ... ok test_load (tests.test_metadata.TestMetadata.test_load) ... ok test_maintainer (tests.test_metadata.TestMetadata.test_maintainer) ... ok test_save (tests.test_metadata.TestMetadata.test_save) ... ok test_short_desc (tests.test_metadata.TestMetadata.test_short_desc) ... ok test_vers (tests.test_metadata.TestMetadata.test_vers) ... ok test_parse (tests.test_model_conf_parser.TestModelConfParser.test_parse) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:59: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if weights_node: /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. if filtering_node: ok test_parse_bad_file (tests.test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... ok test_parse_filtering (tests.test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... ok test_parse_w_bad_value (tests.test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... ok test_parse_w_unkown_tag (tests.test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... ok test_parse_weights (tests.test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok test_parse_wo_filtering (tests.test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok test_parse_wo_weights (tests.test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok test_init (tests.test_package.TestLocalModelIndex.test_init) ... ok test_repos_url (tests.test_package.TestLocalModelIndex.test_repos_url) ... ok test_init (tests.test_package.TestModelIndex.test_init) ... ok test_check (tests.test_package.TestPackage.test_check) ... ok test_check_bad_metadata (tests.test_package.TestPackage.test_check_bad_metadata) ... ok test_check_metadata (tests.test_package.TestPackage.test_check_metadata) ... ok test_check_metadata_no_cite (tests.test_package.TestPackage.test_check_metadata_no_cite) ... ok test_check_metadata_no_copyright (tests.test_package.TestPackage.test_check_metadata_no_copyright) ... ok test_check_metadata_no_desc (tests.test_package.TestPackage.test_check_metadata_no_desc) ... ok test_check_metadata_no_doc (tests.test_package.TestPackage.test_check_metadata_no_doc) ... ok test_check_metadata_no_email (tests.test_package.TestPackage.test_check_metadata_no_email) ... ok test_check_metadata_no_license (tests.test_package.TestPackage.test_check_metadata_no_license) ... ok test_check_metadata_no_maintainer (tests.test_package.TestPackage.test_check_metadata_no_maintainer) ... ok test_check_metadata_no_name (tests.test_package.TestPackage.test_check_metadata_no_name) ... ok test_check_metadata_no_vers (tests.test_package.TestPackage.test_check_metadata_no_vers) ... ok test_check_metadata_with_vers (tests.test_package.TestPackage.test_check_metadata_with_vers) ... ok test_check_model_conf (tests.test_package.TestPackage.test_check_model_conf) ... ok test_check_model_conf_bad_conf (tests.test_package.TestPackage.test_check_model_conf_bad_conf) ... ok test_check_model_conf_no_conf (tests.test_package.TestPackage.test_check_model_conf_no_conf) ... ok test_check_model_consistency (tests.test_package.TestPackage.test_check_model_consistency) ... ok test_check_model_consistency_bad_definitions (tests.test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok test_check_model_consistency_extra_profile (tests.test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok test_check_model_consistency_lack_one_profile (tests.test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok test_check_no_readme_n_no_license (tests.test_package.TestPackage.test_check_no_readme_n_no_license) ... ok test_check_poor_quality_metadata (tests.test_package.TestPackage.test_check_poor_quality_metadata) ... ok test_check_structure (tests.test_package.TestPackage.test_check_structure) ... ok test_check_structure_bad_path (tests.test_package.TestPackage.test_check_structure_bad_path) ... ok test_check_structure_no_def (tests.test_package.TestPackage.test_check_structure_no_def) ... ok test_check_structure_no_license (tests.test_package.TestPackage.test_check_structure_no_license) ... ok test_check_structure_no_metadata (tests.test_package.TestPackage.test_check_structure_no_metadata) ... ok test_check_structure_no_profiles (tests.test_package.TestPackage.test_check_structure_no_profiles) ... ok test_check_structure_no_readme (tests.test_package.TestPackage.test_check_structure_no_readme) ... ok test_find_readme (tests.test_package.TestPackage.test_find_readme) ... ok test_help (tests.test_package.TestPackage.test_help) ... ok test_info (tests.test_package.TestPackage.test_info) ... ok test_info_no_citation (tests.test_package.TestPackage.test_info_no_citation) ... ok test_info_no_doc (tests.test_package.TestPackage.test_info_no_doc) ... ok test_info_no_license (tests.test_package.TestPackage.test_info_no_license) ... ok test_init (tests.test_package.TestPackage.test_init) ... ok test_metadata (tests.test_package.TestPackage.test_metadata) ... ok test_parse_arch_path (tests.test_package.TestPackageFunc.test_parse_arch_path) ... ok test_download (tests.test_package.TestRemoteModelIndex.test_download) ... ok test_get_metadata (tests.test_package.TestRemoteModelIndex.test_get_metadata) ... ok test_init (tests.test_package.TestRemoteModelIndex.test_init) ... ok test_list_package_vers (tests.test_package.TestRemoteModelIndex.test_list_package_vers) ... ok test_list_packages (tests.test_package.TestRemoteModelIndex.test_list_packages) ... ok test_remote_exists (tests.test_package.TestRemoteModelIndex.test_remote_exists) ... ok test_repos_url (tests.test_package.TestRemoteModelIndex.test_repos_url) ... ok test_unarchive (tests.test_package.TestRemoteModelIndex.test_unarchive) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.12/build/macsypy/package.py:110: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. tar.extractall(path, members, numeric_owner=numeric_owner) ok test_url_json (tests.test_package.TestRemoteModelIndex.test_url_json) ... ok test_url_json_reach_limit (tests.test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok test_DefinitionLocationn (tests.test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok test_add_submodel (tests.test_registries.DefinitionLocationTest.test_add_submodel) ... ok test_all (tests.test_registries.DefinitionLocationTest.test_all) ... ok test_eq (tests.test_registries.DefinitionLocationTest.test_eq) ... ok test_family_name (tests.test_registries.DefinitionLocationTest.test_family_name) ... ok test_greater (tests.test_registries.DefinitionLocationTest.test_greater) ... ok test_hash (tests.test_registries.DefinitionLocationTest.test_hash) ... ok test_lesser (tests.test_registries.DefinitionLocationTest.test_lesser) ... ok test_root_name (tests.test_registries.DefinitionLocationTest.test_root_name) ... ok test_separator (tests.test_registries.DefinitionLocationTest.test_separator) ... ok test_split_fqn (tests.test_registries.DefinitionLocationTest.test_split_fqn) ... ok test_str (tests.test_registries.DefinitionLocationTest.test_str) ... ok test_ModelLocation (tests.test_registries.ModelLocationTest.test_ModelLocation) ... ok test_get_all_definitions (tests.test_registries.ModelLocationTest.test_get_all_definitions) ... ok test_get_definition (tests.test_registries.ModelLocationTest.test_get_definition) ... ok test_get_definitions (tests.test_registries.ModelLocationTest.test_get_definitions) ... ok test_get_profile (tests.test_registries.ModelLocationTest.test_get_profile) ... ok test_get_profiles_names (tests.test_registries.ModelLocationTest.test_get_profiles_names) ... ok test_str (tests.test_registries.ModelLocationTest.test_str) ... ok test_version (tests.test_registries.ModelLocationTest.test_version) ... ok test_version_no_metadata (tests.test_registries.ModelLocationTest.test_version_no_metadata) ... ok test_add_get (tests.test_registries.ModelRegistryTest.test_add_get) ... ok test_models (tests.test_registries.ModelRegistryTest.test_models) ... ok test_scan_models_dir (tests.test_registries.ModelRegistryTest.test_scan_models_dir) ... ok test_str (tests.test_registries.ModelRegistryTest.test_str) ... ok test_search (tests.test_search_genes.TestSearchGenes.test_search) ... ok test_search_fail (tests.test_search_genes.TestSearchGenes.test_search_fail) ... ok test_search_recover (tests.test_search_genes.TestSearchGenes.test_search_recover) ... ok test_worker_cpu (tests.test_search_genes.TestSearchGenes.test_worker_cpu) ... ok test_LikelySystemSerializer_txt (tests.test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok test_RejectedClusters_tsv (tests.test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok test_SolutionSerializer_tsv (tests.test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok test_SpecialHitSerializer_tsv (tests.test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok test_SystemSerializer_str (tests.test_serialization.SerializationTest.test_SystemSerializer_str) ... ok test_SystemSerializer_tsv (tests.test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok test_UnlikelySystemSerializer_txt (tests.test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok test_combine_clusters (tests.test_solution.SolutionExplorerTest.test_combine_clusters) ... ok test_combine_multisystems (tests.test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok test_find_best_solution (tests.test_solution.SolutionExplorerTest.test_find_best_solution) ... ok test_average_wholeness (tests.test_solution.SolutionTest.test_average_wholeness) ... ok test_gt (tests.test_solution.SolutionTest.test_gt) ... ok test_hits_number (tests.test_solution.SolutionTest.test_hits_number) ... ok test_hits_positions (tests.test_solution.SolutionTest.test_hits_positions) ... ok test_iteration (tests.test_solution.SolutionTest.test_iteration) ... ok test_lt (tests.test_solution.SolutionTest.test_lt) ... ok test_score (tests.test_solution.SolutionTest.test_score) ... ok test_sorting (tests.test_solution.SolutionTest.test_sorting) ... ok test_systems (tests.test_solution.SolutionTest.test_systems) ... ok test_get_def_to_detect (tests.test_utils.TestUtils.test_get_def_to_detect) ... ok test_get_replicon_names_bad_type (tests.test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok test_get_replicon_names_gembase (tests.test_utils.TestUtils.test_get_replicon_names_gembase) ... ok test_get_replicon_names_ordered (tests.test_utils.TestUtils.test_get_replicon_names_ordered) ... ok test_get_replicon_names_unordered (tests.test_utils.TestUtils.test_get_replicon_names_unordered) ... ok test_parse_time (tests.test_utils.TestUtils.test_parse_time) ... ok test_threads_available (tests.test_utils.TestUtils.test_threads_available) ... ok ---------------------------------------------------------------------- Ran 540 tests in 19.204s OK (skipped=8) create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/macsyfinder/ -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir I: pybuild pybuild:334: cp -a /build/reproducible-path/macsyfinder-2.1.4/debian/etc /build/reproducible-path/macsyfinder-2.1.4/debian/macsyfinder/etc && cd /build/reproducible-path/macsyfinder-2.1.4/doc && make html latexpdf make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.1.4/doc' Running Sphinx v7.4.7 loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 44 source files that are out of date updating environment: [new config] 44 added, 0 changed, 0 removed reading sources... [ 2%] developer_guide/api/cluster reading sources... [ 5%] developer_guide/api/config reading sources... [ 7%] developer_guide/api/database reading sources... [ 9%] developer_guide/api/definition_parser reading sources... [ 11%] developer_guide/api/error reading sources... [ 14%] developer_guide/api/gene reading sources... [ 16%] developer_guide/api/hit reading sources... [ 18%] developer_guide/api/index reading sources... [ 20%] developer_guide/api/model reading sources... [ 23%] developer_guide/api/model_conf_parser reading sources... [ 25%] developer_guide/api/package reading sources... [ 27%] developer_guide/api/profile reading sources... [ 30%] developer_guide/api/registries reading sources... [ 32%] developer_guide/api/report reading sources... [ 34%] developer_guide/api/scripts /build/reproducible-path/macsyfinder-2.1.4/macsypy/scripts/macsydata.py:56: UserWarning: GitPython is not installed, `macsydata init` is disabled () To turn this feature ON: - install git - then run `python -m pip install macsyfinder[model]` in your activated environment. warnings.warn("GitPython is not installed, `macsydata init` is disabled ()\n" reading sources... [ 36%] developer_guide/api/search_genes reading sources... [ 39%] developer_guide/api/serialization reading sources... [ 41%] developer_guide/api/solution reading sources... [ 43%] developer_guide/api/system reading sources... [ 45%] developer_guide/api/utils reading sources... [ 48%] developer_guide/index reading sources... [ 50%] developer_guide/installation reading sources... [ 52%] developer_guide/overview reading sources... [ 55%] index reading sources... [ 57%] modeler_guide/FAQ_modeler reading sources... [ 59%] modeler_guide/gallery reading sources... [ 61%] modeler_guide/helper_tools reading sources... [ 64%] modeler_guide/index reading sources... [ 66%] modeler_guide/installation reading sources... [ 68%] modeler_guide/modeling reading sources... [ 70%] modeler_guide/models_V1ToV2 reading sources... [ 73%] modeler_guide/package reading sources... [ 75%] modeler_guide/publish_package reading sources... [ 77%] user_guide/FAQ reading sources... [ 80%] user_guide/big_data reading sources... [ 82%] user_guide/functioning reading sources... [ 84%] user_guide/gembase_convention reading sources... [ 86%] user_guide/index reading sources... [ 89%] user_guide/input reading sources... [ 91%] user_guide/installation reading sources... [ 93%] user_guide/model_definition reading sources... [ 95%] user_guide/new_v2 reading sources... [ 98%] user_guide/outputs reading sources... [100%] user_guide/quickstart /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:8: ERROR: Unexpected indentation. /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:10: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:11: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/cluster.py:docstring of macsypy.cluster.Cluster.functions:12: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/gene.py:docstring of macsypy.gene.ModelGene.multi_model:3: WARNING: Definition list ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: ERROR: Unexpected indentation. /build/reproducible-path/macsyfinder-2.1.4/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:4: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/macsyfinder-2.1.4/macsypy/system.py:docstring of macsypy.system.MatchMaker.present_genes:4: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying downloadable files... [ 50%] _static/code/pre-push copying downloadable files... [100%] _static/msf_summary.py copying static files... done copying extra files... done copying assets: done writing output... [ 2%] developer_guide/api/cluster writing output... [ 5%] developer_guide/api/config writing output... [ 7%] developer_guide/api/database writing output... [ 9%] developer_guide/api/definition_parser writing output... [ 11%] developer_guide/api/error writing output... [ 14%] developer_guide/api/gene writing output... [ 16%] developer_guide/api/hit writing output... [ 18%] developer_guide/api/index writing output... [ 20%] developer_guide/api/model writing output... [ 23%] developer_guide/api/model_conf_parser writing output... [ 25%] developer_guide/api/package writing output... [ 27%] developer_guide/api/profile writing output... [ 30%] developer_guide/api/registries writing output... [ 32%] developer_guide/api/report writing output... [ 34%] developer_guide/api/scripts writing output... [ 36%] developer_guide/api/search_genes writing output... [ 39%] developer_guide/api/serialization writing output... [ 41%] developer_guide/api/solution writing output... [ 43%] developer_guide/api/system writing output... [ 45%] developer_guide/api/utils writing output... [ 48%] developer_guide/index writing output... [ 50%] developer_guide/installation writing output... [ 52%] developer_guide/overview writing output... [ 55%] index writing output... [ 57%] modeler_guide/FAQ_modeler writing output... [ 59%] modeler_guide/gallery writing output... [ 61%] modeler_guide/helper_tools writing output... [ 64%] modeler_guide/index writing output... [ 66%] modeler_guide/installation writing output... [ 68%] modeler_guide/modeling writing output... [ 70%] modeler_guide/models_V1ToV2 writing output... [ 73%] modeler_guide/package writing output... [ 75%] modeler_guide/publish_package writing output... [ 77%] user_guide/FAQ writing output... [ 80%] user_guide/big_data writing output... [ 82%] user_guide/functioning writing output... [ 84%] user_guide/gembase_convention writing output... [ 86%] user_guide/index writing output... [ 89%] user_guide/input writing output... [ 91%] user_guide/installation writing output... [ 93%] user_guide/model_definition writing output... [ 95%] user_guide/new_v2 writing output... [ 98%] user_guide/outputs writing output... [100%] user_guide/quickstart generating indices... genindex py-modindex done highlighting module code... [ 5%] macsypy.cluster highlighting module code... [ 9%] macsypy.config highlighting module code... [ 14%] macsypy.database highlighting module code... [ 18%] macsypy.definition_parser highlighting module code... [ 23%] macsypy.error highlighting module code... [ 27%] macsypy.gene highlighting module code... [ 32%] macsypy.hit highlighting module code... [ 36%] macsypy.model highlighting module code... [ 41%] macsypy.model_conf_parser highlighting module code... [ 45%] macsypy.package highlighting module code... [ 50%] macsypy.profile highlighting module code... [ 55%] macsypy.registries highlighting module code... [ 59%] macsypy.report highlighting module code... [ 64%] macsypy.scripts.macsyconfig highlighting module code... [ 68%] macsypy.scripts.macsydata highlighting module code... [ 73%] macsypy.scripts.macsyfinder highlighting module code... [ 77%] macsypy.scripts.macsyprofile highlighting module code... [ 82%] macsypy.search_genes highlighting module code... [ 86%] macsypy.serialization highlighting module code... [ 91%] macsypy.solution highlighting module code... [ 95%] macsypy.system highlighting module code... [100%] macsypy.utils writing additional pages... search done copying images... [ 6%] _static/gene_obj_interaction.svg copying images... [ 12%] _static/macsyfinder_classes.svg copying images... [ 19%] _static/logo_macsyfinder.png copying images... [ 25%] _static/figure_main-2.svg copying images... [ 31%] _static/T1SS_example.svg copying images... [ 38%] _static/T3SS_example.svg copying images... [ 44%] _static/logo_macsymodels.png copying images... [ 50%] _static/MSF_modelling.svg copying images... [ 56%] _static/loner.svg copying images... [ 62%] _static/multi_system.svg copying images... [ 69%] _static/multi_model.svg copying images... [ 75%] _static/msf_functionning_step1.svg copying images... [ 81%] _static/msf_functionning_step2.svg copying images... [ 88%] _static/msf_functionning_step3.svg copying images... [ 94%] _static/msf_functionning_step4.svg copying images... [100%] _static/msf_functionning_step5.svg dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 8 warnings. The HTML pages are in build/html. Running Sphinx v7.4.7 loading translations [en]... done making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found copying TeX support files... copying TeX support files... done processing macsyfinder.tex... index user_guide/index user_guide/new_v2 user_guide/installation user_guide/quickstart user_guide/input user_guide/gembase_convention user_guide/outputs user_guide/big_data user_guide/model_definition user_guide/functioning user_guide/FAQ modeler_guide/index modeler_guide/installation modeler_guide/package modeler_guide/modeling modeler_guide/helper_tools modeler_guide/publish_package modeler_guide/gallery modeler_guide/models_V1ToV2 modeler_guide/FAQ_modeler developer_guide/index developer_guide/installation developer_guide/overview developer_guide/api/index developer_guide/api/config developer_guide/api/model_conf_parser developer_guide/api/registries developer_guide/api/definition_parser developer_guide/api/model developer_guide/api/gene developer_guide/api/profile developer_guide/api/hit developer_guide/api/cluster developer_guide/api/system developer_guide/api/report developer_guide/api/search_genes developer_guide/api/solution developer_guide/api/serialization developer_guide/api/database developer_guide/api/error developer_guide/api/utils developer_guide/api/package developer_guide/api/scripts resolving references... done writing... done copying images... [ 6%] _static/logo_macsyfinder.png copying images... [ 12%] _static/figure_main-2.png copying images... [ 19%] _static/msf_functionning_step1.pdf copying images... [ 25%] _static/msf_functionning_step2.pdf copying images... [ 31%] _static/msf_functionning_step3.pdf copying images... [ 38%] _static/msf_functionning_step4.pdf copying images... [ 44%] _static/msf_functionning_step5.pdf copying images... [ 50%] _static/logo_macsymodels.png copying images... [ 56%] _static/MSF_modelling.pdf copying images... [ 62%] _static/loner.pdf copying images... [ 69%] _static/multi_system.pdf copying images... [ 75%] _static/multi_model.pdf copying images... [ 81%] _static/T1SS_example.pdf copying images... [ 88%] _static/T3SS_example.pdf copying images... [ 94%] _static/macsyfinder_classes.pdf copying images... [100%] _static/gene_obj_interaction.pdf 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-2.1.4/doc/build/latex' latexmk -pdf -dvi- -ps- 'macsyfinder.tex' Rc files read: /etc/LatexMk latexmkrc Latexmk: This is Latexmk, John Collins, 7 Apr. 2024. Version 4.85. No existing .aux file, so I'll make a simple one, and require run of *latex. Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Category 'other': Rerun of 'pdflatex' forced or previously required: Reason or flag: 'Initial setup' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2024-11-01> L3 programming layer <2024-11-02> (./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 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxpackageboxes.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty)) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)) (./sphinxlatexnumfig.sty) (./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty ) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip-2001-04-09.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)) (./sphinxmessages.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) Writing index file macsyfinder.idx (/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./macsyfinder.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texmf/fonts/en c/dvips/tex-gyre/q-ec.enc}] [2] No file macsyfinder.toc. [1] [2] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) LaTeX Warning: Hyper reference `user_guide/new_v2:new-v2' on page 1 undefined o n input line 91. LaTeX Warning: Hyper reference `modeler_guide/models_V1ToV2:models-v1-v2' on pa ge 1 undefined on input line 94. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o n page 1 undefined on input line 133. Underfull \hbox (badness 5331) in paragraph at lines 148--154 \T1/qtm/m/n/10 phie S. Mac-SyFinder v2: Im-proved mod-elling and search en-gine to iden-tify molec-u-lar sys-tems in [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} <./logo_macsyfinder.png >] [2 <./figure_main-2.png>] Chapter 1. [3] [4] LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 5 u ndefined on input line 354. [5] LaTeX Warning: Hyper reference `modeler_guide/modeling:components' on page 6 un defined on input line 366. LaTeX Warning: Hyper reference `modeler_guide/modeling:multi-model-label' on pa ge 6 undefined on input line 370. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 6 undef ined on input line 374. LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag e 6 undefined on input line 378. LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 6 un defined on input line 382. LaTeX Warning: Hyper reference `modeler_guide/models_V1ToV2:models-v1-v2' on pa ge 6 undefined on input line 386. LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 6 undefined on input line 395. LaTeX Warning: Hyper reference `user_guide/installation:user-dependencies' on p age 6 undefined on input line 404. LaTeX Warning: Hyper reference `modeler_guide/index:modeler-guide' on page 6 un defined on input line 412. [6] LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 7 un defined on input line 418. LaTeX Warning: Hyper reference `modeler_guide/package:model-configuration' on p age 7 undefined on input line 424. LaTeX Warning: Hyper reference `modeler_guide/helper_tools:macsyprofile' on pag e 7 undefined on input line 431. LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 7 un defined on input line 434. LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 7 un defined on input line 453. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 7 undef ined on input line 474. [7] LaTeX Warning: Hyper reference `developer_guide/installation:dev-installation' on page 8 undefined on input line 516. LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa ge 8 undefined on input line 582. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 8 undef ined on input line 583. [8] [9] [10] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 765. [11] LaTeX Warning: Hyper reference `user_guide/installation:user-installation' on p age 12 undefined on input line 896. LaTeX Warning: Hyper reference `user_guide/input:input-dataset-label' on page 1 2 undefined on input line 913. LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o n page 12 undefined on input line 919. LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 12 u ndefined on input line 921. [12] LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 13 undefined on input line 933. Underfull \hbox (badness 10000) in paragraph at lines 948--950 []\T1/txtt/m/n/10 macsyfinder [][]db[]type unordered [][]sequence[]db unordered _genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 959--961 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir Underfull \hbox (badness 10000) in paragraph at lines 971--973 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag e 13 undefined on input line 976. LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 13 undefined on input line 990. [13] Overfull \hbox (57.99365pt too wide) in paragraph at lines 1035--1039 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_ordered Overfull \hbox (68.49362pt too wide) in paragraph at lines 1045--1048 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_unordered Underfull \hbox (badness 10000) in paragraph at lines 1045--1048 [][]\T1/txtt/m/n/10 models TXSScan all [][]db[]type unordered []w 8 \T1/qtm/m/i t/10 # spec-i-fied out-put folder: mac- LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 14 undefine d on input line 1050. LaTeX Warning: Hyper reference `user_guide/FAQ:faq-search-mode' on page 14 unde fined on input line 1051. LaTeX Warning: Hyper reference `user_guide/input:config-base-label' on page 14 undefined on input line 1073. LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa ge 14 undefined on input line 1073. LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 14 undefined on input line 1076. LaTeX Warning: Hyper reference `user_guide/input:cmd-input-label' on page 14 un defined on input line 1076. LaTeX Warning: Hyper reference `user_guide/gembase_convention:gembase-conventio n' on page 14 undefined on input line 1095. LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 14 undefined on input line 1107. LaTeX Warning: Hyper reference `user_guide/input:cmd-input-label' on page 14 un defined on input line 1108. LaTeX Warning: Hyper reference `user_guide/input:config-base-label' on page 14 undefined on input line 1109. LaTeX Warning: Hyper reference `user_guide/gembase_convention:gembase-conventio n' on page 14 undefined on input line 1113. LaTeX Warning: Hyper reference `user_guide/gembase_convention:topology-files' o n page 14 undefined on input line 1113. [14] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \vbox (2.56042pt too high) detected at line 1174 [15] [16] Underfull \vbox (badness 1226) detected at line 1267 [17] [18] LaTeX Warning: Hyper reference `user_guide/FAQ:cmd-line-examples' on page 19 un defined on input line 1334. LaTeX Warning: Hyper reference `user_guide/quickstart:quickstart' on page 19 un defined on input line 1334. LaTeX Warning: Hyper reference `developer_guide/api/config:configuration' on pa ge 19 undefined on input line 1351. [19] LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 20 undefined on input line 1410. LaTeX Warning: Hyper reference `developer_guide/api/config:configuration' on pa ge 20 undefined on input line 1414. [20] [21] LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 22 undefine d on input line 1693. [22] [23] LaTeX Warning: Hyper reference `user_guide/outputs:ordered-outputs' on page 24 undefined on input line 1837. LaTeX Warning: Hyper reference `user_guide/outputs:unordered-outputs' on page 2 4 undefined on input line 1837. LaTeX Warning: Hyper reference `user_guide/outputs:hmmer-outputs-label' on page 24 undefined on input line 1841. LaTeX Warning: Hyper reference `user_guide/outputs:logs-and-conf' on page 24 un defined on input line 1845. [24] LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 2 5 undefined on input line 1872. LaTeX Warning: Hyper reference `user_guide/outputs:sort-eqt-best-solution' on p age 25 undefined on input line 1874. LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 2 5 undefined on input line 1877. Underfull \hbox (badness 5417) in paragraph at lines 1876--1878 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-loners-tsv' on page 25 undefined on input line 1887. LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-multisystems-t sv' on page 25 undefined on input line 1887. LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-summary-tsv' o n page 25 undefined on input line 1893. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt' on page 25 undefined on input line 1897. LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-tsv' on page 25 undefined on input line 1903. LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-txt' on page 25 undefined on input line 1903. LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-tsv' on page 25 undefined on input line 1905. LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 2 5 undefined on input line 1909. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 25 undefined on input line 1914. [25] LaTeX Warning: Hyper reference `user_guide/functioning:combinatorial-exploratio n' on page 26 undefined on input line 1997. [26] Underfull \vbox (badness 10000) detected at line 2089 Underfull \vbox (badness 10000) detected at line 2089 [27] [28] [29] LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 30 undefined on input line 2248. [30] [31] Underfull \vbox (badness 1226) detected at line 2406 [32] Underfull \vbox (badness 10000) detected at line 2406 Underfull \vbox (badness 10000) detected at line 2406 [33] [34] [35] [36] Overfull \vbox (1.17242pt too high) detected at line 2591 [37] Overfull \vbox (0.91234pt too high) detected at line 2638 [38] Overfull \vbox (1.73233pt too high) detected at line 2761 [39] Underfull \vbox (badness 10000) detected at line 2761 Underfull \vbox (badness 10000) detected at line 2761 [40] LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 4 1 undefined on input line 2771. LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-summary-tsv' o n page 41 undefined on input line 2775. LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 4 1 undefined on input line 2779. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 41 undefined on input line 2783. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt' on page 41 undefined on input line 2783. LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-tsv' on page 41 undefined on input line 2787. LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-txt' on page 41 undefined on input line 2787. [41] LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt-unordered' o n page 42 undefined on input line 2816. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv-unordered' o n page 42 undefined on input line 2820. LaTeX Warning: Hyper reference `user_guide/outputs:uncomplete-unordered' on pag e 42 undefined on input line 2824. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt' on page 42 undefined on input line 2841. [42] LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 43 undefined on input line 2897. [43] Underfull \vbox (badness 10000) detected at line 2936 Underfull \vbox (badness 10000) detected at line 2936 [44] Overfull \vbox (1.17242pt too high) detected at line 2989 [45] [46] pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed LaTeX Warning: Hyper reference `user_guide/installation:user-installation' on p age 47 undefined on input line 3097. [47 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz-bb320 290fa50a2c64c42d68cab416461f9843641.pdf pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag e >] [48] LaTeX Warning: Hyper reference `user_guide/input:general-options' on page 49 un defined on input line 3233. [49] [50] [51] [52] LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 53 undefined on input line 3531. LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 53 undefined on input line 3532. LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 53 undefined on input line 3539. LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa ge 53 undefined on input line 3543. LaTeX Warning: Hyper reference `modeler_guide/index:modeler-guide' on page 53 u ndefined on input line 3553. [53] [54] LaTeX Warning: Hyper reference `user_guide/input:path-options' on page 55 undef ined on input line 3646. LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag e 55 undefined on input line 3654. LaTeX Warning: Hyper reference `user_guide/input:input-dataset-label' on page 5 5 undefined on input line 3666. LaTeX Warning: Hyper reference `modeler_guide/modeling:writing-models' on page 55 undefined on input line 3702. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 55 unde fined on input line 3706. LaTeX Warning: Hyper reference `developer_guide/api/report:hmmreport' on page 5 5 undefined on input line 3706. LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 55 undefined on input line 3708. LaTeX Warning: Hyper reference `developer_guide/api/search_genes:search-genes' on page 55 undefined on input line 3708. [55] LaTeX Warning: Hyper reference `user_guide/input:input-dataset-label' on page 5 6 undefined on input line 3719. LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-genomic -orga' on page 56 undefined on input line 3724. [56 <./msf_functionning_step1.pdf>] LaTeX Warning: Hyper reference `user_guide/functioning:combinatorial-exploratio n' on page 57 undefined on input line 3759. LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-txt' on page 57 undefined on input line 3763. LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv-unordered' o n page 57 undefined on input line 3793. [57 <./msf_functionning_step2.pdf>] LaTeX Warning: Hyper reference `user_guide/outputs:unordered-outputs' on page 5 8 undefined on input line 3805. LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 58 undefine d on input line 3844. LaTeX Warning: Hyper reference `user_guide/input:score-options' on page 58 unde fined on input line 3861. [58] [59 <./msf_functionning_step3.pdf> <./msf_functionning_step4.pdf pdfTeX warning: pdflatex (file ./msf_functionning_step4.pdf): PDF inclusion: mu ltiple pdfs with page group included in a single page >] [60 <./msf_functionning_step5.pdf>] [61] Underfull \hbox (badness 10000) in paragraph at lines 4063--4065 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4071--4073 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4079--4081 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4087--4089 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4098--4100 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir LaTeX Warning: Hyper reference `user_guide/quickstart:quickstart' on page 62 un defined on input line 4103. LaTeX Warning: Hyper reference `user_guide/gembase_convention:gembase-conventio n' on page 62 undefined on input line 4121. [62] LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 63 undefined on input line 4138. LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 63 undefined on input line 4138. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4176. [63] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4221. LaTeX Warning: Hyper reference `user_guide/outputs:ordered-outputs' on page 64 undefined on input line 4258. [64] LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 65 u ndefined on input line 4283. [65] [66] Chapter 2. LaTeX Warning: Hyper reference `modeler_guide/installation:modeler-macsydata' o n page 67 undefined on input line 4352. [67 <./logo_macsymodels.png>] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4393. [68] LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 69 undefined on input line 4527. LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 69 undefined on input line 4528. LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 69 undefined on input line 4535. LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa ge 69 undefined on input line 4539. [69] [70] [71] [72] LaTeX Warning: Hyper reference `user_guide/functioning:combinatorial-exploratio n' on page 73 undefined on input line 4842. LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 73 undefined on input line 4855. LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 73 undefined on input line 4856. LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 73 undefined on input line 4864. LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa ge 73 undefined on input line 4868. [73] LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 74 undefined on input line 4956. [74] LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa ge 75 undefined on input line 5025. [75 <./MSF_modelling.pdf>] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5045. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 58. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 61. Package wrapfig Warning: Collision between wrapping environments on input line 5067. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5067. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 79. [76 <./loner.pdf>] Package wrapfig Warning: Collision between wrapping environments on input line 5091. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5091. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 04. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 07. Overfull \vbox (19.57245pt too high) detected at line 5188 [77 <./multi_system.pdf>] LaTeX Warning: Hyper reference `modeler_guide/gallery:gallery-models' on page 7 8 undefined on input line 5213. [78] LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa ge 79 undefined on input line 5275. [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5531--5536 \T1/txtt/m/n/10 models in conf file XXX. May be these results have been generat ed with an old version [83] LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag e 84 undefined on input line 5549. LaTeX Warning: Hyper reference `modeler_guide/package:model-package' on page 84 undefined on input line 5620. [84] Underfull \hbox (badness 10000) in paragraph at lines 5661--5663 [][][]$\T1/qtm/m/n/10 https : / / the-[]hitchhikers-[]guide-[]to-[]packaging . readthedocs . io / en / latest / speci^^\cation . html # [85] [86] LaTeX Warning: Hyper reference `modeler_guide/gallery:getting-started-with-a-on e-component-system-the-autotransporter-t5ss' on page 87 undefined on input line 5828. LaTeX Warning: Hyper reference `modeler_guide/gallery:a-not-so-simple-example-m odelling-the-t1ss' on page 87 undefined on input line 5832. LaTeX Warning: Hyper reference `modeler_guide/gallery:the-case-of-t3ss-and-bact erial-flagella-or-how-to-distinguish-homologous-cellular-machineries' on page 8 7 undefined on input line 5836. [87] [88] [89 <./T1SS_example.pdf>] LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 90 undefined on input line 5980. [90] Overfull \vbox (0.97131pt too high) detected at line 6075 [91 <./T3SS_example.pdf>] LaTeX Warning: Hyper reference `modeler_guide/models_V1ToV2:ex2' on page 92 und efined on input line 6129. [92] LaTeX Warning: Hyper reference `modeler_guide/publish_package:publish-package' on page 93 undefined on input line 6151. LaTeX Warning: Hyper reference `modeler_guide/package:model-package' on page 93 undefined on input line 6151. [93] [94] Underfull \vbox (badness 1226) detected at line 6332 [95] [96] LaTeX Warning: Hyper reference `modeler_guide/modeling:exchangeables-label' on page 97 undefined on input line 6423. [97 <./multi_model.pdf>] [98] Chapter 3. LaTeX Warning: Hyper reference `modeler_guide/installation:modeler-macsydata' o n page 99 undefined on input line 6440. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 99 unde fined on input line 6461. [99] LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa ge 100 undefined on input line 6542. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 100 und efined on input line 6543. [100] [101] pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [102 <./macsyfinder_classes.pdf>] LaTeX Warning: Hyper reference `developer_guide/api/config:configuration' on pa ge 103 undefined on input line 6746. LaTeX Warning: Hyper reference `developer_guide/api/solution:macsypy.solution.f ind_best_solutions' on page 103 undefined on input line 6813. Underfull \hbox (badness 10000) in paragraph at lines 6812--6817 []\T1/qtm/m/n/10 Among all this po-ten-tial sys-tems, MSF com-pute the best com -bi-na-tion. \T1/txtt/m/sl/10 macsypy.solution. [103] LaTeX Warning: Hyper reference `developer_guide/api/model:model' on page 104 un defined on input line 6822. LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar -label' on page 104 undefined on input line 6825. LaTeX Warning: Hyper reference `developer_guide/api/definition_parser:definitio n-parser' on page 104 undefined on input line 6828. LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o n page 104 undefined on input line 6856. LaTeX Warning: Hyper reference `developer_guide/api/gene:id1' on page 104 undef ined on input line 6863. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 104 undefined on input line 6864. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro file' on page 104 undefined on input line 6866. LaTeX Warning: Hyper reference `developer_guide/overview:profile-implementation ' on page 104 undefined on input line 6868. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 104 undefined on input line 6872. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 104 undefined on input line 6875. LaTeX Warning: Hyper reference `developer_guide/api/gene:id1' on page 104 undef ined on input line 6876. LaTeX Warning: Hyper reference `developer_guide/api/gene:exchangeable-api' on p age 104 undefined on input line 6882. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank' on page 104 undefined on input line 6888. [104] LaTeX Warning: Hyper reference `developer_guide/api/report:macsypy.report.HMMRe port' on page 105 undefined on input line 6905. LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 105 und efined on input line 6910. LaTeX Warning: Hyper reference `user_guide/outputs:hmmer-outputs-label' on page 105 undefined on input line 6911. LaTeX Warning: Hyper reference `developer_guide/api/hit:hit' on page 105 undefi ned on input line 6912. LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa ge 105 undefined on input line 6925. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy Defaults' on page 105 undefined on input line 6929. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 105 undefined on input line 6930. [105] LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy Defaults' on page 106 undefined on input line 6990. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy Defaults' on page 106 undefined on input line 7000. [106] [107] Underfull \hbox (badness 6775) in paragraph at lines 7341--7343 \T1/txtt/bx/n/10 options \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dictionary with opt ion name as keys and values as values\T1/qtm/m/n/10 ) ^^U [108] [109] [110] LaTeX Warning: Hyper reference `developer_guide/api/package:macsypy.package.Pac kage' on page 111 undefined on input line 7767. Underfull \hbox (badness 10000) in paragraph at lines 7868--7871 []\T1/txtt/bx/n/10 allowed_elements \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dict wit h options name as keys and function to [111] LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 112 undefined on input line 7981. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 112 undefined on input line 8037. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 112 undefined on input line 8052. [112] LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 113 undefined on input line 8084. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 113 undefined on input line 8096. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 113 undefined on input line 8143. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 113 undefined on input line 8179. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 113 undefined on input line 8179. [113] LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 114 undefined on input line 8242. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 114 undefined on input line 8266. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 114 undefined on input line 8296. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation.get_all_definitions' on page 114 undefined on input line 8302. [114] LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8384. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8399. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8411. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8435. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8444. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8480. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 8498. [115] LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 116 undefined on input line 8615. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 116 undefined on input line 8638. LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o n page 116 undefined on input line 8652. [116] [117] LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 118 undefined on input line 8787. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC onfig' on page 118 undefined on input line 8787. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.ModelBa nk' on page 118 undefined on input line 8787. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank' on page 118 undefined on input line 8787. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelRegistry' on page 118 undefined on input line 8787. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro fileFactory' on page 118 undefined on input line 8787. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 118 undefined on input line 8796. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC onfig' on page 118 undefined on input line 8796. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.ModelBa nk' on page 118 undefined on input line 8796. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank' on page 118 undefined on input line 8796. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelRegistry' on page 118 undefined on input line 8796. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro fileFactory' on page 118 undefined on input line 8796. LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.ModelIn consistencyError' on page 118 undefined on input line 8861. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 118 undefined on input line 8872. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 118 undefined on input line 8872. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 118 undefined on input line 8898. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 118 undefined on input line 8898. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 118 undefined on input line 8927. [118] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 119 undefined on input line 8942. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 119 undefined on input line 8942. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.Exchangea ble' on page 119 undefined on input line 8942. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 119 undefined on input line 8975. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 119 undefined on input line 9001. LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.ModelIn consistencyError' on page 119 undefined on input line 9013. [119{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}] LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 120 undefined on input line 9105. [120] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 121 undefined on input line 9213. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 121 undefined on input line 9235. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 121 undefined on input line 9309. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 121 undefined on input line 9361. [121] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 122 undefined on input line 9381. LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.ModelIn consistencyError' on page 122 undefined on input line 9449. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 122 undefined on input line 9461. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 122 undefined on input line 9520. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 122 undefined on input line 9520. [122] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 123 undefined on input line 9550. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 123 undefined on input line 9571. [123] LaTeX Warning: Hyper reference `developer_guide/api/gene:id1' on page 124 undef ined on input line 9693. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 124 undefined on input line 9694. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank' on page 124 undefined on input line 9702. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.ModelBa nk' on page 124 undefined on input line 9703. LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac syfinder.main' on page 124 undefined on input line 9704. [124] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 125 undefined on input line 9776. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 125 undefined on input line 9802. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 125 undefined on input line 9861. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro fileFactory' on page 125 undefined on input line 9861. [125] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 126 undefined on input line 9910. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 126 undefined on input line 9910. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank' on page 126 undefined on input line 9911. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 126 undefined on input line 9920. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 126 undefined on input line 9930. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro fileFactory' on page 126 undefined on input line 9930. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 126 undefined on input line 9952. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro fileFactory' on page 126 undefined on input line 9952. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro file' on page 126 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 126 undefined on input line 10015. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 126 undefined on input line 10015. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 126 undefined on input line 10036. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 126 undefined on input line 10036. [126] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.Exchangea ble' on page 127 undefined on input line 10101. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 127 undefined on input line 10119. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 127 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 127 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 127 undefined on input line 10181. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 127 undefined on input line 10216. [127] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 128 undefined on input line 10235. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 128 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 128 undefined on input line 10291. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 128 undefined on input line 10328. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 128 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 128 undefined on input line 10367. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 128 undefined on input line 10367. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 128 undefined on input line 10377. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 128 undefined on input line 10377. [128] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.Exchangea ble' on page 129 undefined on input line 10399. LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy Error' on page 129 undefined on input line 10410. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 129 undefined on input line 10421. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 129 undefined on input line 1. [129] LaTeX Warning: Hyper reference `developer_guide/overview:profile-implementation ' on page 130 undefined on input line 10518. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 130 undefined on input line 10533. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC onfig' on page 130 undefined on input line 10533. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 130 undefined on input line 10546. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC onfig' on page 130 undefined on input line 10546. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 130 undefined on input line 10567. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelLocation' on page 130 undefined on input line 10567. LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro file' on page 130 undefined on input line 10567. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 130 undefined on input line 10601. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 130 undefined on input line 10601. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 130 undefined on input line 10610. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 130 undefined on input line 10610. [130] LaTeX Warning: Hyper reference `developer_guide/api/report:macsypy.report.HMMRe port' on page 131 undefined on input line 10697. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.AbstractCou nterpartHit' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p age 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem ' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS ystem' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi t_4_func' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.sort_model_ hits' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.compute_bes t_MSHit' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi ts' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.AbstractCou nterpartHit' on page 131 undefined on input line 10810. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 []\T1/txtt/m/sl/10 macsypy.hit. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p age 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem ' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS ystem' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi t_4_func' on page 131 undefined on input line 10810. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 []\T1/txtt/m/sl/10 macsypy.hit. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.sort_model_ hits' on page 131 undefined on input line 10810. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.compute_bes t_MSHit' on page 131 undefined on input line 10810. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 []\T1/txtt/m/sl/10 macsypy.hit. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi ts' on page 131 undefined on input line 10810. pdfTeX warning: pdflatex (file ./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f958 9da157.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed pdfTeX warning: pdflatex (file ./gene_obj_interaction.pdf): PDF inclusion: foun d PDF version <1.7>, but at most version <1.5> allowed LaTeX Warning: Float too large for page by 127.0251pt on input line 10847. [131 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>] [132 <./gene_obj_interaction.pdf>] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 133 undefined on input line 10859. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 133 undefined on input line 10865. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 133 undefined on input line 10871. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 133 undefined on input line 10893. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 133 undefined on input line 10928. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 133 undefined on input line 10986. [133] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 134 undefined on input line 11061. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 134 undefined on input line 11061. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 134 undefined on input line 11061. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 134 undefined on input line 11089. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 134 undefined on input line 11101. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 134 undefined on input line 11125. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 134 undefined on input line 11125. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 134 undefined on input line 11125. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene .alternate_of' on page 134 undefined on input line 11140. [134] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 135 undefined on input line 11162. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 135 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 135 undefined on input line 11279. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 135 undefined on input line 11279. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 135 undefined on input line 11279. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 135 undefined on input line 11279. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 135 undefined on input line 11279. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 135 undefined on input line 11288. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 135 undefined on input line 11288. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 135 undefined on input line 11288. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 135 undefined on input line 11288. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 135 undefined on input line 11288. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene .alternate_of' on page 135 undefined on input line 11303. [135] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 136 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 136 undefined on input line 11403. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 136 undefined on input line 11403. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 136 undefined on input line 11403. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 136 undefined on input line 11403. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 136 undefined on input line 11403. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 136 undefined on input line 11412. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 136 undefined on input line 11412. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 136 undefined on input line 11412. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 136 undefined on input line 11412. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 136 undefined on input line 11412. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene .alternate_of' on page 136 undefined on input line 11430. [136] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11492. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 137 undefined on input line 11492. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 137 undefined on input line 11492. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 137 undefined on input line 11492. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11492. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11501. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 137 undefined on input line 11501. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 137 undefined on input line 11501. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 137 undefined on input line 11501. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11501. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene .alternate_of' on page 137 undefined on input line 11519. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11566. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 137 undefined on input line 11566. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 137 undefined on input line 11566. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 137 undefined on input line 11566. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11566. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11589. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 137 undefined on input line 11589. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 137 undefined on input line 11589. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 137 undefined on input line 11589. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 137 undefined on input line 11589. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 137 undefined on input line 11601. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene .alternate_of' on page 137 undefined on input line 11607. [137] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu s' on page 138 undefined on input line 11616. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 138 undefined on input line 11620. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 138 undefined on input line 11763. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 138 undefined on input line 11763. [138] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 139 undefined on input line 11813. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 139 undefined on input line 11816. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 139 undefined on input line 11820. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem ' on page 139 undefined on input line 11838. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS ystem' on page 139 undefined on input line 11838. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 139 undefined on input line 11860. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 139 undefined on input line 11860. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 139 undefined on input line 11860. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 139 undefined on input line 11860. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 139 undefined on input line 11882. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 139 undefined on input line 11896. [139] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 140 undefined on input line 11921. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 140 undefined on input line 11921. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 140 undefined on input line 11930. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 140 undefined on input line 11949. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 140 undefined on input line 11949. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 140 undefined on input line 12017. [140] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight' on page 141 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 141 undefined on input line 12127. LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy Error' on page 141 undefined on input line 12146. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 141 undefined on input line 12186. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 141 undefined on input line 12186. [141] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 142 undefined on input line 12255. LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R epliconInfo' on page 142 undefined on input line 12255. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 142 undefined on input line 12255. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight' on page 142 undefined on input line 12255. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 142 undefined on input line 12312. Underfull \hbox (badness 10000) in paragraph at lines 12315--12317 []\T1/qtm/m/n/10 true_loners: a dict { str func-tion: :class:macsypy.hit.Loner | LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 142 undefined on input line 12342. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec tedCandidate' on page 142 undefined on input line 12343. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel ySystem' on page 142 undefined on input line 12344. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik elySystem' on page 142 undefined on input line 12344. pdfTeX warning: pdflatex (file ./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c662 2aab72.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [142] LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Abstr actSetOfHits' on page 143 undefined on input line 12354. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.MetaS etOfHits' on page 143 undefined on input line 12355. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.MetaS etOfHits' on page 143 undefined on input line 12356. pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 143 undefined on input line 12371. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 143 undefined on input line 12381. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 143 undefined on input line 12402. [143 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf> <./inheritanc e-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12450. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12450. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12450. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12450. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12450. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12453. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 144 undefined on input line 12457. LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy Error' on page 144 undefined on input line 12465. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 144 undefined on input line 12500. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 144 undefined on input line 12500. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec tedCandidate' on page 144 undefined on input line 12500. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 144 undefined on input line 12504. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 144 undefined on input line 12509. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 144 undefined on input line 12517. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec tedCandidate' on page 144 undefined on input line 12517. [144] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 145 undefined on input line 12534. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 145 undefined on input line 12540. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel ySystem' on page 145 undefined on input line 12540. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik elySystem' on page 145 undefined on input line 12540. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 145 undefined on input line 12561. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 145 undefined on input line 12570. [145] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 146 undefined on input line 12716. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 146 undefined on input line 12824. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 146 undefined on input line 12824. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 146 undefined on input line 12824. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 146 undefined on input line 12833. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene ' on page 146 undefined on input line 12837. [146] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 147 undefined on input line 12871. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 147 undefined on input line 12871. LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 147 undefined on input line 12876. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 147 undefined on input line 12880. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem ' on page 147 undefined on input line 12905. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p age 147 undefined on input line 12920. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS ystem' on page 147 undefined on input line 12920. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem ' on page 147 undefined on input line 12935. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS ystem' on page 147 undefined on input line 12935. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 147 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste m' on page 147 undefined on input line 12965. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 147 undefined on input line 12976. [147] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 148 undefined on input line 13105. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 148 undefined on input line 13105. LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu ster' on page 148 undefined on input line 13115. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 148 undefined on input line 13115. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 148 undefined on input line 1. [148] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 149 undefined on input line 13193. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 13193. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 13193. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 13193. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 13193. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 1. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 149 undefined on input line 1. [149] LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model' on page 150 undefined on input line 13365. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 150 undefined on input line 13365. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 150 undefined on input line 13365. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 150 undefined on input line 13365. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o n page 150 undefined on input line 13365. LaTeX Warning: Hyper reference `developer_guide/overview:report-implementation' on page 150 undefined on input line 13442. LaTeX Warning: Hyper reference `user_guide/outputs:hmmer-outputs-label' on page 150 undefined on input line 13443. [150] LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 151 undefined on input line 13456. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 151 undefined on input line 13456. LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene' on page 151 undefined on input line 13469. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 151 undefined on input line 13469. LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on page 151 undefined on input line 13608. [151] Underfull \hbox (badness 10000) in paragraph at lines 13670--13672 \T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (// Output written on macsyfinder.pdf (195 pages, 2554281 bytes). Transcript written on macsyfinder.log. Latexmk: Missing input file 'macsyfinder.toc' (or dependence on it) from following: No file macsyfinder.toc. Latexmk: Missing input file 'macsyfinder.ind' (or dependence on it) from following: No file macsyfinder.ind. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' Latexmk: Examining 'macsyfinder.log' Latexmk: Index file 'macsyfinder.idx' was written Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'macsyfinder.pdf' Have index file 'macsyfinder.idx', macsyfinder.ind macsyfinder Latexmk: applying rule 'makeindex macsyfinder.idx'... Rule 'makeindex macsyfinder.idx': Reasons for rerun Category 'other': Rerun of 'makeindex macsyfinder.idx' forced or previously required: Reason or flag: 'Initial set up of rule' ------------ Run number 1 of rule 'makeindex macsyfinder.idx' ------------ ------------ Running 'makeindex -s python.ist -o "macsyfinder.ind" "macsyfinder.idx"' ------------ This is makeindex, version 2.17 [TeX Live 2025/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file macsyfinder.idx....done (571 entries accepted, 0 rejected). Sorting entries.......done (5710 comparisons). Generating output file macsyfinder.ind....done (830 lines written, 0 warnings). Output written in macsyfinder.ind. Transcript written in macsyfinder.ilg. Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Changed files or newly in use/created: macsyfinder.aux macsyfinder.ind macsyfinder.out macsyfinder.toc ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2024-11-01> L3 programming layer <2024-11-02> (./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 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxpackageboxes.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty)) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)) (./sphinxlatexnumfig.sty) (./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty ) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip-2001-04-09.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)) (./sphinxmessages.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) Writing index file macsyfinder.idx (/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./macsyfinder.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./macsyfinder.out) (./macsyfinder.out) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texmf/fonts/en c/dvips/tex-gyre/q-ec.enc}] [2] (./macsyfinder.toc) [1] [2] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 5331) in paragraph at lines 148--154 \T1/qtm/m/n/10 phie S. Mac-SyFinder v2: Im-proved mod-elling and search en-gine to iden-tify molec-u-lar sys-tems in [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} <./logo_macsyfinder.png >] [2 <./figure_main-2.png>] Chapter 1. [3] [4] [5] [6] [7] [8] [9] [10] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 765. [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 948--950 []\T1/txtt/m/n/10 macsyfinder [][]db[]type unordered [][]sequence[]db unordered _genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 959--961 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir Underfull \hbox (badness 10000) in paragraph at lines 971--973 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [13] Overfull \hbox (57.99365pt too wide) in paragraph at lines 1035--1039 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_ordered Overfull \hbox (68.49362pt too wide) in paragraph at lines 1045--1048 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_unordered Underfull \hbox (badness 10000) in paragraph at lines 1045--1048 [][]\T1/txtt/m/n/10 models TXSScan all [][]db[]type unordered []w 8 \T1/qtm/m/i t/10 # spec-i-fied out-put folder: mac- [14] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \vbox (2.56042pt too high) detected at line 1174 [15] [16] Underfull \vbox (badness 1226) detected at line 1267 [17] [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 5417) in paragraph at lines 1876--1878 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file [25] [26] Underfull \vbox (badness 10000) detected at line 2089 Underfull \vbox (badness 10000) detected at line 2089 [27] [28] [29] [30] [31] Underfull \vbox (badness 1226) detected at line 2406 [32] Underfull \vbox (badness 10000) detected at line 2406 Underfull \vbox (badness 10000) detected at line 2406 [33] [34] [35] [36] Overfull \vbox (1.17242pt too high) detected at line 2591 [37] Overfull \vbox (0.91234pt too high) detected at line 2638 [38] Overfull \vbox (1.73233pt too high) detected at line 2761 [39] Underfull \vbox (badness 10000) detected at line 2761 Underfull \vbox (badness 10000) detected at line 2761 [40] [41] [42] [43] Underfull \vbox (badness 10000) detected at line 2936 Underfull \vbox (badness 10000) detected at line 2936 [44] Overfull \vbox (1.17242pt too high) detected at line 2989 [45] [46] pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed [47 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz-bb320 290fa50a2c64c42d68cab416461f9843641.pdf pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag e >] [48] [49] [50] [51] [52] [53] [54] [55] [56 <./msf_functionning_step1.pdf>] [57 <./msf_functionning_step2.pdf>] [58] [59 <./msf_functionning_step3.pdf> <./msf_functionning_step4.pdf pdfTeX warning: pdflatex (file ./msf_functionning_step4.pdf): PDF inclusion: mu ltiple pdfs with page group included in a single page >] [60 <./msf_functionning_step5.pdf>] [61] Underfull \hbox (badness 10000) in paragraph at lines 4063--4065 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4071--4073 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4079--4081 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4087--4089 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4098--4100 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir [62] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4176. [63] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4221. [64] [65] [66] Chapter 2. [67 <./logo_macsymodels.png>] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4393. [68] [69] [70] [71] [72] [73] [74] [75 <./MSF_modelling.pdf>] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5045. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 58. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 61. Package wrapfig Warning: Collision between wrapping environments on input line 5067. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5067. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 79. [76 <./loner.pdf>] Package wrapfig Warning: Collision between wrapping environments on input line 5091. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5091. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 04. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 07. Overfull \vbox (19.57245pt too high) detected at line 5188 [77 <./multi_system.pdf>] [78] [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5531--5536 \T1/txtt/m/n/10 models in conf file XXX. May be these results have been generat ed with an old version [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 5661--5663 [][][]$\T1/qtm/m/n/10 https : / / the-[]hitchhikers-[]guide-[]to-[]packaging . readthedocs . io / en / latest / speci^^\cation . html # [85] [86] [87] [88] [89 <./T1SS_example.pdf>] [90] Overfull \vbox (0.97131pt too high) detected at line 6075 [91 <./T3SS_example.pdf>] [92] [93] [94] Underfull \vbox (badness 1226) detected at line 6332 [95] [96] [97 <./multi_model.pdf>] [98] Chapter 3. [99] [100] [101] pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [102 <./macsyfinder_classes.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 6812--6817 []\T1/qtm/m/n/10 Among all this po-ten-tial sys-tems, MSF com-pute the best com -bi-na-tion. [][]\T1/txtt/m/sl/10 macsypy.solution. [103] [104] [105] [106] [107] Underfull \hbox (badness 6775) in paragraph at lines 7341--7343 \T1/txtt/bx/n/10 options \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dictionary with opt ion name as keys and values as values\T1/qtm/m/n/10 ) ^^U [108] [109] [110] Underfull \hbox (badness 10000) in paragraph at lines 7868--7871 []\T1/txtt/bx/n/10 allowed_elements \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dict wit h options name as keys and function to [111] [112] [113] [114] [115] [116] [117] [118] [119{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. pdfTeX warning: pdflatex (file ./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f958 9da157.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed pdfTeX warning: pdflatex (file ./gene_obj_interaction.pdf): PDF inclusion: foun d PDF version <1.7>, but at most version <1.5> allowed LaTeX Warning: Float too large for page by 127.0251pt on input line 10847. [131 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>] [132 <./gene_obj_interaction.pdf>] [133] [134] [135] [136] [137] [138] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 12315--12317 []\T1/qtm/m/n/10 true_loners: a dict { str func-tion: :class:macsypy.hit.Loner | pdfTeX warning: pdflatex (file ./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c662 2aab72.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [142] pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [143 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf> <./inheritanc e-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [144] [145] [146] [147] [148] [149] [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 13670--13672 \T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (// Output written on macsyfinder.pdf (206 pages, 2644667 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' Latexmk: Examining 'macsyfinder.log' Latexmk: Index file 'macsyfinder.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'macsyfinder.pdf' Have index file 'macsyfinder.idx', macsyfinder.ind macsyfinder Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Changed files or newly in use/created: macsyfinder.aux macsyfinder.out macsyfinder.toc ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2024-11-01> L3 programming layer <2024-11-02> (./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 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))) (/usr/share/texmf/tex/latex/tex-gyre/tgheros.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (./sphinxoptionshyperref.sty) (./sphinxoptionsgeometry.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (./sphinxlatexgraphics.sty) (./sphinxpackageboxes.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.sty (/usr/share/texlive/texmf-dist/tex/latex/pict2e/pict2e.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pict2e/p2e-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ellipse/ellipse.sty)) (./sphinxlatexadmonitions.sty (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)) (./sphinxlatexliterals.sty (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty)) (./sphinxlatexshadowbox.sty) (./sphinxlatexcontainers.sty) (./sphinxhighlight.sty) (./sphinxlatextables.sty (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) (/usr/share/texlive/texmf-dist/tex/latex/colortbl/colortbl.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)) (./sphinxlatexnumfig.sty) (./sphinxlatexlists.sty) (./sphinxpackagefootnote.sty ) (./sphinxlatexindbibtoc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)) (./sphinxlatexstylepage.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip-2001-04-09.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty)) (./sphinxlatexstyleheadings.sty (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)) (./sphinxlatexstyletext.sty) (./sphinxlatexobjects.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hypcap/hypcap.sty (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)) (./sphinxmessages.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) Writing index file macsyfinder.idx (/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./macsyfinder.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./macsyfinder.out) (./macsyfinder.out) (/usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texmf/fonts/en c/dvips/tex-gyre/q-ec.enc}] [2] (./macsyfinder.toc) [1] [2] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 5331) in paragraph at lines 148--154 \T1/qtm/m/n/10 phie S. Mac-SyFinder v2: Im-proved mod-elling and search en-gine to iden-tify molec-u-lar sys-tems in [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} <./logo_macsyfinder.png >] [2 <./figure_main-2.png>] Chapter 1. [3] [4] [5] [6] [7] [8] [9] [10] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 765. [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 948--950 []\T1/txtt/m/n/10 macsyfinder [][]db[]type unordered [][]sequence[]db unordered _genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 959--961 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir Underfull \hbox (badness 10000) in paragraph at lines 971--973 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [13] Overfull \hbox (57.99365pt too wide) in paragraph at lines 1035--1039 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_ordered Overfull \hbox (68.49362pt too wide) in paragraph at lines 1045--1048 []\T1/txtt/m/n/10 macsyfinder [][]sequence[]db VICH001.B.00001.C001.fasta []o m acsyfinder_TXSScan_VICH001_unordered Underfull \hbox (badness 10000) in paragraph at lines 1045--1048 [][]\T1/txtt/m/n/10 models TXSScan all [][]db[]type unordered []w 8 \T1/qtm/m/i t/10 # spec-i-fied out-put folder: mac- [14] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \vbox (2.56042pt too high) detected at line 1174 [15] [16] Underfull \vbox (badness 1226) detected at line 1267 [17] [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 5417) in paragraph at lines 1876--1878 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file [25] [26] Underfull \vbox (badness 10000) detected at line 2089 Underfull \vbox (badness 10000) detected at line 2089 [27] [28] [29] [30] [31] Underfull \vbox (badness 1226) detected at line 2406 [32] Underfull \vbox (badness 10000) detected at line 2406 Underfull \vbox (badness 10000) detected at line 2406 [33] [34] [35] [36] Overfull \vbox (1.17242pt too high) detected at line 2591 [37] Overfull \vbox (0.91234pt too high) detected at line 2638 [38] Overfull \vbox (1.73233pt too high) detected at line 2761 [39] Underfull \vbox (badness 10000) detected at line 2761 Underfull \vbox (badness 10000) detected at line 2761 [40] [41] [42] [43] Underfull \vbox (badness 10000) detected at line 2936 Underfull \vbox (badness 10000) detected at line 2936 [44] Overfull \vbox (1.17242pt too high) detected at line 2989 [45] [46] pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all owed [47 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz-bb320 290fa50a2c64c42d68cab416461f9843641.pdf pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843 641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag e >] [48] [49] [50] [51] [52] [53] [54] [55] [56 <./msf_functionning_step1.pdf>] [57 <./msf_functionning_step2.pdf>] [58] [59 <./msf_functionning_step3.pdf> <./msf_functionning_step4.pdf pdfTeX warning: pdflatex (file ./msf_functionning_step4.pdf): PDF inclusion: mu ltiple pdfs with page group included in a single page >] [60 <./msf_functionning_step5.pdf>] [61] Underfull \hbox (badness 10000) in paragraph at lines 4063--4065 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4071--4073 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4079--4081 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4087--4089 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 4098--4100 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir [62] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4176. [63] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4221. [64] [65] [66] Chapter 2. [67 <./logo_macsymodels.png>] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 4393. [68] [69] [70] [71] [72] [73] [74] [75 <./MSF_modelling.pdf>] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5045. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 58. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 61. Package wrapfig Warning: Collision between wrapping environments on input line 5067. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5067. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 50 79. [76 <./loner.pdf>] Package wrapfig Warning: Collision between wrapping environments on input line 5091. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 5091. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 04. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 51 07. Overfull \vbox (19.57245pt too high) detected at line 5188 [77 <./multi_system.pdf>] [78] [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5531--5536 \T1/txtt/m/n/10 models in conf file XXX. May be these results have been generat ed with an old version [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 5661--5663 [][][]$\T1/qtm/m/n/10 https : / / the-[]hitchhikers-[]guide-[]to-[]packaging . readthedocs . io / en / latest / speci^^\cation . html # [85] [86] [87] [88] [89 <./T1SS_example.pdf>] [90] Overfull \vbox (0.97131pt too high) detected at line 6075 [91 <./T3SS_example.pdf>] [92] [93] [94] Underfull \vbox (badness 1226) detected at line 6332 [95] [96] [97 <./multi_model.pdf>] [98] Chapter 3. [99] [100] [101] pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [102 <./macsyfinder_classes.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 6812--6817 []\T1/qtm/m/n/10 Among all this po-ten-tial sys-tems, MSF com-pute the best com -bi-na-tion. [][]\T1/txtt/m/sl/10 macsypy.solution. [103] [104] [105] [106] [107] Underfull \hbox (badness 6775) in paragraph at lines 7341--7343 \T1/txtt/bx/n/10 options \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dictionary with opt ion name as keys and values as values\T1/qtm/m/n/10 ) ^^U [108] [109] [110] Underfull \hbox (badness 10000) in paragraph at lines 7868--7871 []\T1/txtt/bx/n/10 allowed_elements \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 a dict wit h options name as keys and function to [111] [112] [113] [114] [115] [116] [117] [118] [119{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. Underfull \hbox (badness 10000) in paragraph at lines 10810--10810 [][][]\T1/txtt/m/sl/10 macsypy.hit. pdfTeX warning: pdflatex (file ./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f958 9da157.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed pdfTeX warning: pdflatex (file ./gene_obj_interaction.pdf): PDF inclusion: foun d PDF version <1.7>, but at most version <1.5> allowed LaTeX Warning: Float too large for page by 127.0251pt on input line 10847. [131 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>] [132 <./gene_obj_interaction.pdf>] [133] [134] [135] [136] [137] [138] [139] [140] [141] Underfull \hbox (badness 10000) in paragraph at lines 12315--12317 []\T1/qtm/m/n/10 true_loners: a dict { str func-tion: :class:macsypy.hit.Loner | pdfTeX warning: pdflatex (file ./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c662 2aab72.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [142] pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [143 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf> <./inheritanc e-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c 5ae428.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [144] [145] [146] [147] [148] [149] [150] [151] Underfull \hbox (badness 10000) in paragraph at lines 13670--13672 \T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (// Output written on macsyfinder.pdf (206 pages, 2645050 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' Latexmk: Examining 'macsyfinder.log' Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Log file says output to 'macsyfinder.pdf' Have index file 'macsyfinder.idx', macsyfinder.ind macsyfinder Latexmk: All targets (macsyfinder.pdf) are up-to-date make[2]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.4/doc/build/latex' make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.4/doc' dh_installdocs -O--buildsystem=pybuild dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/macsyfinder-2.1.4' dh_fixperms find debian -name "test_*.fa" -executable -exec chmod -x \{\} \; find debian -name "*.prt" -executable -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/macsyfinder-2.1.4' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'macsyfinder' in '../macsyfinder_2.1.4-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../macsyfinder_2.1.4-1_arm64.buildinfo dpkg-genchanges --build=binary -O../macsyfinder_2.1.4-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/4023626/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4023626/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/4023626 and its subdirectories I: Current time: Fri Jan 2 09:37:42 +14 2026 I: pbuilder-time-stamp: 1767296262