W: cgroups are not available on the host, not using them.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Jan 21 11:15:54 -12 2025
I: pbuilder-time-stamp: 1737501354
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
dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.1.4-1.dsc: unsupported subcommand
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/3899812/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3899812'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wmdEMdHe/pbuilderrc_zkEz --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wmdEMdHe/b1 --logfile b1/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+12'
USER='root'
_='/usr/sbin/chroot'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3899812/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19964 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} 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} libffi8{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libkpathsea6{a} liblab-gamut1{a} liblapack3{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpathplan4{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsvtav1enc2{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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} procps{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} python3.13{a} python3.13-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 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 linux-sysctl-defaults lmodern lynx mupdf okular psmisc 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, 218 newly installed, 0 to remove and 0 not upgraded.
Need to get 227 MB of archives. After unpacking 874 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 libpython3.13-minimal arm64 3.13.1-3 [852 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 python3.13-minimal arm64 3.13.1-3 [1990 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 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 2025a-1 [259 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B]
Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.0-2 [1385 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B]
Get: 32 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 33 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0048 [42.0 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 37 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 47 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 48 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 49 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 50 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 51 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 52 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 53 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB]
Get: 65 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB]
Get: 66 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB]
Get: 67 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 68 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get: 69 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.45-1 [273 kB]
Get: 70 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get: 71 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 72 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 73 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB]
Get: 74 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB]
Get: 75 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2 [462 kB]
Get: 76 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 77 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB]
Get: 78 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB]
Get: 79 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-2+b2 [39.4 kB]
Get: 80 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-2+b2 [61.2 kB]
Get: 81 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.11.0-1 [1690 kB]
Get: 82 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB]
Get: 83 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB]
Get: 84 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3 [491 kB]
Get: 85 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-9 [654 kB]
Get: 86 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB]
Get: 87 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get: 88 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1899.20250103-1 [136 kB]
Get: 89 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.1.1-1 [109 kB]
Get: 90 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB]
Get: 91 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.5-1 [11.2 kB]
Get: 92 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB]
Get: 93 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.5-1 [15.1 kB]
Get: 94 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.5-1 [438 kB]
Get: 95 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB]
Get: 96 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB]
Get: 97 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB]
Get: 98 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get: 99 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB]
Get: 100 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB]
Get: 101 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB]
Get: 102 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB]
Get: 104 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB]
Get: 105 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get: 106 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get: 107 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB]
Get: 108 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get: 109 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 110 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get: 111 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB]
Get: 112 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB]
Get: 113 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB]
Get: 114 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB]
Get: 115 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB]
Get: 116 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB]
Get: 117 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB]
Get: 118 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB]
Get: 119 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get: 120 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.5.4-2 [415 kB]
Get: 121 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB]
Get: 122 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB]
Get: 123 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB]
Get: 124 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB]
Get: 125 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB]
Get: 126 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB]
Get: 127 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-2+b2 [41.4 kB]
Get: 128 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-2+b2 [629 kB]
Get: 129 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-2+b2 [182 kB]
Get: 130 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-2+b2 [198 kB]
Get: 131 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.2 [216 kB]
Get: 132 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB]
Get: 133 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB]
Get: 134 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB]
Get: 135 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB]
Get: 136 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB]
Get: 137 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-2+b2 [576 kB]
Get: 138 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB]
Get: 139 http://deb.debian.org/debian unstable/main arm64 hmmer arm64 3.4+dfsg-2+b1 [977 kB]
Get: 140 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB]
Get: 141 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3 [16.3 kB]
Get: 142 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3 [16.1 kB]
Get: 143 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5+b1 [154 kB]
Get: 144 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5+b1 [48.2 kB]
Get: 145 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5+b1 [60.6 kB]
Get: 146 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5+b1 [106 kB]
Get: 147 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB]
Get: 148 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB]
Get: 149 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB]
Get: 150 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB]
Get: 151 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB]
Get: 152 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB]
Get: 153 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5+b1 [7357 kB]
Get: 154 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 155 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20250114-1 [22.8 MB]
Get: 156 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20250114-1 [1282 kB]
Get: 157 http://deb.debian.org/debian unstable/main arm64 latexmk all 1:4.86~ds-1 [507 kB]
Get: 158 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B]
Get: 159 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB]
Get: 160 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 161 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 162 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB]
Get: 163 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB]
Get: 164 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB]
Get: 165 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 166 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 167 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 168 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 169 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB]
Get: 170 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB]
Get: 171 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB]
Get: 172 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB]
Get: 173 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB]
Get: 174 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB]
Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-toml all 0.10.2-1 [16.2 kB]
Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.45.1-1 [56.7 kB]
Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.2-1 [36.0 kB]
Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB]
Get: 179 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20250108 [11.6 kB]
Get: 180 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB]
Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.16.0-1 [114 kB]
Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.12.14+ds-1 [9624 B]
Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB]
Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-colorama all 0.4.6-4 [36.2 kB]
Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-colorlog all 6.9.0-1 [27.5 kB]
Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB]
Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB]
Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-2 [120 kB]
Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB]
Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB]
Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.2-1 [31.0 kB]
Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB]
Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 205 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-4 [616 kB]
Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-4 [468 kB]
Get: 207 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB]
Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB]
Get: 210 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b1 [148 kB]
Get: 211 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 212 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get: 213 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB]
Get: 214 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB]
Get: 215 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB]
Get: 216 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB]
Get: 217 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB]
Get: 218 http://deb.debian.org/debian unstable/main arm64 texlive-plain-generic all 2024.20250114-1 [28.9 MB]
Fetched 227 MB in 1s (208 MB/s)
Preconfiguring packages ...
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 ... 19964 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 libpython3.13-minimal:arm64.
Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ...
Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ...
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 python3.13-minimal.
Preparing to unpack .../python3.13-minimal_3.13.1-3_arm64.deb ...
Unpacking python3.13-minimal (3.13.1-3) ...
Setting up libpython3.13-minimal:arm64 (3.13.1-3) ...
Setting up libexpat1:arm64 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.1-3) ...
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 ... 20324 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ...
Unpacking python3-minimal (3.13.1-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../2-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../3-tzdata_2025a-1_all.deb ...
Unpacking tzdata (2025a-1) ...
Selecting previously unselected package libffi8:arm64.
Preparing to unpack .../4-libffi8_3.4.6-1_arm64.deb ...
Unpacking libffi8:arm64 (3.4.6-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../5-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:arm64.
Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ...
Selecting previously unselected package libpython3.13-stdlib:arm64.
Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ...
Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ...
Selecting previously unselected package python3.13.
Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ...
Unpacking python3.13 (3.13.1-3) ...
Selecting previously unselected package libpython3-stdlib:arm64.
Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_arm64.deb ...
Unpacking libpython3-stdlib:arm64 (3.13.1-2) ...
Setting up python3-minimal (3.13.1-2) ...
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 ... 21334 files and directories currently installed.)
Preparing to unpack .../000-python3_3.13.1-2_arm64.deb ...
Unpacking python3 (3.13.1-2) ...
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 libproc2-0:arm64.
Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_arm64.deb ...
Unpacking libproc2-0:arm64 (2:4.0.4-6) ...
Selecting previously unselected package procps.
Preparing to unpack .../003-procps_2%3a4.0.4-6_arm64.deb ...
Unpacking procps (2:4.0.4-6) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package openssl.
Preparing to unpack .../005-openssl_3.4.0-2_arm64.deb ...
Unpacking openssl (3.4.0-2) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../006-ca-certificates_20241223_all.deb ...
Unpacking ca-certificates (20241223) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../007-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 .../008-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../009-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../010-gettext-base_0.23.1-1_arm64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../011-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 .../012-groff-base_1.23.0-7_arm64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../013-bsdextrautils_2.40.4-1_arm64.deb ...
Unpacking bsdextrautils (2.40.4-1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package libtext-charwidth-perl:arm64.
Preparing to unpack .../016-libtext-charwidth-perl_0.04-11+b4_arm64.deb ...
Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ...
Selecting previously unselected package libtext-wrapi18n-perl.
Preparing to unpack .../017-libtext-wrapi18n-perl_0.06-10_all.deb ...
Unpacking libtext-wrapi18n-perl (0.06-10) ...
Selecting previously unselected package ucf.
Preparing to unpack .../018-ucf_3.0048_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0048) ...
Selecting previously unselected package m4.
Preparing to unpack .../019-m4_1.4.19-5_arm64.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../020-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../021-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../022-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 .../023-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../024-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../025-libtool_2.5.4-2_all.deb ...
Unpacking libtool (2.5.4-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../026-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../027-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 .../028-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../029-dh-strip-nondeterminism_1.14.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-1) ...
Selecting previously unselected package libelf1t64:arm64.
Preparing to unpack .../030-libelf1t64_0.192-4_arm64.deb ...
Unpacking libelf1t64:arm64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../031-dwz_0.15-1+b1_arm64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:arm64.
Preparing to unpack .../032-libunistring5_1.3-1_arm64.deb ...
Unpacking libunistring5:arm64 (1.3-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../033-libicu72_72.1-6_arm64.deb ...
Unpacking libicu72:arm64 (72.1-6) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../034-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 .../035-gettext_0.23.1-1_arm64.deb ...
Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../036-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 .../037-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../038-debhelper_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Selecting previously unselected package python3-autocommand.
Preparing to unpack .../039-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 .../040-python3-more-itertools_10.6.0-1_all.deb ...
Unpacking python3-more-itertools (10.6.0-1) ...
Selecting previously unselected package python3-typing-extensions.
Preparing to unpack .../041-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 .../042-python3-typeguard_4.4.1-1_all.deb ...
Unpacking python3-typeguard (4.4.1-1) ...
Selecting previously unselected package python3-inflect.
Preparing to unpack .../043-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 .../044-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 .../045-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 .../046-python3-pkg-resources_75.6.0-1_all.deb ...
Unpacking python3-pkg-resources (75.6.0-1) ...
Selecting previously unselected package python3-jaraco.text.
Preparing to unpack .../047-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 .../048-python3-zipp_3.21.0-1_all.deb ...
Unpacking python3-zipp (3.21.0-1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../049-python3-setuptools_75.6.0-1_all.deb ...
Unpacking python3-setuptools (75.6.0-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../050-dh-python_6.20250108_all.deb ...
Unpacking dh-python (6.20250108) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../051-xml-core_0.19_all.deb ...
Unpacking xml-core (0.19) ...
Selecting previously unselected package docutils-common.
Preparing to unpack .../052-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 .../053-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 .../054-libpng16-16t64_1.6.45-1_arm64.deb ...
Unpacking libpng16-16t64:arm64 (1.6.45-1) ...
Selecting previously unselected package libfreetype6:arm64.
Preparing to unpack .../055-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 .../056-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 .../057-fonts-dejavu-core_2.37-8_all.deb ...
Unpacking fonts-dejavu-core (2.37-8) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../058-fontconfig-config_2.15.0-2_arm64.deb ...
Unpacking fontconfig-config (2.15.0-2) ...
Selecting previously unselected package libfontconfig1:arm64.
Preparing to unpack .../059-libfontconfig1_2.15.0-2_arm64.deb ...
Unpacking libfontconfig1:arm64 (2.15.0-2) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../060-fontconfig_2.15.0-2_arm64.deb ...
Unpacking fontconfig (2.15.0-2) ...
Selecting previously unselected package fonts-font-awesome.
Preparing to unpack .../061-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 .../062-fonts-lmodern_2.005-1_all.deb ...
Unpacking fonts-lmodern (2.005-1) ...
Selecting previously unselected package libann0.
Preparing to unpack .../063-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 .../064-libcdt5_2.42.4-2+b2_arm64.deb ...
Unpacking libcdt5:arm64 (2.42.4-2+b2) ...
Selecting previously unselected package libcgraph6:arm64.
Preparing to unpack .../065-libcgraph6_2.42.4-2+b2_arm64.deb ...
Unpacking libcgraph6:arm64 (2.42.4-2+b2) ...
Selecting previously unselected package libaom3:arm64.
Preparing to unpack .../066-libaom3_3.11.0-1_arm64.deb ...
Unpacking libaom3:arm64 (3.11.0-1) ...
Selecting previously unselected package libdav1d7:arm64.
Preparing to unpack .../067-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 .../068-libabsl20230802_20230802.1-4_arm64.deb ...
Unpacking libabsl20230802:arm64 (20230802.1-4) ...
Selecting previously unselected package libgav1-1:arm64.
Preparing to unpack .../069-libgav1-1_0.19.0-3_arm64.deb ...
Unpacking libgav1-1:arm64 (0.19.0-3) ...
Selecting previously unselected package librav1e0.7:arm64.
Preparing to unpack .../070-librav1e0.7_0.7.1-9_arm64.deb ...
Unpacking librav1e0.7:arm64 (0.7.1-9) ...
Selecting previously unselected package libsvtav1enc2:arm64.
Preparing to unpack .../071-libsvtav1enc2_2.3.0+dfsg-1_arm64.deb ...
Unpacking libsvtav1enc2:arm64 (2.3.0+dfsg-1) ...
Selecting previously unselected package libjpeg62-turbo:arm64.
Preparing to unpack .../072-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 .../073-libyuv0_0.0.1899.20250103-1_arm64.deb ...
Unpacking libyuv0:arm64 (0.0.1899.20250103-1) ...
Selecting previously unselected package libavif16:arm64.
Preparing to unpack .../074-libavif16_1.1.1-1_arm64.deb ...
Unpacking libavif16:arm64 (1.1.1-1) ...
Selecting previously unselected package libsharpyuv0:arm64.
Preparing to unpack .../075-libsharpyuv0_1.5.0-0.1_arm64.deb ...
Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ...
Selecting previously unselected package libheif-plugin-dav1d:arm64.
Preparing to unpack .../076-libheif-plugin-dav1d_1.19.5-1_arm64.deb ...
Unpacking libheif-plugin-dav1d:arm64 (1.19.5-1) ...
Selecting previously unselected package libde265-0:arm64.
Preparing to unpack .../077-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 .../078-libheif-plugin-libde265_1.19.5-1_arm64.deb ...
Unpacking libheif-plugin-libde265:arm64 (1.19.5-1) ...
Selecting previously unselected package libheif1:arm64.
Preparing to unpack .../079-libheif1_1.19.5-1_arm64.deb ...
Unpacking libheif1:arm64 (1.19.5-1) ...
Selecting previously unselected package libimagequant0:arm64.
Preparing to unpack .../080-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 .../081-libfribidi0_1.0.16-1_arm64.deb ...
Unpacking libfribidi0:arm64 (1.0.16-1) ...
Selecting previously unselected package libglib2.0-0t64:arm64.
Preparing to unpack .../082-libglib2.0-0t64_2.82.4-2_arm64.deb ...
Unpacking libglib2.0-0t64:arm64 (2.82.4-2) ...
Selecting previously unselected package libgraphite2-3:arm64.
Preparing to unpack .../083-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 .../084-libharfbuzz0b_10.2.0-1_arm64.deb ...
Unpacking libharfbuzz0b:arm64 (10.2.0-1) ...
Selecting previously unselected package libraqm0:arm64.
Preparing to unpack .../085-libraqm0_0.10.2-1_arm64.deb ...
Unpacking libraqm0:arm64 (0.10.2-1) ...
Selecting previously unselected package libdeflate0:arm64.
Preparing to unpack .../086-libdeflate0_1.23-1+b1_arm64.deb ...
Unpacking libdeflate0:arm64 (1.23-1+b1) ...
Selecting previously unselected package libjbig0:arm64.
Preparing to unpack .../087-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 .../088-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 .../089-libwebp7_1.5.0-0.1_arm64.deb ...
Unpacking libwebp7:arm64 (1.5.0-0.1) ...
Selecting previously unselected package libtiff6:arm64.
Preparing to unpack .../090-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 .../091-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 .../092-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 .../093-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 .../094-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 .../095-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 .../096-libxpm4_1%3a3.5.17-1+b3_arm64.deb ...
Unpacking libxpm4:arm64 (1:3.5.17-1+b3) ...
Selecting previously unselected package libgd3:arm64.
Preparing to unpack .../097-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 .../098-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 .../099-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 .../100-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 .../101-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 .../102-libxext6_2%3a1.3.4-1+b3_arm64.deb ...
Unpacking libxext6:arm64 (2:1.3.4-1+b3) ...
Selecting previously unselected package libxrender1:arm64.
Preparing to unpack .../103-libxrender1_1%3a0.9.10-1.1+b3_arm64.deb ...
Unpacking libxrender1:arm64 (1:0.9.10-1.1+b3) ...
Selecting previously unselected package libcairo2:arm64.
Preparing to unpack .../104-libcairo2_1.18.2-2_arm64.deb ...
Unpacking libcairo2:arm64 (1.18.2-2) ...
Selecting previously unselected package libltdl7:arm64.
Preparing to unpack .../105-libltdl7_2.5.4-2_arm64.deb ...
Unpacking libltdl7:arm64 (2.5.4-2) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../106-libthai-data_0.1.29-2_all.deb ...
Unpacking libthai-data (0.1.29-2) ...
Selecting previously unselected package libdatrie1:arm64.
Preparing to unpack .../107-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 .../108-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 .../109-libpango-1.0-0_1.56.1-1_arm64.deb ...
Unpacking libpango-1.0-0:arm64 (1.56.1-1) ...
Selecting previously unselected package libpangoft2-1.0-0:arm64.
Preparing to unpack .../110-libpangoft2-1.0-0_1.56.1-1_arm64.deb ...
Unpacking libpangoft2-1.0-0:arm64 (1.56.1-1) ...
Selecting previously unselected package libpangocairo-1.0-0:arm64.
Preparing to unpack .../111-libpangocairo-1.0-0_1.56.1-1_arm64.deb ...
Unpacking libpangocairo-1.0-0:arm64 (1.56.1-1) ...
Selecting previously unselected package libpathplan4:arm64.
Preparing to unpack .../112-libpathplan4_2.42.4-2+b2_arm64.deb ...
Unpacking libpathplan4:arm64 (2.42.4-2+b2) ...
Selecting previously unselected package libgvc6.
Preparing to unpack .../113-libgvc6_2.42.4-2+b2_arm64.deb ...
Unpacking libgvc6 (2.42.4-2+b2) ...
Selecting previously unselected package libgvpr2:arm64.
Preparing to unpack .../114-libgvpr2_2.42.4-2+b2_arm64.deb ...
Unpacking libgvpr2:arm64 (2.42.4-2+b2) ...
Selecting previously unselected package liblab-gamut1:arm64.
Preparing to unpack .../115-liblab-gamut1_2.42.4-2+b2_arm64.deb ...
Unpacking liblab-gamut1:arm64 (2.42.4-2+b2) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../116-x11-common_1%3a7.7+23.2_all.deb ...
Unpacking x11-common (1:7.7+23.2) ...
Selecting previously unselected package libice6:arm64.
Preparing to unpack .../117-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 .../118-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 .../119-libxt6t64_1%3a1.2.1-1.2+b2_arm64.deb ...
Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b2) ...
Selecting previously unselected package libxmu6:arm64.
Preparing to unpack .../120-libxmu6_2%3a1.1.3-3+b4_arm64.deb ...
Unpacking libxmu6:arm64 (2:1.1.3-3+b4) ...
Selecting previously unselected package libxaw7:arm64.
Preparing to unpack .../121-libxaw7_2%3a1.0.16-1_arm64.deb ...
Unpacking libxaw7:arm64 (2:1.0.16-1) ...
Selecting previously unselected package graphviz.
Preparing to unpack .../122-graphviz_2.42.4-2+b2_arm64.deb ...
Unpacking graphviz (2.42.4-2+b2) ...
Selecting previously unselected package libdivsufsort3:arm64.
Preparing to unpack .../123-libdivsufsort3_2.0.1-6+b1_arm64.deb ...
Unpacking libdivsufsort3:arm64 (2.0.1-6+b1) ...
Selecting previously unselected package hmmer.
Preparing to unpack .../124-hmmer_3.4+dfsg-2+b1_arm64.deb ...
Unpacking hmmer (3.4+dfsg-2+b1) ...
Selecting previously unselected package tex-common.
Preparing to unpack .../125-tex-common_6.18_all.deb ...
Unpacking tex-common (6.18) ...
Selecting previously unselected package libpaper2:arm64.
Preparing to unpack .../126-libpaper2_2.2.5-0.3_arm64.deb ...
Unpacking libpaper2:arm64 (2.2.5-0.3) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../127-libpaper-utils_2.2.5-0.3_arm64.deb ...
Unpacking libpaper-utils (2.2.5-0.3) ...
Selecting previously unselected package libkpathsea6:arm64.
Preparing to unpack .../128-libkpathsea6_2024.20240313.70630+ds-5+b1_arm64.deb ...
Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-5+b1) ...
Selecting previously unselected package libptexenc1:arm64.
Preparing to unpack .../129-libptexenc1_2024.20240313.70630+ds-5+b1_arm64.deb ...
Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-5+b1) ...
Selecting previously unselected package libsynctex2:arm64.
Preparing to unpack .../130-libsynctex2_2024.20240313.70630+ds-5+b1_arm64.deb ...
Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-5+b1) ...
Selecting previously unselected package libtexlua53-5:arm64.
Preparing to unpack .../131-libtexlua53-5_2024.20240313.70630+ds-5+b1_arm64.deb ...
Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-5+b1) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../132-t1utils_1.41-4+b1_arm64.deb ...
Unpacking t1utils (1.41-4+b1) ...
Selecting previously unselected package libmpfi0:arm64.
Preparing to unpack .../133-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 .../134-libpotrace0_1.16-2+b2_arm64.deb ...
Unpacking libpotrace0:arm64 (1.16-2+b2) ...
Selecting previously unselected package libteckit0:arm64.
Preparing to unpack .../135-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 .../136-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 .../137-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 .../138-texlive-binaries_2024.20240313.70630+ds-5+b1_arm64.deb ...
Unpacking texlive-binaries (2024.20240313.70630+ds-5+b1) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../139-xdg-utils_1.2.1-2_all.deb ...
Unpacking xdg-utils (1.2.1-2) ...
Selecting previously unselected package texlive-base.
Preparing to unpack .../140-texlive-base_2024.20250114-1_all.deb ...
Unpacking texlive-base (2024.20250114-1) ...
Selecting previously unselected package texlive-latex-base.
Preparing to unpack .../141-texlive-latex-base_2024.20250114-1_all.deb ...
Unpacking texlive-latex-base (2024.20250114-1) ...
Selecting previously unselected package latexmk.
Preparing to unpack .../142-latexmk_1%3a4.86~ds-1_all.deb ...
Unpacking latexmk (1:4.86~ds-1) ...
Selecting previously unselected package libapache-pom-java.
Preparing to unpack .../143-libapache-pom-java_33-2_all.deb ...
Unpacking libapache-pom-java (33-2) ...
Selecting previously unselected package libblas3:arm64.
Preparing to unpack .../144-libblas3_3.12.0-4_arm64.deb ...
Unpacking libblas3:arm64 (3.12.0-4) ...
Selecting previously unselected package libcommons-parent-java.
Preparing to unpack .../145-libcommons-parent-java_56-1_all.deb ...
Unpacking libcommons-parent-java (56-1) ...
Selecting previously unselected package libcommons-logging-java.
Preparing to unpack .../146-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 .../147-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 .../148-libfontenc1_1%3a1.1.8-1+b2_arm64.deb ...
Unpacking libfontenc1:arm64 (1:1.1.8-1+b2) ...
Selecting previously unselected package libgfortran5:arm64.
Preparing to unpack .../149-libgfortran5_14.2.0-14_arm64.deb ...
Unpacking libgfortran5:arm64 (14.2.0-14) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../150-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 .../151-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 .../152-libjs-sphinxdoc_8.1.3-4_all.deb ...
Unpacking libjs-sphinxdoc (8.1.3-4) ...
Selecting previously unselected package libjson-perl.
Preparing to unpack .../153-libjson-perl_4.10000-1_all.deb ...
Unpacking libjson-perl (4.10000-1) ...
Selecting previously unselected package liblapack3:arm64.
Preparing to unpack .../154-liblapack3_3.12.0-4_arm64.deb ...
Unpacking liblapack3:arm64 (3.12.0-4) ...
Selecting previously unselected package libpdfbox-java.
Preparing to unpack .../155-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 .../156-libyaml-0-2_0.2.5-2_arm64.deb ...
Unpacking libyaml-0-2:arm64 (0.2.5-2) ...
Selecting previously unselected package preview-latex-style.
Preparing to unpack .../157-preview-latex-style_13.2-1_all.deb ...
Unpacking preview-latex-style (13.2-1) ...
Selecting previously unselected package python3-packaging.
Preparing to unpack .../158-python3-packaging_24.2-1_all.deb ...
Unpacking python3-packaging (24.2-1) ...
Selecting previously unselected package python3-pyproject-hooks.
Preparing to unpack .../159-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 .../160-python3-toml_0.10.2-1_all.deb ...
Unpacking python3-toml (0.10.2-1) ...
Selecting previously unselected package python3-wheel.
Preparing to unpack .../161-python3-wheel_0.45.1-1_all.deb ...
Unpacking python3-wheel (0.45.1-1) ...
Selecting previously unselected package python3-build.
Preparing to unpack .../162-python3-build_1.2.2-1_all.deb ...
Unpacking python3-build (1.2.2-1) ...
Selecting previously unselected package python3-installer.
Preparing to unpack .../163-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 .../164-pybuild-plugin-pyproject_6.20250108_all.deb ...
Unpacking pybuild-plugin-pyproject (6.20250108) ...
Selecting previously unselected package python-babel-localedata.
Preparing to unpack .../165-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 .../166-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 .../167-python3-babel_2.16.0-1_all.deb ...
Unpacking python3-babel (2.16.0-1) ...
Selecting previously unselected package python3-certifi.
Preparing to unpack .../168-python3-certifi_2024.12.14+ds-1_all.deb ...
Unpacking python3-certifi (2024.12.14+ds-1) ...
Selecting previously unselected package python3-chardet.
Preparing to unpack .../169-python3-chardet_5.2.0+dfsg-2_all.deb ...
Unpacking python3-chardet (5.2.0+dfsg-2) ...
Selecting previously unselected package python3-charset-normalizer.
Preparing to unpack .../170-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 .../171-python3-colorama_0.4.6-4_all.deb ...
Unpacking python3-colorama (0.4.6-4) ...
Selecting previously unselected package python3-colorlog.
Preparing to unpack .../172-python3-colorlog_6.9.0-1_all.deb ...
Unpacking python3-colorlog (6.9.0-1) ...
Selecting previously unselected package python3-dateutil.
Preparing to unpack .../173-python3-dateutil_2.9.0-3_all.deb ...
Unpacking python3-dateutil (2.9.0-3) ...
Selecting previously unselected package python3-defusedxml.
Preparing to unpack .../174-python3-defusedxml_0.7.1-3_all.deb ...
Unpacking python3-defusedxml (0.7.1-3) ...
Selecting previously unselected package python3-roman.
Preparing to unpack .../175-python3-roman_4.2-1_all.deb ...
Unpacking python3-roman (4.2-1) ...
Selecting previously unselected package python3-docutils.
Preparing to unpack .../176-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 .../177-python3-idna_3.8-2_all.deb ...
Unpacking python3-idna (3.8-2) ...
Selecting previously unselected package python3-imagesize.
Preparing to unpack .../178-python3-imagesize_1.4.1-1_all.deb ...
Unpacking python3-imagesize (1.4.1-1) ...
Selecting previously unselected package python3-markupsafe.
Preparing to unpack .../179-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 .../180-python3-jinja2_3.1.3-2_all.deb ...
Unpacking python3-jinja2 (3.1.3-2) ...
Selecting previously unselected package python3-networkx.
Preparing to unpack .../181-python3-networkx_3.2.1-5_all.deb ...
Unpacking python3-networkx (3.2.1-5) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../182-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ...
Unpacking python3-numpy (1:1.26.4+ds-13) ...
Selecting previously unselected package python3-tz.
Preparing to unpack .../183-python3-tz_2024.2-1_all.deb ...
Unpacking python3-tz (2024.2-1) ...
Selecting previously unselected package python3-pandas-lib:arm64.
Preparing to unpack .../184-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 .../185-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 .../186-python3-pygments_2.18.0+dfsg-2_all.deb ...
Unpacking python3-pygments (2.18.0+dfsg-2) ...
Selecting previously unselected package python3-urllib3.
Preparing to unpack .../187-python3-urllib3_2.3.0-1_all.deb ...
Unpacking python3-urllib3 (2.3.0-1) ...
Selecting previously unselected package python3-requests.
Preparing to unpack .../188-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 .../189-python3-snowballstemmer_2.2.0-4_all.deb ...
Unpacking python3-snowballstemmer (2.2.0-4) ...
Selecting previously unselected package sphinx-common.
Preparing to unpack .../190-sphinx-common_8.1.3-4_all.deb ...
Unpacking sphinx-common (8.1.3-4) ...
Selecting previously unselected package python3-sphinx.
Preparing to unpack .../191-python3-sphinx_8.1.3-4_all.deb ...
Unpacking python3-sphinx (8.1.3-4) ...
Selecting previously unselected package sphinx-rtd-theme-common.
Preparing to unpack .../192-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ...
Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ...
Selecting previously unselected package python3-sphinxcontrib.jquery.
Preparing to unpack .../193-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 .../194-python3-sphinx-rtd-theme_3.0.2+dfsg-2_all.deb ...
Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-2) ...
Selecting previously unselected package python3-yaml.
Preparing to unpack .../195-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 .../196-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 .../197-xfonts-utils_1%3a7.7+7_arm64.deb ...
Unpacking xfonts-utils (1:7.7+7) ...
Selecting previously unselected package tex-gyre.
Preparing to unpack .../198-tex-gyre_20180621-6_all.deb ...
Unpacking tex-gyre (20180621-6) ...
Selecting previously unselected package texlive-fonts-recommended.
Preparing to unpack .../199-texlive-fonts-recommended_2024.20250114-1_all.deb ...
Unpacking texlive-fonts-recommended (2024.20250114-1) ...
Selecting previously unselected package texlive-latex-recommended.
Preparing to unpack .../200-texlive-latex-recommended_2024.20250114-1_all.deb ...
Unpacking texlive-latex-recommended (2024.20250114-1) ...
Selecting previously unselected package texlive-pictures.
Preparing to unpack .../201-texlive-pictures_2024.20250114-1_all.deb ...
Unpacking texlive-pictures (2024.20250114-1) ...
Selecting previously unselected package texlive-latex-extra.
Preparing to unpack .../202-texlive-latex-extra_2024.20250114-1_all.deb ...
Unpacking texlive-latex-extra (2024.20250114-1) ...
Selecting previously unselected package texlive-plain-generic.
Preparing to unpack .../203-texlive-plain-generic_2024.20250114-1_all.deb ...
Unpacking texlive-plain-generic (2024.20250114-1) ...
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 libtext-charwidth-perl:arm64 (0.04-11+b4) ...
Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
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 libxcb1:arm64 (1.17.0-2+b1) ...
Setting up fonts-lato (2.015-1) ...
Setting up libicu72:arm64 (72.1-6) ...
Setting up liblerc4:arm64 (4.0.0+ds-5) ...
Setting up bsdextrautils (2.40.4-1) ...
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 (0.2.5-2) ...
Setting up libdebhelper-perl (13.24.1) ...
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+b2) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up x11-common (1:7.7+23.2) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libdeflate0:arm64 (1.23-1+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libtext-wrapi18n-perl (0.06-10) ...
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 tzdata (2025a-1) ...
Current default time zone: 'Etc/UTC'
Local time is now: Tue Jan 21 23:16:42 UTC 2025.
Universal Time is now: Tue Jan 21 23:16:42 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ...
Setting up autotools-dev (20220109.1) ...
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 (2.3.0+dfsg-1) ...
Setting up libteckit0:arm64 (2.5.12+ds1-1+b1) ...
Setting up libpathplan4:arm64 (2.42.4-2+b2) ...
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 (1.0.16-1) ...
Setting up t1utils (1.41-4+b1) ...
Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libimagequant0:arm64 (2.18.0-1+b2) ...
Setting up libproc2-0:arm64 (2:4.0.4-6) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:arm64 (1.6.45-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up libmpfi0:arm64 (1.5.4+ds-4) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libltdl7:arm64 (2.5.4-2) ...
Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libgfortran5:arm64 (14.2.0-14) ...
Setting up autoconf (2.72-3) ...
Setting up libwebp7:arm64 (1.5.0-0.1) ...
Setting up libffi8:arm64 (3.4.6-1) ...
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 (0.7.1-9) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up procps (2:4.0.4-6) ...
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 sgml-base (1.31) ...
Setting up libcdt5:arm64 (2.42.4-2+b2) ...
Setting up libcgraph6:arm64 (2.42.4-2+b2) ...
Setting up libpaper2:arm64 (2.2.5-0.3) ...
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 (3.4.0-2) ...
Setting up libyuv0:arm64 (0.0.1899.20250103-1) ...
Setting up readline-common (8.2-6) ...
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-2) ...
Setting up xdg-utils (1.2.1-2) ...
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+b1) ...
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 (1.14.1-1) ...
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 (0.23.1-1) ...
Setting up libpdfbox-java (1:1.8.16-5) ...
Setting up libxpm4:arm64 (1:3.5.17-1+b3) ...
Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ...
Setting up libtool (2.5.4-2) ...
Setting up fontconfig-config (2.15.0-2) ...
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+b3) ...
Setting up libpaper-utils (2.2.5-0.3) ...
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 (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libglib2.0-0t64:arm64 (2.82.4-2) ...
No schema files found: doing nothing.
Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ...
Setting up libgav1-1:arm64 (0.19.0-3) ...
Setting up ucf (3.0048) ...
Setting up libjs-sphinxdoc (8.1.3-4) ...
Setting up libreadline8t64:arm64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-1) ...
Setting up libgvpr2:arm64 (2.42.4-2+b2) ...
Setting up groff-base (1.23.0-7) ...
Setting up xml-core (0.19) ...
Setting up hmmer (3.4+dfsg-2+b1) ...
Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ...
Setting up libfontconfig1:arm64 (2.15.0-2) ...
Setting up libsm6:arm64 (2:1.2.4-1) ...
Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ...
Setting up libpython3-stdlib:arm64 (3.13.1-2) ...
Setting up fontconfig (2.15.0-2) ...
Regenerating fonts cache... done.
Setting up libavif16:arm64 (1.1.1-1) ...
Setting up libxi6:arm64 (2:1.8.2-1) ...
Setting up python3.13 (3.13.1-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpango-1.0-0:arm64 (1.56.1-1) ...
Setting up python3 (3.13.1-2) ...
Setting up python3-zipp (3.21.0-1) ...
Setting up xfonts-utils (1:7.7+7) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3-markupsafe (2.1.5-1+b3) ...
Setting up python3-wheel (0.45.1-1) ...
Setting up libcairo2:arm64 (1.18.2-2) ...
Setting up python3-tz (2024.2-1) ...
Setting up tex-common (6.18) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up python3-roman (4.2-1) ...
Setting up python3-jinja2 (3.1.3-2) ...
Setting up python3-pygments (2.18.0+dfsg-2) ...
Setting up python3-packaging (24.2-1) ...
Setting up python3-chardet (5.2.0+dfsg-2) ...
Setting up python3-pyproject-hooks (1.2.0-1) ...
Setting up python3-certifi (2024.12.14+ds-1) ...
Setting up python3-snowballstemmer (2.2.0-4) ...
Setting up libraqm0:arm64 (0.10.2-1) ...
Setting up sphinx-common (8.1.3-4) ...
Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ...
Setting up python3-idna (3.8-2) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up python3-numpy (1:1.26.4+ds-13) ...
Setting up python3-toml (0.10.2-1) ...
Setting up python3-installer (0.7.0+dfsg1-3) ...
Setting up python3-urllib3 (2.3.0-1) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ...
Setting up python3-build (1.2.2-1) ...
Setting up tex-gyre (20180621-6) ...
Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ...
Setting up python3-imagesize (1.4.1-1) ...
Setting up python3-more-itertools (10.6.0-1) ...
Setting up libxmu6:arm64 (2:1.1.3-3+b4) ...
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 (0.7.1-3) ...
Setting up python3-charset-normalizer (3.4.0-1+b1) ...
Setting up python3-alabaster (0.7.16-0.1) ...
Setting up preview-latex-style (13.2-1) ...
Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ...
Setting up python3-typeguard (4.4.1-1) ...
Setting up python3-yaml (6.0.2-1+b1) ...
Setting up debhelper (13.24.1) ...
Setting up libxaw7:arm64 (2:1.0.16-1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pandas (2.2.3+dfsg-5) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-requests (2.32.3+dfsg-1) ...
Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ...
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 (2024.20250114-1) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
Setting up python3-pkg-resources (75.6.0-1) ...
Setting up python3-setuptools (75.6.0-1) ...
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 texlive-plain-generic (2024.20250114-1) ...
Setting up python3-networkx (3.2.1-5) ...
Setting up texlive-latex-base (2024.20250114-1) ...
Setting up texlive-latex-recommended (2024.20250114-1) ...
Setting up texlive-pictures (2024.20250114-1) ...
Setting up texlive-fonts-recommended (2024.20250114-1) ...
Setting up dh-python (6.20250108) ...
Setting up pybuild-plugin-pyproject (6.20250108) ...
Setting up latexmk (1:4.86~ds-1) ...
Setting up texlive-latex-extra (2024.20250114-1) ...
Setting up libheif-plugin-dav1d:arm64 (1.19.5-1) ...
Setting up libheif-plugin-libde265:arm64 (1.19.5-1) ...
Setting up libheif1:arm64 (1.19.5-1) ...
Setting up libgd3:arm64 (2.3.3-12+b1) ...
Setting up libgvc6 (2.42.4-2+b2) ...
Setting up graphviz (2.42.4-2+b2) ...
Processing triggers for libc-bin (2.40-5) ...
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 (8.1.3-4) ...
Setting up python3-sphinxcontrib.jquery (4.1-5) ...
Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for tex-common (6.18) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
This may take some time... done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/macsyfinder-2.1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../macsyfinder_2.1.4-1_source.changes
dpkg-buildpackage: info: source package macsyfinder
dpkg-buildpackage: info: source version 2.1.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
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 python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13
* 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_3.13/.tmp-1poxb4l3/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 python3.13 with "installer" module
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v
/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/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_3.13/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_3.13/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_3.13/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_3.13/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_3.13/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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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_3.13/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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: 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/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp4tovvy5z/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/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpjy_uvz4u/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/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpujoonygr/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/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpvp8w7wzb/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_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpjfjctvhu/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_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpjfjctvhu/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_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpw9hxx8ko/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_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpw9hxx8ko/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_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpghvd6c78/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_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpghvd6c78/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_3.13/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/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp64xnrswp' 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_3.13/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_3.13/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_3.13/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 17.745s
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 python3.13 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 v8.1.3
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. [docutils]
/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. [docutils]
/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. [docutils]
/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. [docutils]
/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. [docutils]
/build/reproducible-path/macsyfinder-2.1.4/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: ERROR: Unexpected indentation. [docutils]
/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. [docutils]
/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. [docutils]
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...
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/language_data.js
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/documentation_options.js
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/basic.css
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/js/versions.js
copying static files: done
copying extra files...
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 v8.1.3
loading translations [en]... done
making output directory... done
loading pickled environment... The configuration has changed (3 options: 'html_css_files', 'html_permalinks_icon', 'jquery_use_sri')
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
preparing documents... done
copying assets...
copying TeX support files... Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/make.bat
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/latexmkrc
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/latexmkjarc
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/Makefile
done
copying assets: 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...
processing macsyfinder.tex: 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
Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/sphinxmessages.sty
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, 11 Dec. 2024. Version 4.86.
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> patch level 1
L3 programming layer <2024-12-25>
(./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<<t1.cmap>>)
(/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)
(./sphinxpackagefootnote.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) (./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/etoolbox/etoolbox.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/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)<<ot1.cmap>><<oml.cmap>><<oms.cma
p>><<omx.cmap>> (/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.
LaTeX Warning: Hyper reference `modeler_guide/modeling:components' on page 5 un
defined on input line 366.
LaTeX Warning: Hyper reference `modeler_guide/modeling:multi-model-label' on pa
ge 5 undefined on input line 370.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 5 undef
ined on input line 374.
LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag
e 5 undefined on input line 378.
LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 5 un
defined on input line 382.
LaTeX Warning: Hyper reference `modeler_guide/models_V1ToV2:models-v1-v2' on pa
ge 5 undefined on input line 386.
LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 5 undefined
on input line 395.
[5]
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.
LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 6 un
defined on input line 418.
LaTeX Warning: Hyper reference `modeler_guide/package:model-configuration' on p
age 6 undefined on input line 424.
LaTeX Warning: Hyper reference `modeler_guide/helper_tools:macsyprofile' on pag
e 6 undefined on input line 431.
LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 6 un
defined on input line 434.
LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 6 un
defined on input line 453.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 6 undef
ined on input line 474.
[6]
LaTeX Warning: Hyper reference `developer_guide/installation:dev-installation'
on page 7 undefined on input line 516.
LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa
ge 7 undefined on input line 582.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 7 undef
ined on input line 583.
[7]
[8]
[9]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 765.
[10]
LaTeX Warning: Hyper reference `user_guide/installation:user-installation' on p
age 11 undefined on input line 896.
LaTeX Warning: Hyper reference `user_guide/input:input-dataset-label' on page 1
1 undefined on input line 913.
LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o
n page 11 undefined on input line 919.
LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 11 u
ndefined on input line 921.
LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 11
undefined on input line 933.
[11]
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 12 undefined on input line 976.
LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 12
undefined on input line 990.
[12]
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 13 undefine
d on input line 1050.
LaTeX Warning: Hyper reference `user_guide/FAQ:faq-search-mode' on page 13 unde
fined on input line 1051.
LaTeX Warning: Hyper reference `user_guide/input:config-base-label' on page 13
undefined on input line 1073.
LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa
ge 13 undefined on input line 1073.
LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 13
undefined on input line 1076.
LaTeX Warning: Hyper reference `user_guide/input:cmd-input-label' on page 13 un
defined on input line 1076.
LaTeX Warning: Hyper reference `user_guide/gembase_convention:gembase-conventio
n' on page 13 undefined on input line 1095.
LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 13
undefined on input line 1107.
LaTeX Warning: Hyper reference `user_guide/input:cmd-input-label' on page 13 un
defined on input line 1108.
LaTeX Warning: Hyper reference `user_guide/input:config-base-label' on page 13
undefined on input line 1109.
LaTeX Warning: Hyper reference `user_guide/gembase_convention:gembase-conventio
n' on page 13 undefined on input line 1113.
LaTeX Warning: Hyper reference `user_guide/gembase_convention:topology-files' o
n page 13 undefined on input line 1113.
[13] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd)
[14]
[15]
[16]
Overfull \vbox (2.32195pt too high) detected at line 1330
[17]
LaTeX Warning: Hyper reference `user_guide/FAQ:cmd-line-examples' on page 18 un
defined on input line 1334.
LaTeX Warning: Hyper reference `user_guide/quickstart:quickstart' on page 18 un
defined on input line 1334.
LaTeX Warning: Hyper reference `developer_guide/api/config:configuration' on pa
ge 18 undefined on input line 1351.
[18]
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 19 undefined on input line 1410.
LaTeX Warning: Hyper reference `developer_guide/api/config:configuration' on pa
ge 19 undefined on input line 1414.
[19]
[20]
LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 21 undefine
d on input line 1693.
[21]
[22]
LaTeX Warning: Hyper reference `user_guide/outputs:ordered-outputs' on page 23
undefined on input line 1837.
LaTeX Warning: Hyper reference `user_guide/outputs:unordered-outputs' on page 2
3 undefined on input line 1837.
LaTeX Warning: Hyper reference `user_guide/outputs:hmmer-outputs-label' on page
23 undefined on input line 1841.
LaTeX Warning: Hyper reference `user_guide/outputs:logs-and-conf' on page 23 un
defined on input line 1845.
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 2
3 undefined on input line 1872.
LaTeX Warning: Hyper reference `user_guide/outputs:sort-eqt-best-solution' on p
age 23 undefined on input line 1874.
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 2
3 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 23 undefined on input line 1887.
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-multisystems-t
sv' on page 23 undefined on input line 1887.
[23]
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-summary-tsv' o
n page 24 undefined on input line 1893.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt' on page 24
undefined on input line 1897.
LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-tsv' on
page 24 undefined on input line 1903.
LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-txt' on
page 24 undefined on input line 1903.
LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-tsv' on
page 24 undefined on input line 1905.
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 2
4 undefined on input line 1909.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 24
undefined on input line 1914.
LaTeX Warning: Hyper reference `user_guide/functioning:combinatorial-exploratio
n' on page 24 undefined on input line 1997.
[24]
Underfull \vbox (badness 10000) detected at line 2089
Overfull \vbox (3.12196pt too high) detected at line 2089
[25]
[26]
[27]
Underfull \vbox (badness 10000) detected at line 2232
[28]
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 29
undefined on input line 2248.
[29]
[30]
Underfull \vbox (badness 1226) detected at line 2406
[31]
Underfull \vbox (badness 10000) detected at line 2406
Underfull \vbox (badness 10000) detected at line 2406
[32]
[33]
Overfull \vbox (1.2275pt too high) detected at line 2545
[34]
[35]
[36]
[37]
[38]
Underfull \vbox (badness 10000) detected at line 2761
Underfull \vbox (badness 10000) detected at line 2761
[39]
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 4
0 undefined on input line 2771.
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-summary-tsv' o
n page 40 undefined on input line 2775.
LaTeX Warning: Hyper reference `user_guide/outputs:best-solution-tsv' on page 4
0 undefined on input line 2779.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 40
undefined on input line 2783.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt' on page 40
undefined on input line 2783.
LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-tsv' on
page 40 undefined on input line 2787.
LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-txt' on
page 40 undefined on input line 2787.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt-unordered' o
n page 40 undefined on input line 2816.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv-unordered' o
n page 40 undefined on input line 2820.
LaTeX Warning: Hyper reference `user_guide/outputs:uncomplete-unordered' on pag
e 40 undefined on input line 2824.
[40]
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-txt' on page 41
undefined on input line 2841.
[41]
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv' on page 42
undefined on input line 2897.
[42]
[43]
[44]
pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec
df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all
owed
pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843
641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all
owed
LaTeX Warning: Hyper reference `user_guide/installation:user-installation' on p
age 45 undefined on input line 3097.
[45]
[46 <./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
>]
[47]
LaTeX Warning: Hyper reference `user_guide/input:general-options' on page 48 un
defined on input line 3233.
[48]
[49]
[50]
[51]
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 52 undefined on input line 3531.
LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 52
undefined on input line 3532.
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 52 undefined on input line 3539.
LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa
ge 52 undefined on input line 3543.
LaTeX Warning: Hyper reference `modeler_guide/index:modeler-guide' on page 52 u
ndefined on input line 3553.
[52]
LaTeX Warning: Hyper reference `user_guide/input:path-options' on page 53 undef
ined on input line 3646.
LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag
e 53 undefined on input line 3654.
LaTeX Warning: Hyper reference `user_guide/input:input-dataset-label' on page 5
3 undefined on input line 3666.
[53]
LaTeX Warning: Hyper reference `modeler_guide/modeling:writing-models' on page
54 undefined on input line 3702.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 54 unde
fined on input line 3706.
LaTeX Warning: Hyper reference `developer_guide/api/report:hmmreport' on page 5
4 undefined on input line 3706.
LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 54
undefined on input line 3708.
LaTeX Warning: Hyper reference `developer_guide/api/search_genes:search-genes'
on page 54 undefined on input line 3708.
LaTeX Warning: Hyper reference `user_guide/input:input-dataset-label' on page 5
4 undefined on input line 3719.
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-genomic
-orga' on page 54 undefined on input line 3724.
[54 <./msf_functionning_step1.pdf>]
LaTeX Warning: Hyper reference `user_guide/functioning:combinatorial-exploratio
n' on page 55 undefined on input line 3759.
LaTeX Warning: Hyper reference `user_guide/outputs:rejected-candidates-txt' on
page 55 undefined on input line 3763.
LaTeX Warning: Hyper reference `user_guide/outputs:all-systems-tsv-unordered' o
n page 55 undefined on input line 3793.
[55 <./msf_functionning_step2.pdf>]
LaTeX Warning: Hyper reference `user_guide/outputs:unordered-outputs' on page 5
6 undefined on input line 3805.
LaTeX Warning: Hyper reference `user_guide/outputs:outputs' on page 56 undefine
d on input line 3844.
LaTeX Warning: Hyper reference `user_guide/input:score-options' on page 56 unde
fined on input line 3861.
[56]
[57 <./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
>]
[58 <./msf_functionning_step5.pdf>]
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
[59]
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 60 un
defined on input line 4103.
LaTeX Warning: Hyper reference `user_guide/gembase_convention:gembase-conventio
n' on page 60 undefined on input line 4121.
LaTeX Warning: Hyper reference `user_guide/input:command-line-label' on page 60
undefined on input line 4138.
LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 60
undefined on input line 4138.
[60]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4176.
[61]
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 62
undefined on input line 4258.
LaTeX Warning: Hyper reference `user_guide/installation:macsydata' on page 62 u
ndefined on input line 4283.
[62]
[63]
[64]
Chapter 2.
LaTeX Warning: Hyper reference `modeler_guide/installation:modeler-macsydata' o
n page 65 undefined on input line 4352.
[65 <./logo_macsymodels.png>]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4393.
[66]
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 67 undefined on input line 4527.
LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 67
undefined on input line 4528.
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 67 undefined on input line 4535.
LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa
ge 67 undefined on input line 4539.
[67]
[68]
[69]
[70]
LaTeX Warning: Hyper reference `user_guide/functioning:combinatorial-exploratio
n' on page 71 undefined on input line 4842.
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 71 undefined on input line 4855.
LaTeX Warning: Hyper reference `user_guide/functioning:functioning' on page 71
undefined on input line 4856.
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 71 undefined on input line 4864.
LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa
ge 71 undefined on input line 4868.
[71]
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 72 undefined on input line 4956.
[72]
LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa
ge 73 undefined on input line 5025.
[73 <./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.
[74 <./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
[75 <./multi_system.pdf>]
LaTeX Warning: Hyper reference `modeler_guide/gallery:gallery-models' on page 7
6 undefined on input line 5213.
[76]
LaTeX Warning: Hyper reference `modeler_guide/modeling:provide-hmm-label' on pa
ge 77 undefined on input line 5275.
[77]
Overfull \vbox (2.5072pt too high) detected at line 5384
[78]
[79]
[80]
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
LaTeX Warning: Hyper reference `modeler_guide/package:package-structure' on pag
e 81 undefined on input line 5549.
[81]
LaTeX Warning: Hyper reference `modeler_guide/package:model-package' on page 82
undefined on input line 5620.
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 #
[82]
Underfull \vbox (badness 10000) detected at line 5739
Overfull \vbox (1.56999pt too high) detected at line 5739
[83]
Overfull \vbox (1.35179pt too high) detected at line 5805
[84]
LaTeX Warning: Hyper reference `modeler_guide/gallery:getting-started-with-a-on
e-component-system-the-autotransporter-t5ss' on page 85 undefined on input line
5828.
LaTeX Warning: Hyper reference `modeler_guide/gallery:a-not-so-simple-example-m
odelling-the-t1ss' on page 85 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
5 undefined on input line 5836.
[85]
[86 <./T1SS_example.pdf>]
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 87 undefined on input line 5980.
[87]
[88 <./T3SS_example.pdf>]
LaTeX Warning: Hyper reference `modeler_guide/models_V1ToV2:ex2' on page 89 und
efined on input line 6129.
[89]
LaTeX Warning: Hyper reference `modeler_guide/publish_package:publish-package'
on page 90 undefined on input line 6151.
LaTeX Warning: Hyper reference `modeler_guide/package:model-package' on page 90
undefined on input line 6151.
[90]
[91]
Underfull \vbox (badness 1226) detected at line 6332
[92]
[93]
LaTeX Warning: Hyper reference `modeler_guide/modeling:exchangeables-label' on
page 94 undefined on input line 6423.
[94 <./multi_model.pdf>]
Chapter 3.
LaTeX Warning: Hyper reference `modeler_guide/installation:modeler-macsydata' o
n page 95 undefined on input line 6440.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 95 unde
fined on input line 6461.
[95]
LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa
ge 96 undefined on input line 6542.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 96 unde
fined on input line 6543.
[96]
pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found
PDF version <1.7>, but at most version <1.5> allowed
[97]
[98 <./macsyfinder_classes.pdf>]
LaTeX Warning: Hyper reference `developer_guide/api/config:configuration' on pa
ge 99 undefined on input line 6746.
LaTeX Warning: Hyper reference `developer_guide/api/solution:macsypy.solution.f
ind_best_solutions' on page 99 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.
LaTeX Warning: Hyper reference `developer_guide/api/model:model' on page 99 und
efined on input line 6822.
LaTeX Warning: Hyper reference `modeler_guide/modeling:model-definition-grammar
-label' on page 99 undefined on input line 6825.
LaTeX Warning: Hyper reference `developer_guide/api/definition_parser:definitio
n-parser' on page 99 undefined on input line 6828.
[99]
LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o
n page 100 undefined on input line 6856.
LaTeX Warning: Hyper reference `developer_guide/api/gene:id1' on page 100 undef
ined on input line 6863.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 100 undefined on input line 6864.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
file' on page 100 undefined on input line 6866.
LaTeX Warning: Hyper reference `developer_guide/overview:profile-implementation
' on page 100 undefined on input line 6868.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 100 undefined on input line 6872.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 100 undefined on input line 6875.
LaTeX Warning: Hyper reference `developer_guide/api/gene:id1' on page 100 undef
ined on input line 6876.
LaTeX Warning: Hyper reference `developer_guide/api/gene:exchangeable-api' on p
age 100 undefined on input line 6882.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank'
on page 100 undefined on input line 6888.
LaTeX Warning: Hyper reference `developer_guide/api/report:macsypy.report.HMMRe
port' on page 100 undefined on input line 6905.
LaTeX Warning: Hyper reference `user_guide/input:hmmer-options' on page 100 und
efined on input line 6910.
LaTeX Warning: Hyper reference `user_guide/outputs:hmmer-outputs-label' on page
100 undefined on input line 6911.
LaTeX Warning: Hyper reference `developer_guide/api/hit:hit' on page 100 undefi
ned on input line 6912.
[100]
LaTeX Warning: Hyper reference `user_guide/input:config-definition-label' on pa
ge 101 undefined on input line 6925.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 101 undefined on input line 6929.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 101 undefined on input line 6930.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 101 undefined on input line 7000.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 101 undefined on input line 7013.
[101]
[102]
Underfull \hbox (badness 6775) in paragraph at lines 7400--7402
\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
[103]
[104]
[105]
LaTeX Warning: Hyper reference `developer_guide/api/package:macsypy.package.Pac
kage' on page 106 undefined on input line 7893.
Underfull \hbox (badness 10000) in paragraph at lines 8008--8011
[]\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
[106]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 107 undefined on input line 8134.
[107]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 108 undefined on input line 8200.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 108 undefined on input line 8218.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 108 undefined on input line 8256.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 108 undefined on input line 8271.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 108 undefined on input line 8315.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 108 undefined on input line 8358.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 108 undefined on input line 8358.
[108]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 109 undefined on input line 8427.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 109 undefined on input line 8454.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 109 undefined on input line 8487.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation.get_all_definitions' on page 109 undefined on input line 8493.
[109]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8586.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8604.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8619.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8649.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8661.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8704.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 110 undefined on input line 8725.
[110]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 111 undefined on input line 8858.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 111 undefined on input line 8881.
LaTeX Warning: Hyper reference `user_guide/model_definition:model-definition' o
n page 111 undefined on input line 8895.
[111]
[112]
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 113 undefined on input line 9033.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC
onfig' on page 113 undefined on input line 9033.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.ModelBa
nk' on page 113 undefined on input line 9033.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank'
on page 113 undefined on input line 9033.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelRegistry' on page 113 undefined on input line 9033.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
fileFactory' on page 113 undefined on input line 9033.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 113 undefined on input line 9045.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC
onfig' on page 113 undefined on input line 9045.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.ModelBa
nk' on page 113 undefined on input line 9045.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank'
on page 113 undefined on input line 9045.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelRegistry' on page 113 undefined on input line 9045.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
fileFactory' on page 113 undefined on input line 9045.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.ModelIn
consistencyError' on page 113 undefined on input line 9114.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 113 undefined on input line 9128.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 113 undefined on input line 9128.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 113 undefined on input line 9157.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 113 undefined on input line 9157.
[113]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 114 undefined on input line 9189.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 114 undefined on input line 9207.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 114 undefined on input line 9207.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.Exchangea
ble' on page 114 undefined on input line 9207.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 114 undefined on input line 9243.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 114 undefined on input line 9272.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.ModelIn
consistencyError' on page 114 undefined on input line 9284.
[114{/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 115 undefined on input line 9379.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 115 undefined on input line 9491.
[115]
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 116 undefined on input line 9516.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 116 undefined on input line 9603.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 116 undefined on input line 9661.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 116 undefined on input line 9684.
[116]
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.ModelIn
consistencyError' on page 117 undefined on input line 9758.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 117 undefined on input line 9773.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 117 undefined on input line 9840.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 117 undefined on input line 9840.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 117 undefined on input line 9873.
[117]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 118 undefined on input line 9897.
LaTeX Warning: Hyper reference `developer_guide/api/gene:id1' on page 118 undef
ined on input line 10025.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 118 undefined on input line 10026.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank'
on page 118 undefined on input line 10034.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.ModelBa
nk' on page 118 undefined on input line 10035.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syfinder.main' on page 118 undefined on input line 10036.
[118]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 119 undefined on input line 10112.
[119]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 120 undefined on input line 10141.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 120 undefined on input line 10210.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
fileFactory' on page 120 undefined on input line 10210.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 120 undefined on input line 10262.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 120 undefined on input line 10262.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneBank'
on page 120 undefined on input line 10263.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 120 undefined on input line 10272.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 120 undefined on input line 10285.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
fileFactory' on page 120 undefined on input line 10285.
[120]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 121 undefined on input line 10313.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
fileFactory' on page 121 undefined on input line 10313.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
file' on page 121 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 121 undefined on input line 10383.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 121 undefined on input line 10383.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 121 undefined on input line 10410.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 121 undefined on input line 10410.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.Exchangea
ble' on page 121 undefined on input line 10482.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 121 undefined on input line 10503.
[121]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 122 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 122 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 122 undefined on input line 10571.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 122 undefined on input line 10610.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 122 undefined on input line 10632.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 122 undefined on input line 1.
[122]
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 123 undefined on input line 10691.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 123 undefined on input line 10732.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 123 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 123 undefined on input line 10775.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 123 undefined on input line 10775.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 123 undefined on input line 10788.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 123 undefined on input line 10788.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.Exchangea
ble' on page 123 undefined on input line 10813.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 123 undefined on input line 10824.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 123 undefined on input line 10838.
[123]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 124 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/overview:profile-implementation
' on page 124 undefined on input line 10943.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 124 undefined on input line 10961.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC
onfig' on page 124 undefined on input line 10961.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 124 undefined on input line 10977.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.NoneC
onfig' on page 124 undefined on input line 10977.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 124 undefined on input line 11002.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 124 undefined on input line 11002.
LaTeX Warning: Hyper reference `developer_guide/api/profile:macsypy.profile.Pro
file' on page 124 undefined on input line 11002.
[124]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 125 undefined on input line 11039.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 125 undefined on input line 11039.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 125 undefined on input line 11051.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 125 undefined on input line 11051.
LaTeX Warning: Hyper reference `developer_guide/api/report:macsypy.report.HMMRe
port' on page 125 undefined on input line 11151.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.AbstractCou
nterpartHit' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS
ystem' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight'
on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi
t_4_func' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.sort_model_
hits' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.compute_bes
t_MSHit' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi
ts' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.AbstractCou
nterpartHit' on page 125 undefined on input line 11264.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[]\T1/txtt/m/sl/10 macsypy.hit.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS
ystem' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight'
on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi
t_4_func' on page 125 undefined on input line 11264.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[]\T1/txtt/m/sl/10 macsypy.hit.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.sort_model_
hits' on page 125 undefined on input line 11264.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.compute_bes
t_MSHit' on page 125 undefined on input line 11264.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[]\T1/txtt/m/sl/10 macsypy.hit.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.get_best_hi
ts' on page 125 undefined on input line 11264.
[125]
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 11301.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 126 undefined on input line 11316.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 126 undefined on input line 11322.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 126 undefined on input line 11331.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 126 undefined on input line 11356.
[126 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>]
[127 <./gene_obj_interaction.pdf>]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 128 undefined on input line 11397.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 128 undefined on input line 11458.
[128]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 129 undefined on input line 11543.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 129 undefined on input line 11543.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 129 undefined on input line 11543.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 129 undefined on input line 11574.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 129 undefined on input line 11589.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 129 undefined on input line 11619.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 129 undefined on input line 11619.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 129 undefined on input line 11619.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
.alternate_of' on page 129 undefined on input line 11634.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 129 undefined on input line 11659.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 129 undefined on input line 1.
[129]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 130 undefined on input line 11787.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 130 undefined on input line 11787.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 130 undefined on input line 11787.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 130 undefined on input line 11787.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 130 undefined on input line 11787.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 130 undefined on input line 11799.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 130 undefined on input line 11799.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 130 undefined on input line 11799.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 130 undefined on input line 11799.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 130 undefined on input line 11799.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
.alternate_of' on page 130 undefined on input line 11814.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 130 undefined on input line 1.
[130]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 11923.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 131 undefined on input line 11923.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 131 undefined on input line 11923.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 131 undefined on input line 11923.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 11923.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 11935.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 131 undefined on input line 11935.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 131 undefined on input line 11935.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 131 undefined on input line 11935.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 11935.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
.alternate_of' on page 131 undefined on input line 11953.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 12019.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 131 undefined on input line 12019.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 131 undefined on input line 12019.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 131 undefined on input line 12019.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 12019.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 12031.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 131 undefined on input line 12031.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 131 undefined on input line 12031.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 131 undefined on input line 12031.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 131 undefined on input line 12031.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
.alternate_of' on page 131 undefined on input line 12049.
[131]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 132 undefined on input line 12100.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 132 undefined on input line 12100.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 132 undefined on input line 12100.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 132 undefined on input line 12100.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 132 undefined on input line 12100.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 132 undefined on input line 12126.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 132 undefined on input line 12126.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 132 undefined on input line 12126.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 132 undefined on input line 12126.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 132 undefined on input line 12126.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 132 undefined on input line 12138.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
.alternate_of' on page 132 undefined on input line 12144.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.GeneStatu
s' on page 132 undefined on input line 12153.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 132 undefined on input line 12157.
[132]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 133 undefined on input line 12325.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 133 undefined on input line 12325.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 133 undefined on input line 12378.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 133 undefined on input line 12381.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 133 undefined on input line 12385.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 133 undefined on input line 12406.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS
ystem' on page 133 undefined on input line 12406.
[133]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 134 undefined on input line 12431.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 134 undefined on input line 12431.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 134 undefined on input line 12431.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 134 undefined on input line 12431.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 134 undefined on input line 12453.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 134 undefined on input line 12467.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 134 undefined on input line 12495.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 134 undefined on input line 12495.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 134 undefined on input line 12507.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 134 undefined on input line 12529.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 134 undefined on input line 12529.
[134]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 135 undefined on input line 12607.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight'
on page 135 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 135 undefined on input line 12723.
[135]
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 136 undefined on input line 12742.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 136 undefined on input line 12786.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 136 undefined on input line 12786.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 136 undefined on input line 12860.
LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R
epliconInfo' on page 136 undefined on input line 12860.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 136 undefined on input line 12860.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.HitWeight'
on page 136 undefined on input line 12860.
[136]
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 137 undefined on input line 12917.
Underfull \hbox (badness 10000) in paragraph at lines 12920--12922
[]\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 137 undefined on input line 12947.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 137 undefined on input line 12948.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 137 undefined on input line 12949.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik
elySystem' on page 137 undefined on input line 12949.
pdfTeX warning: pdflatex (file ./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c662
2aab72.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5>
allowed
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Abstr
actSetOfHits' on page 137 undefined on input line 12959.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.MetaS
etOfHits' on page 137 undefined on input line 12960.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.MetaS
etOfHits' on page 137 undefined on input line 12961.
pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c
5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5>
allowed
[137 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf>]
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 138 undefined on input line 12979.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 138 undefined on input line 12992.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 138 undefined on input line 13017.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13071.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13071.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13071.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13071.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13071.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13074.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 138 undefined on input line 13078.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 138 undefined on input line 13086.
[138 <./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf>]
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 139 undefined on input line 13130.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 139 undefined on input line 13130.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 139 undefined on input line 13130.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 139 undefined on input line 13134.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 139 undefined on input line 13139.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 139 undefined on input line 13147.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 139 undefined on input line 13147.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 139 undefined on input line 13167.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 139 undefined on input line 13176.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 139 undefined on input line 13176.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik
elySystem' on page 139 undefined on input line 13176.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 139 undefined on input line 13200.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 139 undefined on input line 13212.
[139]
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 140 undefined on input line 13374.
[140]
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 141 undefined on input line 13495.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 141 undefined on input line 13495.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 141 undefined on input line 13495.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 141 undefined on input line 13507.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 141 undefined on input line 13511.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 141 undefined on input line 13551.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 141 undefined on input line 13551.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 141 undefined on input line 13556.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 141 undefined on input line 13560.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 141 undefined on input line 13591.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 141 undefined on input line 13609.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS
ystem' on page 141 undefined on input line 13609.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 141 undefined on input line 13627.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS
ystem' on page 141 undefined on input line 13627.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 141 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 141 undefined on input line 13661.
[141]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 142 undefined on input line 13672.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 142 undefined on input line 13814.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 142 undefined on input line 13814.
[142]
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 143 undefined on input line 13824.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 13824.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 143 undefined on input line 13913.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 13913.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 13913.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 13913.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 13913.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 143 undefined on input line 1.
[143]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 144 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/model:macsypy.model.Model'
on page 144 undefined on input line 14103.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 144 undefined on input line 14103.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 144 undefined on input line 14103.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 144 undefined on input line 14103.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.ModelHit' o
n page 144 undefined on input line 14103.
[144]
LaTeX Warning: Hyper reference `developer_guide/overview:report-implementation'
on page 145 undefined on input line 14184.
LaTeX Warning: Hyper reference `user_guide/outputs:hmmer-outputs-label' on page
145 undefined on input line 14185.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 145 undefined on input line 14201.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 145 undefined on input line 14201.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 145 undefined on input line 14217.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 145 undefined on input line 14217.
[145]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 146 undefined on input line 14375.
Underfull \hbox (badness 10000) in paragraph at lines 14440--14442
\T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (<it
ertools._grouper object at
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 146 undefined on input line 14463.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 146 undefined on input line 14478.
[146]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 147 undefined on input line 14517.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 147 undefined on input line 14517.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 147 undefined on input line 14561.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 147 undefined on input line 14561.
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.CoreGene'
on page 147 undefined on input line 14605.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 147 undefined on input line 14605.
[147]
LaTeX Warning: Hyper reference `developer_guide/api/gene:macsypy.gene.ModelGene
' on page 148 undefined on input line 14675.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 148 undefined on input line 14675.
LaTeX Warning: Hyper reference `developer_guide/api/report:macsypy.report.HMMRe
port' on page 148 undefined on input line 14675.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 148 undefined on input line 14707.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 148 undefined on input line 14765.
[148]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 149 undefined on input line 14829.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 149 undefined on input line 14896.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 149 undefined on input line 14896.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 149 undefined on input line 1.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 149 undefined on input line 14996.
[149]
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 150 undefined on input line 15009.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 150 undefined on input line 15010.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.LonerMultiS
ystem' on page 150 undefined on input line 15011.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 150 undefined on input line 15025.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 150 undefined on input line 15042.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 150 undefined on input line 15042.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 150 undefined on input line 15051.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 150 undefined on input line 15052.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 150 undefined on input line 15062.
LaTeX Warning: Hyper reference `developer_guide/api/cluster:macsypy.cluster.Clu
ster' on page 150 undefined on input line 15063.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 150 undefined on input line 15080.
LaTeX Warning: Hyper reference `developer_guide/api/solution:macsypy.solution.S
olution' on page 150 undefined on input line 15080.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 150 undefined on input line 15083.
LaTeX Warning: Hyper reference `developer_guide/api/solution:macsypy.solution.S
olution' on page 150 undefined on input line 15092.
[150]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 151 undefined on input line 15175.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 151 undefined on input line 15175.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 151 undefined on input line 15178.
LaTeX Warning: Hyper reference `developer_guide/api/solution:macsypy.solution.S
olution' on page 151 undefined on input line 15244.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 151 undefined on input line 15244.
LaTeX Warning: Hyper reference `developer_guide/api/serialization:macsypy.seria
lization.TsvSystemSerializer.serialize' on page 151 undefined on input line 152
65.
[151]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 152 undefined on input line 15297.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 152 undefined on input line 15297.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 152 undefined on input line 15369.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 152 undefined on input line 15394.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 152 undefined on input line 15394.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 152 undefined on input line 15416.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 152 undefined on input line 15416.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.Loner' on p
age 152 undefined on input line 15420.
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.MultiSystem
' on page 152 undefined on input line 15420.
[152]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 153 undefined on input line 15450.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 153 undefined on input line 15450.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 153 undefined on input line 15484.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 153 undefined on input line 15484.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik
elySystem' on page 153 undefined on input line 15530.
LaTeX Warning: Hyper reference `user_guide/gembase_convention:topology-files' o
n page 153 undefined on input line 15566.
[153]
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 154 undefined on input line 15588.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 154 undefined on input line 15606.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 154 undefined on input line 15615.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 154 undefined on input line 15633.
[154]
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 155 undefined on input line 15908.
LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R
epliconInfo' on page 155 undefined on input line 15943.
[155]
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 156 undefined on input line 15969.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 156 undefined on input line 15973.
LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R
epliconInfo' on page 156 undefined on input line 16070.
[156]
LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R
epliconInfo' on page 157 undefined on input line 16136.
LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R
epliconInfo' on page 157 undefined on input line 16154.
LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R
epliconInfo' on page 157 undefined on input line 16172.
[157]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelRegistry' on page 158 undefined on input line 16393.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 158 undefined on input line 16393.
Underfull \hbox (badness 10000) in paragraph at lines 16397--16400
[]\T1/txtt/bx/n/10 models \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 list of tuple with t
he following structure: [(\TS1/txtt/m/sl/10 '\T1/txtt/m/sl/10 model_fqn\TS1/txt
t/m/sl/10 '\T1/txtt/m/sl/10 ,
[158]
Underfull \hbox (badness 10000) in paragraph at lines 16556--16560
\T1/qtm/m/n/10 Unar-chive and un-com-press a pack-age un-der \T1/qtm/m/it/10 <r
e-mote cache>/<organization name>/<package
[159]
[160]
[161]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 162 undefined on input line 17103.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 162 undefined on input line 17144.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 162 undefined on input line 17144.
[162]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 163 undefined on input line 17177.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik
elySystem' on page 163 undefined on input line 17177.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 163 undefined on input line 17242.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 163 undefined on input line 17242.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 163 undefined on input line 17287.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 163 undefined on input line 17287.
[163]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 164 undefined on input line 17354.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 164 undefined on input line 17419.
[164]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 165 undefined on input line 17477.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 165 undefined on input line 17521.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 165 undefined on input line 17565.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelRegistry' on page 165 undefined on input line 17565.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 165 undefined on input line 17565.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 165 undefined on input line 17565.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Likel
ySystem' on page 165 undefined on input line 17565.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Rejec
tedCandidate' on page 165 undefined on input line 17565.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik
elySystem' on page 165 undefined on input line 17565.
[165]
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 166 undefined on input line 17595.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelRegistry' on page 166 undefined on input line 17599.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.DefinitionLocation' on page 166 undefined on input line 17603.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 166 undefined on input line 17618.
LaTeX Warning: Hyper reference `developer_guide/api/solution:macsypy.solution.S
olution' on page 166 undefined on input line 17632.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 166 undefined on input line 17632.
[166]
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 167 undefined on input line 17740.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 167 undefined on input line 17740.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Syste
m' on page 167 undefined on input line 17788.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.HitSy
stemTracker' on page 167 undefined on input line 17788.
LaTeX Warning: Hyper reference `developer_guide/api/system:macsypy.system.Unlik
elySystem' on page 167 undefined on input line 17836.
[167]
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelRegistry' on page 168 undefined on input line 17884.
LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri
es.ModelLocation' on page 168 undefined on input line 17902.
LaTeX Warning: Hyper reference `developer_guide/api/package:macsypy.package.Rem
oteModelIndex' on page 168 undefined on input line 17945.
LaTeX Warning: Hyper reference `developer_guide/api/package:macsypy.package.Rem
oteModelIndex' on page 168 undefined on input line 17982.
[168]
[169]
[170]
[171]
[172]
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 173 undefined on input line 18729.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 173 undefined on input line 18826.
[173]
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 174 undefined on input line 18870.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 174 undefined on input line 18910.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 174 undefined on input line 18950.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 174 undefined on input line 18990.
[174]
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 175 undefined on input line 19030.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 175 undefined on input line 19070.
LaTeX Warning: Hyper reference `developer_guide/api/error:macsypy.error.Macsypy
Error' on page 175 undefined on input line 19110.
[175]
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 176 undefined on input line 19206.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 176 undefined on input line 19234.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 176 undefined on input line 19234.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 176 undefined on input line 19266.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 176 undefined on input line 19266.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 176 undefined on input line 19298.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 176 undefined on input line 19298.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 176 undefined on input line 19330.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 176 undefined on input line 19330.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 176 undefined on input line 19362.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Macsy
Defaults' on page 176 undefined on input line 19362.
[176]
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syconfig.ConfigParserWithComments' on page 177 undefined on input line 19394.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 177 undefined on input line 19443.
LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi
g' on page 177 undefined on input line 19455.
[177]
LaTeX Warning: Hyper reference `developer_guide/api/hit:macsypy.hit.CoreHit' on
page 178 undefined on input line 19566.
LaTeX Warning: Hyper reference `developer_guide/api/scripts:macsypy.scripts.mac
syprofile.LightHit' on page 178 undefined on input line 19646.
[178]
[179]
[180]
Chapter 4.
[181]
[182]
LaTeX Warning: Reference `developer_guide/api/database:module-macsypy.database'
on page 183 undefined on input line 19969.
LaTeX Warning: Reference `developer_guide/api/definition_parser:module-macsypy.
definition_parser' on page 183 undefined on input line 19970.
LaTeX Warning: Reference `developer_guide/api/error:module-macsypy.error' on pa
ge 183 undefined on input line 19971.
LaTeX Warning: Reference `developer_guide/api/model_conf_parser:module-macsypy.
model_conf_parser' on page 183 undefined on input line 19972.
LaTeX Warning: Reference `developer_guide/api/scripts:module-macsypy.scripts.ma
csyconfig' on page 183 undefined on input line 19973.
LaTeX Warning: Reference `developer_guide/api/scripts:module-macsypy.scripts.ma
csydata' on page 183 undefined on input line 19974.
LaTeX Warning: Reference `developer_guide/api/scripts:module-macsypy.scripts.ma
csyfinder' on page 183 undefined on input line 19975.
LaTeX Warning: Reference `developer_guide/api/scripts:module-macsypy.scripts.ma
csyprofile' on page 183 undefined on input line 19976.
LaTeX Warning: Reference `developer_guide/api/search_genes:module-macsypy.searc
h_genes' on page 183 undefined on input line 19977.
[183]
No file macsyfinder.ind.
(./macsyfinder.aux)
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Package rerunfilecheck Warning: File `macsyfinder.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
)
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/q
hvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvbi.pfb></usr/share/tex
mf/fonts/type1/public/tex-gyre/qhvr.pfb></usr/share/texmf/fonts/type1/public/te
x-gyre/qtmb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmbi.pfb></usr/s
hare/texmf/fonts/type1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/p
ublic/tex-gyre/qtmri.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfo
nts/t1xbtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/txfonts/tcxbtt.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb>
Output written on macsyfinder.pdf (187 pages, 2547202 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: 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: 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 (568 entries accepted, 0 rejected).
Sorting entries.......done (5839 comparisons).
Generating output file macsyfinder.ind....done (825 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> patch level 1
L3 programming layer <2024-12-25>
(./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<<t1.cmap>>)
(/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)
(./sphinxpackagefootnote.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) (./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/etoolbox/etoolbox.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/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)<<ot1.cmap>><<oml.cmap>><<oms.cma
p>><<omx.cmap>> (/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]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 765.
[10]
[11]
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
[12]
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-
[13] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd)
[14]
[15]
[16]
Overfull \vbox (2.32195pt too high) detected at line 1330
[17]
[18]
[19]
[20]
[21]
[22]
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
[23]
[24]
Underfull \vbox (badness 10000) detected at line 2089
Overfull \vbox (3.12196pt too high) detected at line 2089
[25]
[26]
[27]
Underfull \vbox (badness 10000) detected at line 2232
[28]
[29]
[30]
Underfull \vbox (badness 1226) detected at line 2406
[31]
Underfull \vbox (badness 10000) detected at line 2406
Underfull \vbox (badness 10000) detected at line 2406
[32]
[33]
Overfull \vbox (1.2275pt too high) detected at line 2545
[34]
[35]
[36]
[37]
[38]
Underfull \vbox (badness 10000) detected at line 2761
Underfull \vbox (badness 10000) detected at line 2761
[39]
[40]
[41]
[42]
[43]
[44]
pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec
df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all
owed
pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843
641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all
owed
[45]
[46 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz-bb320
290fa50a2c64c42d68cab416461f9843641.pdf
pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843
641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag
e
>]
[47]
[48]
[49]
[50]
[51]
[52]
[53]
[54 <./msf_functionning_step1.pdf>]
[55 <./msf_functionning_step2.pdf>]
[56]
[57 <./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
>]
[58 <./msf_functionning_step5.pdf>]
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
[59]
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
[60]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4176.
[61]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4221.
[62]
[63]
[64]
Chapter 2.
[65 <./logo_macsymodels.png>]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4393.
[66]
[67]
[68]
[69]
[70]
[71]
[72]
[73 <./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.
[74 <./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
[75 <./multi_system.pdf>]
[76]
[77]
Overfull \vbox (2.5072pt too high) detected at line 5384
[78]
[79]
[80]
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
[81]
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 #
[82]
Underfull \vbox (badness 10000) detected at line 5739
Overfull \vbox (1.56999pt too high) detected at line 5739
[83]
Overfull \vbox (1.35179pt too high) detected at line 5805
[84]
[85]
[86 <./T1SS_example.pdf>]
[87]
[88 <./T3SS_example.pdf>]
[89]
[90]
[91]
Underfull \vbox (badness 1226) detected at line 6332
[92]
[93]
[94 <./multi_model.pdf>]
Chapter 3.
[95]
[96]
pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found
PDF version <1.7>, but at most version <1.5> allowed
[97]
[98 <./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.
[99]
[100]
[101]
[102]
Underfull \hbox (badness 6775) in paragraph at lines 7400--7402
\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
[103]
[104]
[105]
Underfull \hbox (badness 10000) in paragraph at lines 8008--8011
[]\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
[106]
[107]
[108]
[109]
[110]
[111]
[112]
[113]
[114{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}]
[115]
[116]
[117]
[118]
[119]
[120]
[121]
[122]
[123]
[124]
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[][][]\T1/txtt/m/sl/10 macsypy.hit.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[][][]\T1/txtt/m/sl/10 macsypy.hit.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[][][]\T1/txtt/m/sl/10 macsypy.hit.
[125]
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 11301.
[126 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>]
[127 <./gene_obj_interaction.pdf>]
[128]
[129]
[130]
[131]
[132]
[133]
[134]
[135]
[136]
Underfull \hbox (badness 10000) in paragraph at lines 12920--12922
[]\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
pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c
5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5>
allowed
[137 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf>]
[138 <./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf>]
[139]
[140]
[141]
[142]
[143]
[144]
[145]
Underfull \hbox (badness 10000) in paragraph at lines 14440--14442
\T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (<it
ertools._grouper object at
[146]
[147]
[148]
[149]
[150]
[151]
[152]
[153]
[154]
[155]
[156]
[157]
Underfull \hbox (badness 10000) in paragraph at lines 16397--16400
[]\T1/txtt/bx/n/10 models \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 list of tuple with t
he following structure: [(\TS1/txtt/m/sl/10 '\T1/txtt/m/sl/10 model_fqn\TS1/txt
t/m/sl/10 '\T1/txtt/m/sl/10 ,
[158]
Underfull \hbox (badness 10000) in paragraph at lines 16556--16560
\T1/qtm/m/n/10 Unar-chive and un-com-press a pack-age un-der \T1/qtm/m/it/10 <r
e-mote cache>/<organization name>/<package
[159]
[160]
[161]
[162]
[163]
[164]
[165]
[166]
[167]
[168]
[169]
[170]
[171]
[172]
[173]
[174]
[175]
[176]
[177]
[178]
[179]
[180]
Chapter 4.
[181]
[182]
[183] (./macsyfinder.ind
[184]
Underfull \hbox (badness 10000) in paragraph at lines 10--11
[]\T1/txtt/m/n/10 __contains__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.datab
ase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 11--12
[]\T1/txtt/m/n/10 __contains__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene.
GeneBank method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 14--16
[]\T1/txtt/m/n/10 __delattr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 20--22
[]\T1/txtt/m/n/10 __eq__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries.
DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 24--26
[]\T1/txtt/m/n/10 __eq__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.mac
syprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 27--28
[]\T1/txtt/m/n/10 __getitem__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.databa
se.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 30--32
[]\T1/txtt/m/n/10 __getitem__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.regist
ries.ModelRegistry
Underfull \hbox (badness 10000) in paragraph at lines 35--37
[]\T1/txtt/m/n/10 __gt__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries.
DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 45--47
[]\T1/txtt/m/n/10 __hash__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 47--49
[]\T1/txtt/m/n/10 __hash__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyconfig.Theme
Underfull \hbox (badness 6608) in paragraph at lines 51--52
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.config.Ma
csyDefaults method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 5403) in paragraph at lines 53--54
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.database.
RepliconDB method\T1/qtm/m/n/10 ),
Overfull \hbox (1.16237pt too wide) in paragraph at lines 54--56
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.definitio
n_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 60--62
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abstr
actCounterpartHit
Underfull \hbox (badness 8170) in paragraph at lines 65--66
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Loner
MultiSystem method\T1/qtm/m/n/10 ),
Overfull \hbox (15.04237pt too wide) in paragraph at lines 70--72
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.model_con
f_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 72--74
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.A
bstractModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 74--75
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.L
ocalModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 76--78
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.R
emoteModelIndex
[185]
Underfull \hbox (badness 7081) in paragraph at lines 79--80
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.profile.P
rofileFactory method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 80--82
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 82--84
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.ModelLocation
Underfull \hbox (badness 10000) in paragraph at lines 84--86
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.ModelRegistry
Underfull \hbox (badness 10000) in paragraph at lines 87--89
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 91--93
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 94--96
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Ab
stractClusterizedHits
Underfull \hbox (badness 10000) in paragraph at lines 96--98
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Ab
stractSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 98--100
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Ab
stractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 100--101
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Hi
tSystemTracker
Underfull \hbox (badness 10000) in paragraph at lines 102--104
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Or
deredMatchMaker
Underfull \hbox (badness 10000) in paragraph at lines 104--106
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Re
jectedCandidate
Underfull \hbox (badness 10000) in paragraph at lines 117--119
[]\T1/txtt/m/n/10 __lt__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries.
DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 122--124
[]\T1/txtt/m/n/10 __repr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 124--126
[]\T1/txtt/m/n/10 __repr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 127--129
[]\T1/txtt/m/n/10 __setattr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 132--134
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abstra
ctCounterpartHit
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries
.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 143--145
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.ma
csyprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 146--147
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Rej
ectedCandidate
Underfull \hbox (badness 10000) in paragraph at lines 148--149
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Unl
ikelySystem method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 153--154
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.config.N
oneConfig at-tribute\T1/qtm/m/n/10 ),
Overfull \hbox (6.41235pt too wide) in paragraph at lines 156--158
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.definiti
on_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 166--167
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.model.Mo
delBank at-tribute\T1/qtm/m/n/10 ),
Overfull \hbox (20.29236pt too wide) in paragraph at lines 167--169
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.model_co
nf_parser.ModelConfParser
[186]
Underfull \hbox (badness 10000) in paragraph at lines 177--179
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.ModelLocation
Underfull \hbox (badness 10000) in paragraph at lines 179--181
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.ModelRegistry at-
Overfull \hbox (0.55235pt too wide) in paragraph at lines 184--186
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.
macsyprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 188--190
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.SystemSerializer
Overfull \hbox (53.63235pt too wide) in paragraph at lines 190--192
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvRejectedCandidatesSerializer
Overfull \hbox (7.43233pt too wide) in paragraph at lines 192--194
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSolutionSerializer
Overfull \hbox (16.31233pt too wide) in paragraph at lines 194--196
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSpecialHitSerializer
Underfull \hbox (badness 10000) in paragraph at lines 197--199
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.A
bstractSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 199--201
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.H
itSystemTracker at-
Underfull \hbox (badness 10000) in paragraph at lines 202--203
[]\T1/txtt/m/n/10 _build_my_db() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.repor
t.HMMReport
Underfull \hbox (badness 10000) in paragraph at lines 203--205
[]\T1/txtt/m/n/10 _build_my_db() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 205--207
[]\T1/txtt/m/n/10 _build_my_indexes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
database.Indexes
Underfull \hbox (badness 10000) in paragraph at lines 207--208
[]\T1/txtt/m/n/10 _check_metadata() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.pa
ckage.Package
Underfull \hbox (badness 10000) in paragraph at lines 208--209
[]\T1/txtt/m/n/10 _check_model_conf() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
package.Package
Underfull \hbox (badness 10000) in paragraph at lines 209--211
[]\T1/txtt/m/n/10 _check_model_consistency() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 211--213
[]\T1/txtt/m/n/10 _check_replicon_consistency() \T1/qtm/m/n/10 (\T1/qtm/m/it/10
mac-
Underfull \hbox (badness 10000) in paragraph at lines 213--214
[]\T1/txtt/m/n/10 _check_structure() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.p
ackage.Package
Underfull \hbox (badness 10000) in paragraph at lines 214--216
[]\T1/txtt/m/n/10 _check_syntax() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 214--216
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 216--218
[]\T1/txtt/m/n/10 _config_file_2_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-syp
y.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 218--220
[]\T1/txtt/m/n/10 _create_exchangeable_map() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 220--222
[]\T1/txtt/m/n/10 _create_model() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 220--222
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 222--224
[]\T1/txtt/m/n/10 _fill_gembase_min_max() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 224--226
[]\T1/txtt/m/n/10 _fill_gene_bank() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 224--226
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Overfull \hbox (11.05232pt too wide) in paragraph at lines 227--229
[]\T1/txtt/m/n/10 _fill_my_db() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 229--231
[]\T1/txtt/m/n/10 _fill_ordered_min_max() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 231--232
[]\T1/txtt/m/n/10 _fill_topology() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.dat
abase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 234--236
[]\T1/txtt/m/n/10 _find_installed_package() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 237--239
[]\T1/txtt/m/n/10 _get_model_conf_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 237--239
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 239--241
[]\T1/txtt/m/n/10 _get_model_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 239--241
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 241--243
[]\T1/txtt/m/n/10 _get_remote_available_versions() \T1/qtm/m/n/10 (\T1/qtm/m/it
/10 in mod-ule
Underfull \hbox (badness 10000) in paragraph at lines 243--245
[]\T1/txtt/m/n/10 _get_replicon_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 243--245
\T1/qtm/m/it/10 sypy.report.GembaseHMMReport method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 245--247
[]\T1/txtt/m/n/10 _get_replicon_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 245--247
\T1/qtm/m/it/10 sypy.report.GeneralHMMReport method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 249--251
[]\T1/txtt/m/n/10 _get_replicon_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 249--251
\T1/qtm/m/it/10 sypy.report.OrderedHMMReport method\T1/qtm/m/n/10 ),
Overfull \hbox (5.80234pt too wide) in paragraph at lines 252--254
[]\T1/txtt/m/n/10 _hit_start() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts
.macsyprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 255--256
[]\T1/txtt/m/n/10 _load_metadata() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.pac
kage.Package
Underfull \hbox (badness 10000) in paragraph at lines 256--258
[]\T1/txtt/m/n/10 _loner_warning() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 258--260
[]\T1/txtt/m/n/10 _outfile_header() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 260--262
[]\T1/txtt/m/n/10 _parse_exchangeable() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 260--262
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
[187]
Underfull \hbox (badness 10000) in paragraph at lines 262--264
[]\T1/txtt/m/n/10 _parse_genes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 262--264
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 264--265
[]\T1/txtt/m/n/10 _parse_hmm_body() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.re
port.HMMReport
Underfull \hbox (badness 10000) in paragraph at lines 265--267
[]\T1/txtt/m/n/10 _parse_hmm_body() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 267--269
[]\T1/txtt/m/n/10 _parse_hmm_header() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
report.HMMReport
Underfull \hbox (badness 10000) in paragraph at lines 269--271
[]\T1/txtt/m/n/10 _parse_hmm_header() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 271--273
[]\T1/txtt/m/n/10 _parse_section() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 271--273
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 273--274
[]\T1/txtt/m/n/10 _profile_features() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
profile.Profile
Underfull \hbox (badness 10000) in paragraph at lines 274--276
[]\T1/txtt/m/n/10 _scan_definitions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 274--276
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 278--280
[]\T1/txtt/m/n/10 _search_in_desc() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 282--284
[]\T1/txtt/m/n/10 _search_in_pack_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod
-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 286--288
[]\T1/txtt/m/n/10 _set_command_line_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 289--290
[]\T1/txtt/m/n/10 _set_default_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-syp
y.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 290--292
[]\T1/txtt/m/n/10 _set_inter_gene_max_space() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 292--293
[]\T1/txtt/m/n/10 _set_log_level() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.con
fig.Config method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 293--294
[]\T1/txtt/m/n/10 _set_max_nb_genes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
config.Config
Underfull \hbox (badness 10000) in paragraph at lines 296--298
[]\T1/txtt/m/n/10 _set_min_mandatory_genes_required() \T1/qtm/m/n/10 (\T1/qtm/m
/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 298--299
[]\T1/txtt/m/n/10 _set_model_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
config.Config
Underfull \hbox (badness 10000) in paragraph at lines 302--303
[]\T1/txtt/m/n/10 _set_no_cut_ga() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.con
fig.Config method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 304--306
[]\T1/txtt/m/n/10 _set_previous_run_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 306--308
[]\T1/txtt/m/n/10 _set_project_config_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 308--310
[]\T1/txtt/m/n/10 _set_replicon_topology() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
sypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 311--313
[]\T1/txtt/m/n/10 _set_system_models_dir() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
sypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 315--316
[]\T1/txtt/m/n/10 _set_topology_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 316--318
[]\T1/txtt/m/n/10 _set_user_config_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-s
ypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 318--320
[]\T1/txtt/m/n/10 _set_user_wide_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-s
ypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 320--321
[]\T1/txtt/m/n/10 _sorted_systems() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.so
lution.Solution
Underfull \hbox (badness 10000) in paragraph at lines 322--323
[]\T1/txtt/m/n/10 _url_json() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.
RemoteModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 332--334
[]\T1/txtt/m/n/10 accessory_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.AbstractUnordered
Overfull \hbox (74.65233pt too wide) in paragraph at lines 335--337
[]\T1/txtt/m/n/10 add_comment() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyconfig.ConfigParserWithComments
Underfull \hbox (badness 10000) in paragraph at lines 337--338
[]\T1/txtt/m/n/10 add_exchangeable() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.g
ene.Exchangeable
Underfull \hbox (badness 10000) in paragraph at lines 338--339
[]\T1/txtt/m/n/10 add_exchangeable() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.g
ene.ModelGene
Underfull \hbox (badness 10000) in paragraph at lines 340--341
[]\T1/txtt/m/n/10 add_new_gene() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene.
GeneBank method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 341--343
[]\T1/txtt/m/n/10 add_subdefinition() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 341--343
\T1/qtm/m/it/10 sypy.registries.DefinitionLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 343--345
[]\T1/txtt/m/n/10 alarm_handler() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule ma
c-
[188]
Underfull \hbox (badness 10000) in paragraph at lines 346--348
[]\T1/txtt/m/n/10 allowed_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.
AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 357--359
[]\T1/txtt/m/n/10 build_arg_parser() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 365--366
[]\T1/txtt/m/n/10 check_choice() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac
-
Underfull \hbox (badness 10000) in paragraph at lines 366--368
[]\T1/txtt/m/n/10 check_consistency() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 366--368
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 371--372
[]\T1/txtt/m/n/10 check_float() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 372--374
[]\T1/txtt/m/n/10 check_positive_int() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u
le mac-
Underfull \hbox (badness 10000) in paragraph at lines 380--381
[]\T1/txtt/m/n/10 combine_multisystems() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod
-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 383--385
[]\T1/txtt/m/n/10 ConfigParserWithComments \T1/qtm/m/n/10 (\T1/qtm/m/it/10 clas
s in mac-
Underfull \hbox (badness 10000) in paragraph at lines 392--393
[]\T1/txtt/m/n/10 count() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Abstr
actSetOfHits method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 393--395
[]\T1/txtt/m/n/10 counterpart \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abst
ractCounterpartHit
Underfull \hbox (badness 10000) in paragraph at lines 399--400
[]\T1/txtt/m/n/10 DefinitionParser \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in mac
-
Underfull \hbox (badness 10000) in paragraph at lines 400--401
[]\T1/txtt/m/n/10 do_available() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac
-
Underfull \hbox (badness 10000) in paragraph at lines 407--409
[]\T1/txtt/m/n/10 do_init_package() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 412--414
[]\T1/txtt/m/n/10 do_show_definition() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u
le mac-
Underfull \hbox (badness 10000) in paragraph at lines 414--415
[]\T1/txtt/m/n/10 do_uninstall() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac
-
Underfull \hbox (badness 10000) in paragraph at lines 416--417
[]\T1/txtt/m/n/10 download() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.R
emoteModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 430--432
[]\T1/txtt/m/n/10 family_name \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 434--435
[]\T1/txtt/m/n/10 find_best_solutions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
[189]
Underfull \hbox (badness 10000) in paragraph at lines 435--436
[]\T1/txtt/m/n/10 find_my_indexes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.da
tabase.Indexes
Underfull \hbox (badness 10000) in paragraph at lines 436--438
[]\T1/txtt/m/n/10 forbidden_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 438--439
[]\T1/txtt/m/n/10 fulfilled_function() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.cluster.Cluster
Underfull \hbox (badness 10000) in paragraph at lines 439--441
[]\T1/txtt/m/n/10 fulfilled_function() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 439--441
\T1/qtm/m/it/10 sypy.system.AbstractClusterizedHits method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 453--455
[]\T1/txtt/m/n/10 get_all_definitions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 453--455
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 460--462
[]\T1/txtt/m/n/10 get_definitions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 460--462
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 463--465
[]\T1/txtt/m/n/10 get_gene_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 465--467
[]\T1/txtt/m/n/10 get_hits_encoding_multisystem() \T1/qtm/m/n/10 (\T1/qtm/m/it/
10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 472--473
[]\T1/txtt/m/n/10 get_profile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.profil
e.ProfileFactory
Underfull \hbox (badness 10000) in paragraph at lines 473--475
[]\T1/txtt/m/n/10 get_profile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.regist
ries.ModelLocation
Underfull \hbox (badness 10000) in paragraph at lines 475--477
[]\T1/txtt/m/n/10 get_profile_len() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 477--479
[]\T1/txtt/m/n/10 get_profiles_names() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 477--479
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 480--482
[]\T1/txtt/m/n/10 get_version_message() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 482--484
[]\T1/txtt/m/n/10 get_version_message() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 484--486
[]\T1/txtt/m/n/10 get_version_message() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 486--487
[]\T1/txtt/m/n/10 getter_maker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.MetaSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 487--489
[]\T1/txtt/m/n/10 guess_if_really_gembase() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac
-
Underfull \hbox (badness 10000) in paragraph at lines 513--514
[]\T1/txtt/m/n/10 init_logger() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 514--516
[]\T1/txtt/m/n/10 inter_gene_max_space \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.gene.ModelGene
Underfull \hbox (badness 10000) in paragraph at lines 517--519
[]\T1/txtt/m/n/10 inter_gene_max_space() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sy
py.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 520--521
[]\T1/txtt/m/n/10 is_compatible() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syst
em.System method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 522--523
[]\T1/txtt/m/n/10 is_exchangeable \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene
.ModelGene prop-
[190]
Underfull \hbox (badness 10000) in paragraph at lines 535--537
[]\T1/txtt/m/n/10 likely_systems_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo
d-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 537--539
[]\T1/txtt/m/n/10 likely_systems_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo
d-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 540--541
[]\T1/txtt/m/n/10 list_models() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 541--543
[]\T1/txtt/m/n/10 list_package_vers() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 541--543
\T1/qtm/m/it/10 sypy.package.RemoteModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 543--545
[]\T1/txtt/m/n/10 list_packages() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 543--545
\T1/qtm/m/it/10 sypy.package.RemoteModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 5417) in paragraph at lines 552--553
[]\T1/txtt/m/n/10 loner \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.AbstractCo
unterpartHit prop-erty\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 556--558
[]\T1/txtt/m/n/10 loners_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 588--590
[]\T1/txtt/m/n/10 mandatory_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 591--592
[]\T1/txtt/m/n/10 match() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Unord
eredMatchMaker
Underfull \hbox (badness 10000) in paragraph at lines 601--602
[]\T1/txtt/m/n/10 min_genes_required \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.m
odel.Model prop-
Underfull \hbox (badness 10000) in paragraph at lines 602--603
[]\T1/txtt/m/n/10 min_genes_required() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 603--605
[]\T1/txtt/m/n/10 min_mandatory_genes_required \T1/qtm/m/n/10 (\T1/qtm/m/it/10
mac-
Underfull \hbox (badness 10000) in paragraph at lines 605--607
[]\T1/txtt/m/n/10 min_mandatory_genes_required() \T1/qtm/m/n/10 (\T1/qtm/m/it/1
0 mac-
Underfull \hbox (badness 10000) in paragraph at lines 611--612
[]\T1/txtt/m/n/10 model_family_name \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.ge
ne.CoreGene prop-
Underfull \hbox (badness 10000) in paragraph at lines 613--614
[]\T1/txtt/m/n/10 ModelConfParser \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in mac-
[191]
Underfull \hbox (badness 10000) in paragraph at lines 638--639
[]\T1/txtt/m/n/10 multi_system \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene.Mo
delGene prop-erty\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 639--641
[]\T1/txtt/m/n/10 multi_system \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abs
tractCounterpartHit
Underfull \hbox (badness 10000) in paragraph at lines 644--646
[]\T1/txtt/m/n/10 multisystems_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 651--653
[]\T1/txtt/m/n/10 neutral_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.
AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 666--668
[]\T1/txtt/m/n/10 parse() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.definition_p
arser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 670--672
[]\T1/txtt/m/n/10 parse() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.macs
yprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 674--675
[]\T1/txtt/m/n/10 parse_args() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 675--677
[]\T1/txtt/m/n/10 parse_filtering() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 675--677
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 678--680
[]\T1/txtt/m/n/10 parse_weights() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 678--680
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 681--682
[]\T1/txtt/m/n/10 present_genes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syst
em.MatchMaker
Underfull \hbox (badness 6188) in paragraph at lines 693--695
[]\T1/txtt/m/n/10 rejected_candidates_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10
in mod-ule mac-
Underfull \hbox (badness 6188) in paragraph at lines 695--697
[]\T1/txtt/m/n/10 rejected_candidates_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10
in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 698--700
[]\T1/txtt/m/n/10 remote_exists() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 698--700
\T1/qtm/m/it/10 sypy.package.RemoteModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 702--703
[]\T1/txtt/m/n/10 replicon_infos() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.dat
abase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 704--706
[]\T1/txtt/m/n/10 replicon_name \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system
.AbstractSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 706--707
[]\T1/txtt/m/n/10 replicon_names() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.dat
abase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 709--711
[]\T1/txtt/m/n/10 root_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 715--716
[]\T1/txtt/m/n/10 save_extract() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.repor
t.HMMReport
[192]
Underfull \hbox (badness 10000) in paragraph at lines 721--723
[]\T1/txtt/m/n/10 search_systems() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Overfull \hbox (25.85234pt too wide) in paragraph at lines 724--726
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvLikelySystemSerializer
Overfull \hbox (53.63235pt too wide) in paragraph at lines 726--728
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvRejectedCandidatesSerializer
Overfull \hbox (7.43233pt too wide) in paragraph at lines 728--730
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSolutionSerializer
Overfull \hbox (16.31233pt too wide) in paragraph at lines 730--732
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSpecialHitSerializer
Overfull \hbox (1.41234pt too wide) in paragraph at lines 732--734
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSystemSerializer
Overfull \hbox (25.49234pt too wide) in paragraph at lines 734--736
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TxtLikelySystemSerializer
Overfull \hbox (1.05234pt too wide) in paragraph at lines 736--738
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TxtSystemSerializer
Overfull \hbox (31.85233pt too wide) in paragraph at lines 738--740
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TxtUnikelySystemSerializer
Underfull \hbox (badness 10000) in paragraph at lines 740--742
[]\T1/txtt/m/n/10 set_base_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 742--744
[]\T1/txtt/m/n/10 set_general_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 744--746
[]\T1/txtt/m/n/10 set_hmmer_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul
e mac-
Underfull \hbox (badness 10000) in paragraph at lines 746--748
[]\T1/txtt/m/n/10 set_path_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 748--750
[]\T1/txtt/m/n/10 set_score_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul
e mac-
Underfull \hbox (badness 10000) in paragraph at lines 750--751
[]\T1/txtt/m/n/10 set_section() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 756--758
[]\T1/txtt/m/n/10 solutions_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 758--760
[]\T1/txtt/m/n/10 sort_hits_by_status() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 762--764
[]\T1/txtt/m/n/10 split_fqn() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 766--768
[]\T1/txtt/m/n/10 summary_best_solution() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo
d-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 772--774
[]\T1/txtt/m/n/10 systems_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 774--776
[]\T1/txtt/m/n/10 systems_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 784--785
[]\T1/txtt/m/n/10 topology \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.database.Re
pliconInfo at-tribute\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 785--787
[]\T1/txtt/m/n/10 TsvLikelySystemSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 cla
ss in mac-
Underfull \hbox (badness 10000) in paragraph at lines 789--790
[]\T1/txtt/m/n/10 TsvSolutionSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class i
n mac-
Underfull \hbox (badness 10000) in paragraph at lines 790--792
[]\T1/txtt/m/n/10 TsvSpecialHitSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class
in mac-
Underfull \hbox (badness 10000) in paragraph at lines 793--795
[]\T1/txtt/m/n/10 TxtLikelySystemSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 cla
ss in mac-
Underfull \hbox (badness 10000) in paragraph at lines 796--798
[]\T1/txtt/m/n/10 TxtUnikelySystemSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 cl
ass in mac-
Underfull \hbox (badness 10000) in paragraph at lines 801--803
[]\T1/txtt/m/n/10 unarchive_package() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 801--803
\T1/qtm/m/it/10 sypy.package.AbstractModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 803--805
[]\T1/txtt/m/n/10 unlikely_systems_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 811--813
[]\T1/txtt/m/n/10 verbosity_to_log_level() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 813--815
[]\T1/txtt/m/n/10 verbosity_to_log_level() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 819--820
[]\T1/txtt/m/n/10 wholeness \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Abs
tractSetOfHits prop-
Overfull \hbox (43.15242pt too wide) in paragraph at lines 822--824
[]\T1/txtt/m/n/10 write() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.macs
yconfig.ConfigParserWithComments
[193]
[194]) (./macsyfinder.aux)
Package rerunfilecheck Warning: File `macsyfinder.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
)
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/q
hvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvbi.pfb></usr/share/tex
mf/fonts/type1/public/tex-gyre/qhvr.pfb></usr/share/texmf/fonts/type1/public/te
x-gyre/qtmb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmbi.pfb></usr/s
hare/texmf/fonts/type1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/p
ublic/tex-gyre/qtmri.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfo
nts/t1xbtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/txfonts/tcxbtt.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb>
Output written on macsyfinder.pdf (198 pages, 2637296 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> patch level 1
L3 programming layer <2024-12-25>
(./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<<t1.cmap>>)
(/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)
(./sphinxpackagefootnote.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) (./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/etoolbox/etoolbox.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/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)<<ot1.cmap>><<oml.cmap>><<oms.cma
p>><<omx.cmap>> (/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]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 765.
[10]
[11]
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
[12]
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-
[13] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd)
[14]
[15]
[16]
Overfull \vbox (2.32195pt too high) detected at line 1330
[17]
[18]
[19]
[20]
[21]
[22]
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
[23]
[24]
Underfull \vbox (badness 10000) detected at line 2089
Overfull \vbox (3.12196pt too high) detected at line 2089
[25]
[26]
[27]
Underfull \vbox (badness 10000) detected at line 2232
[28]
[29]
[30]
Underfull \vbox (badness 1226) detected at line 2406
[31]
Underfull \vbox (badness 10000) detected at line 2406
Underfull \vbox (badness 10000) detected at line 2406
[32]
[33]
Overfull \vbox (1.2275pt too high) detected at line 2545
[34]
[35]
[36]
[37]
[38]
Underfull \vbox (badness 10000) detected at line 2761
Underfull \vbox (badness 10000) detected at line 2761
[39]
[40]
[41]
[42]
[43]
[44]
pdfTeX warning: pdflatex (file ./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eec
df0.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all
owed
pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843
641.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> all
owed
[45]
[46 <./graphviz-f93ec17dfa5e6a44dcc511504e87d52305eecdf0.pdf> <./graphviz-bb320
290fa50a2c64c42d68cab416461f9843641.pdf
pdfTeX warning: pdflatex (file ./graphviz-bb320290fa50a2c64c42d68cab416461f9843
641.pdf): PDF inclusion: multiple pdfs with page group included in a single pag
e
>]
[47]
[48]
[49]
[50]
[51]
[52]
[53]
[54 <./msf_functionning_step1.pdf>]
[55 <./msf_functionning_step2.pdf>]
[56]
[57 <./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
>]
[58 <./msf_functionning_step5.pdf>]
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
[59]
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
[60]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4176.
[61]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4221.
[62]
[63]
[64]
Chapter 2.
[65 <./logo_macsymodels.png>]
Package hyperref Warning: Token not allowed in a PDF string (Unicode):
(hyperref) removing `\sphinxtitleref' on input line 4393.
[66]
[67]
[68]
[69]
[70]
[71]
[72]
[73 <./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.
[74 <./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
[75 <./multi_system.pdf>]
[76]
[77]
Overfull \vbox (2.5072pt too high) detected at line 5384
[78]
[79]
[80]
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
[81]
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 #
[82]
Underfull \vbox (badness 10000) detected at line 5739
Overfull \vbox (1.56999pt too high) detected at line 5739
[83]
Overfull \vbox (1.35179pt too high) detected at line 5805
[84]
[85]
[86 <./T1SS_example.pdf>]
[87]
[88 <./T3SS_example.pdf>]
[89]
[90]
[91]
Underfull \vbox (badness 1226) detected at line 6332
[92]
[93]
[94 <./multi_model.pdf>]
Chapter 3.
[95]
[96]
pdfTeX warning: pdflatex (file ./macsyfinder_classes.pdf): PDF inclusion: found
PDF version <1.7>, but at most version <1.5> allowed
[97]
[98 <./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.
[99]
[100]
[101]
[102]
Underfull \hbox (badness 6775) in paragraph at lines 7400--7402
\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
[103]
[104]
[105]
Underfull \hbox (badness 10000) in paragraph at lines 8008--8011
[]\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
[106]
[107]
[108]
[109]
[110]
[111]
[112]
[113]
[114{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}]
[115]
[116]
[117]
[118]
[119]
[120]
[121]
[122]
[123]
[124]
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[][][]\T1/txtt/m/sl/10 macsypy.hit.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[][][]\T1/txtt/m/sl/10 macsypy.hit.
Underfull \hbox (badness 10000) in paragraph at lines 11264--11264
[][][]\T1/txtt/m/sl/10 macsypy.hit.
[125]
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 11301.
[126 <./inheritance-83b34b40613bc1e14b9a1c8cafe3b8f9589da157.pdf>]
[127 <./gene_obj_interaction.pdf>]
[128]
[129]
[130]
[131]
[132]
[133]
[134]
[135]
[136]
Underfull \hbox (badness 10000) in paragraph at lines 12920--12922
[]\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
pdfTeX warning: pdflatex (file ./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c
5ae428.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5>
allowed
[137 <./inheritance-7c6ce73e7deb2ae58cdffa96bafb81c6622aab72.pdf>]
[138 <./inheritance-9ba8cb50536aed57391419cf7d6ad8df2c5ae428.pdf>]
[139]
[140]
[141]
[142]
[143]
[144]
[145]
Underfull \hbox (badness 10000) in paragraph at lines 14440--14442
\T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (<it
ertools._grouper object at
[146]
[147]
[148]
[149]
[150]
[151]
[152]
[153]
[154]
[155]
[156]
[157]
Underfull \hbox (badness 10000) in paragraph at lines 16397--16400
[]\T1/txtt/bx/n/10 models \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 list of tuple with t
he following structure: [(\TS1/txtt/m/sl/10 '\T1/txtt/m/sl/10 model_fqn\TS1/txt
t/m/sl/10 '\T1/txtt/m/sl/10 ,
[158]
Underfull \hbox (badness 10000) in paragraph at lines 16556--16560
\T1/qtm/m/n/10 Unar-chive and un-com-press a pack-age un-der \T1/qtm/m/it/10 <r
e-mote cache>/<organization name>/<package
[159]
[160]
[161]
[162]
[163]
[164]
[165]
[166]
[167]
[168]
[169]
[170]
[171]
[172]
[173]
[174]
[175]
[176]
[177]
[178]
[179]
[180]
Chapter 4.
[181]
[182]
[183] (./macsyfinder.ind
[184]
Underfull \hbox (badness 10000) in paragraph at lines 10--11
[]\T1/txtt/m/n/10 __contains__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.datab
ase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 11--12
[]\T1/txtt/m/n/10 __contains__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene.
GeneBank method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 14--16
[]\T1/txtt/m/n/10 __delattr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 20--22
[]\T1/txtt/m/n/10 __eq__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries.
DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 24--26
[]\T1/txtt/m/n/10 __eq__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.mac
syprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 27--28
[]\T1/txtt/m/n/10 __getitem__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.databa
se.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 30--32
[]\T1/txtt/m/n/10 __getitem__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.regist
ries.ModelRegistry
Underfull \hbox (badness 10000) in paragraph at lines 35--37
[]\T1/txtt/m/n/10 __gt__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries.
DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 45--47
[]\T1/txtt/m/n/10 __hash__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 47--49
[]\T1/txtt/m/n/10 __hash__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyconfig.Theme
Underfull \hbox (badness 6608) in paragraph at lines 51--52
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.config.Ma
csyDefaults method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 5403) in paragraph at lines 53--54
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.database.
RepliconDB method\T1/qtm/m/n/10 ),
Overfull \hbox (1.16237pt too wide) in paragraph at lines 54--56
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.definitio
n_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 60--62
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abstr
actCounterpartHit
Underfull \hbox (badness 8170) in paragraph at lines 65--66
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Loner
MultiSystem method\T1/qtm/m/n/10 ),
Overfull \hbox (15.04237pt too wide) in paragraph at lines 70--72
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.model_con
f_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 72--74
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.A
bstractModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 74--75
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.L
ocalModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 76--78
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.R
emoteModelIndex
[185]
Underfull \hbox (badness 7081) in paragraph at lines 79--80
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.profile.P
rofileFactory method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 80--82
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 82--84
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.ModelLocation
Underfull \hbox (badness 10000) in paragraph at lines 84--86
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registrie
s.ModelRegistry
Underfull \hbox (badness 10000) in paragraph at lines 87--89
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 91--93
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 94--96
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Ab
stractClusterizedHits
Underfull \hbox (badness 10000) in paragraph at lines 96--98
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Ab
stractSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 98--100
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Ab
stractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 100--101
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Hi
tSystemTracker
Underfull \hbox (badness 10000) in paragraph at lines 102--104
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Or
deredMatchMaker
Underfull \hbox (badness 10000) in paragraph at lines 104--106
[]\T1/txtt/m/n/10 __init__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Re
jectedCandidate
Underfull \hbox (badness 10000) in paragraph at lines 117--119
[]\T1/txtt/m/n/10 __lt__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries.
DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 122--124
[]\T1/txtt/m/n/10 __repr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 124--126
[]\T1/txtt/m/n/10 __repr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.m
acsyprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 127--129
[]\T1/txtt/m/n/10 __setattr__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyconfig.Theme
Underfull \hbox (badness 10000) in paragraph at lines 132--134
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abstra
ctCounterpartHit
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registries
.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 143--145
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.ma
csyprofile.LightHit
Underfull \hbox (badness 10000) in paragraph at lines 146--147
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Rej
ectedCandidate
Underfull \hbox (badness 10000) in paragraph at lines 148--149
[]\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Unl
ikelySystem method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 153--154
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.config.N
oneConfig at-tribute\T1/qtm/m/n/10 ),
Overfull \hbox (6.41235pt too wide) in paragraph at lines 156--158
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.definiti
on_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 166--167
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.model.Mo
delBank at-tribute\T1/qtm/m/n/10 ),
Overfull \hbox (20.29236pt too wide) in paragraph at lines 167--169
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.model_co
nf_parser.ModelConfParser
[186]
Underfull \hbox (badness 10000) in paragraph at lines 177--179
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.ModelLocation
Underfull \hbox (badness 10000) in paragraph at lines 179--181
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.ModelRegistry at-
Overfull \hbox (0.55235pt too wide) in paragraph at lines 184--186
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.
macsyprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 188--190
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.SystemSerializer
Overfull \hbox (53.63235pt too wide) in paragraph at lines 190--192
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvRejectedCandidatesSerializer
Overfull \hbox (7.43233pt too wide) in paragraph at lines 192--194
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSolutionSerializer
Overfull \hbox (16.31233pt too wide) in paragraph at lines 194--196
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSpecialHitSerializer
Underfull \hbox (badness 10000) in paragraph at lines 197--199
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.A
bstractSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 199--201
[]\T1/txtt/m/n/10 __weakref__ \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.H
itSystemTracker at-
Underfull \hbox (badness 10000) in paragraph at lines 202--203
[]\T1/txtt/m/n/10 _build_my_db() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.repor
t.HMMReport
Underfull \hbox (badness 10000) in paragraph at lines 203--205
[]\T1/txtt/m/n/10 _build_my_db() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 205--207
[]\T1/txtt/m/n/10 _build_my_indexes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
database.Indexes
Underfull \hbox (badness 10000) in paragraph at lines 207--208
[]\T1/txtt/m/n/10 _check_metadata() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.pa
ckage.Package
Underfull \hbox (badness 10000) in paragraph at lines 208--209
[]\T1/txtt/m/n/10 _check_model_conf() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
package.Package
Underfull \hbox (badness 10000) in paragraph at lines 209--211
[]\T1/txtt/m/n/10 _check_model_consistency() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 211--213
[]\T1/txtt/m/n/10 _check_replicon_consistency() \T1/qtm/m/n/10 (\T1/qtm/m/it/10
mac-
Underfull \hbox (badness 10000) in paragraph at lines 213--214
[]\T1/txtt/m/n/10 _check_structure() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.p
ackage.Package
Underfull \hbox (badness 10000) in paragraph at lines 214--216
[]\T1/txtt/m/n/10 _check_syntax() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 214--216
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 216--218
[]\T1/txtt/m/n/10 _config_file_2_dict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-syp
y.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 218--220
[]\T1/txtt/m/n/10 _create_exchangeable_map() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 220--222
[]\T1/txtt/m/n/10 _create_model() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 220--222
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 222--224
[]\T1/txtt/m/n/10 _fill_gembase_min_max() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 224--226
[]\T1/txtt/m/n/10 _fill_gene_bank() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 224--226
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Overfull \hbox (11.05232pt too wide) in paragraph at lines 227--229
[]\T1/txtt/m/n/10 _fill_my_db() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 229--231
[]\T1/txtt/m/n/10 _fill_ordered_min_max() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 231--232
[]\T1/txtt/m/n/10 _fill_topology() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.dat
abase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 234--236
[]\T1/txtt/m/n/10 _find_installed_package() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 237--239
[]\T1/txtt/m/n/10 _get_model_conf_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 237--239
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 239--241
[]\T1/txtt/m/n/10 _get_model_node() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 239--241
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 241--243
[]\T1/txtt/m/n/10 _get_remote_available_versions() \T1/qtm/m/n/10 (\T1/qtm/m/it
/10 in mod-ule
Underfull \hbox (badness 10000) in paragraph at lines 243--245
[]\T1/txtt/m/n/10 _get_replicon_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 243--245
\T1/qtm/m/it/10 sypy.report.GembaseHMMReport method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 245--247
[]\T1/txtt/m/n/10 _get_replicon_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 245--247
\T1/qtm/m/it/10 sypy.report.GeneralHMMReport method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 249--251
[]\T1/txtt/m/n/10 _get_replicon_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 249--251
\T1/qtm/m/it/10 sypy.report.OrderedHMMReport method\T1/qtm/m/n/10 ),
Overfull \hbox (5.80234pt too wide) in paragraph at lines 252--254
[]\T1/txtt/m/n/10 _hit_start() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts
.macsyprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 255--256
[]\T1/txtt/m/n/10 _load_metadata() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.pac
kage.Package
Underfull \hbox (badness 10000) in paragraph at lines 256--258
[]\T1/txtt/m/n/10 _loner_warning() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 258--260
[]\T1/txtt/m/n/10 _outfile_header() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 260--262
[]\T1/txtt/m/n/10 _parse_exchangeable() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 260--262
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
[187]
Underfull \hbox (badness 10000) in paragraph at lines 262--264
[]\T1/txtt/m/n/10 _parse_genes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 262--264
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 264--265
[]\T1/txtt/m/n/10 _parse_hmm_body() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.re
port.HMMReport
Underfull \hbox (badness 10000) in paragraph at lines 265--267
[]\T1/txtt/m/n/10 _parse_hmm_body() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 267--269
[]\T1/txtt/m/n/10 _parse_hmm_header() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
report.HMMReport
Underfull \hbox (badness 10000) in paragraph at lines 269--271
[]\T1/txtt/m/n/10 _parse_hmm_header() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 271--273
[]\T1/txtt/m/n/10 _parse_section() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 271--273
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 273--274
[]\T1/txtt/m/n/10 _profile_features() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
profile.Profile
Underfull \hbox (badness 10000) in paragraph at lines 274--276
[]\T1/txtt/m/n/10 _scan_definitions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 274--276
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 278--280
[]\T1/txtt/m/n/10 _search_in_desc() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 282--284
[]\T1/txtt/m/n/10 _search_in_pack_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod
-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 286--288
[]\T1/txtt/m/n/10 _set_command_line_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 289--290
[]\T1/txtt/m/n/10 _set_default_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-syp
y.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 290--292
[]\T1/txtt/m/n/10 _set_inter_gene_max_space() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 292--293
[]\T1/txtt/m/n/10 _set_log_level() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.con
fig.Config method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 293--294
[]\T1/txtt/m/n/10 _set_max_nb_genes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
config.Config
Underfull \hbox (badness 10000) in paragraph at lines 296--298
[]\T1/txtt/m/n/10 _set_min_mandatory_genes_required() \T1/qtm/m/n/10 (\T1/qtm/m
/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 298--299
[]\T1/txtt/m/n/10 _set_model_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.
config.Config
Underfull \hbox (badness 10000) in paragraph at lines 302--303
[]\T1/txtt/m/n/10 _set_no_cut_ga() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.con
fig.Config method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 304--306
[]\T1/txtt/m/n/10 _set_previous_run_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 306--308
[]\T1/txtt/m/n/10 _set_project_config_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 308--310
[]\T1/txtt/m/n/10 _set_replicon_topology() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
sypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 311--313
[]\T1/txtt/m/n/10 _set_system_models_dir() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
sypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 315--316
[]\T1/txtt/m/n/10 _set_topology_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 316--318
[]\T1/txtt/m/n/10 _set_user_config_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-s
ypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 318--320
[]\T1/txtt/m/n/10 _set_user_wide_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-s
ypy.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 320--321
[]\T1/txtt/m/n/10 _sorted_systems() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.so
lution.Solution
Underfull \hbox (badness 10000) in paragraph at lines 322--323
[]\T1/txtt/m/n/10 _url_json() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.
RemoteModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 332--334
[]\T1/txtt/m/n/10 accessory_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.AbstractUnordered
Overfull \hbox (74.65233pt too wide) in paragraph at lines 335--337
[]\T1/txtt/m/n/10 add_comment() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.script
s.macsyconfig.ConfigParserWithComments
Underfull \hbox (badness 10000) in paragraph at lines 337--338
[]\T1/txtt/m/n/10 add_exchangeable() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.g
ene.Exchangeable
Underfull \hbox (badness 10000) in paragraph at lines 338--339
[]\T1/txtt/m/n/10 add_exchangeable() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.g
ene.ModelGene
Underfull \hbox (badness 10000) in paragraph at lines 340--341
[]\T1/txtt/m/n/10 add_new_gene() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene.
GeneBank method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 341--343
[]\T1/txtt/m/n/10 add_subdefinition() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 341--343
\T1/qtm/m/it/10 sypy.registries.DefinitionLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 343--345
[]\T1/txtt/m/n/10 alarm_handler() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule ma
c-
[188]
Underfull \hbox (badness 10000) in paragraph at lines 346--348
[]\T1/txtt/m/n/10 allowed_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.
AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 357--359
[]\T1/txtt/m/n/10 build_arg_parser() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 365--366
[]\T1/txtt/m/n/10 check_choice() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac
-
Underfull \hbox (badness 10000) in paragraph at lines 366--368
[]\T1/txtt/m/n/10 check_consistency() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 366--368
\T1/qtm/m/it/10 sypy.definition_parser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 371--372
[]\T1/txtt/m/n/10 check_float() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 372--374
[]\T1/txtt/m/n/10 check_positive_int() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u
le mac-
Underfull \hbox (badness 10000) in paragraph at lines 380--381
[]\T1/txtt/m/n/10 combine_multisystems() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod
-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 383--385
[]\T1/txtt/m/n/10 ConfigParserWithComments \T1/qtm/m/n/10 (\T1/qtm/m/it/10 clas
s in mac-
Underfull \hbox (badness 10000) in paragraph at lines 392--393
[]\T1/txtt/m/n/10 count() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Abstr
actSetOfHits method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 393--395
[]\T1/txtt/m/n/10 counterpart \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abst
ractCounterpartHit
Underfull \hbox (badness 10000) in paragraph at lines 399--400
[]\T1/txtt/m/n/10 DefinitionParser \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in mac
-
Underfull \hbox (badness 10000) in paragraph at lines 400--401
[]\T1/txtt/m/n/10 do_available() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac
-
Underfull \hbox (badness 10000) in paragraph at lines 407--409
[]\T1/txtt/m/n/10 do_init_package() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 412--414
[]\T1/txtt/m/n/10 do_show_definition() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u
le mac-
Underfull \hbox (badness 10000) in paragraph at lines 414--415
[]\T1/txtt/m/n/10 do_uninstall() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac
-
Underfull \hbox (badness 10000) in paragraph at lines 416--417
[]\T1/txtt/m/n/10 download() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.package.R
emoteModelIndex
Underfull \hbox (badness 10000) in paragraph at lines 430--432
[]\T1/txtt/m/n/10 family_name \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 434--435
[]\T1/txtt/m/n/10 find_best_solutions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
[189]
Underfull \hbox (badness 10000) in paragraph at lines 435--436
[]\T1/txtt/m/n/10 find_my_indexes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.da
tabase.Indexes
Underfull \hbox (badness 10000) in paragraph at lines 436--438
[]\T1/txtt/m/n/10 forbidden_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 438--439
[]\T1/txtt/m/n/10 fulfilled_function() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.cluster.Cluster
Underfull \hbox (badness 10000) in paragraph at lines 439--441
[]\T1/txtt/m/n/10 fulfilled_function() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 439--441
\T1/qtm/m/it/10 sypy.system.AbstractClusterizedHits method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 453--455
[]\T1/txtt/m/n/10 get_all_definitions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 453--455
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 460--462
[]\T1/txtt/m/n/10 get_definitions() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 460--462
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 463--465
[]\T1/txtt/m/n/10 get_gene_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 465--467
[]\T1/txtt/m/n/10 get_hits_encoding_multisystem() \T1/qtm/m/n/10 (\T1/qtm/m/it/
10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 472--473
[]\T1/txtt/m/n/10 get_profile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.profil
e.ProfileFactory
Underfull \hbox (badness 10000) in paragraph at lines 473--475
[]\T1/txtt/m/n/10 get_profile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.regist
ries.ModelLocation
Underfull \hbox (badness 10000) in paragraph at lines 475--477
[]\T1/txtt/m/n/10 get_profile_len() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 477--479
[]\T1/txtt/m/n/10 get_profiles_names() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 477--479
\T1/qtm/m/it/10 sypy.registries.ModelLocation method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 480--482
[]\T1/txtt/m/n/10 get_version_message() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 482--484
[]\T1/txtt/m/n/10 get_version_message() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 484--486
[]\T1/txtt/m/n/10 get_version_message() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 486--487
[]\T1/txtt/m/n/10 getter_maker() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.MetaSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 487--489
[]\T1/txtt/m/n/10 guess_if_really_gembase() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac
-
Underfull \hbox (badness 10000) in paragraph at lines 513--514
[]\T1/txtt/m/n/10 init_logger() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 514--516
[]\T1/txtt/m/n/10 inter_gene_max_space \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.gene.ModelGene
Underfull \hbox (badness 10000) in paragraph at lines 517--519
[]\T1/txtt/m/n/10 inter_gene_max_space() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sy
py.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 520--521
[]\T1/txtt/m/n/10 is_compatible() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syst
em.System method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 522--523
[]\T1/txtt/m/n/10 is_exchangeable \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene
.ModelGene prop-
[190]
Underfull \hbox (badness 10000) in paragraph at lines 535--537
[]\T1/txtt/m/n/10 likely_systems_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo
d-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 537--539
[]\T1/txtt/m/n/10 likely_systems_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo
d-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 540--541
[]\T1/txtt/m/n/10 list_models() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 541--543
[]\T1/txtt/m/n/10 list_package_vers() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 541--543
\T1/qtm/m/it/10 sypy.package.RemoteModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 543--545
[]\T1/txtt/m/n/10 list_packages() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 543--545
\T1/qtm/m/it/10 sypy.package.RemoteModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 5417) in paragraph at lines 552--553
[]\T1/txtt/m/n/10 loner \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.AbstractCo
unterpartHit prop-erty\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 556--558
[]\T1/txtt/m/n/10 loners_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule ma
c-
Underfull \hbox (badness 10000) in paragraph at lines 588--590
[]\T1/txtt/m/n/10 mandatory_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syste
m.AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 591--592
[]\T1/txtt/m/n/10 match() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Unord
eredMatchMaker
Underfull \hbox (badness 10000) in paragraph at lines 601--602
[]\T1/txtt/m/n/10 min_genes_required \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.m
odel.Model prop-
Underfull \hbox (badness 10000) in paragraph at lines 602--603
[]\T1/txtt/m/n/10 min_genes_required() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy
.config.Config
Underfull \hbox (badness 10000) in paragraph at lines 603--605
[]\T1/txtt/m/n/10 min_mandatory_genes_required \T1/qtm/m/n/10 (\T1/qtm/m/it/10
mac-
Underfull \hbox (badness 10000) in paragraph at lines 605--607
[]\T1/txtt/m/n/10 min_mandatory_genes_required() \T1/qtm/m/n/10 (\T1/qtm/m/it/1
0 mac-
Underfull \hbox (badness 10000) in paragraph at lines 611--612
[]\T1/txtt/m/n/10 model_family_name \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.ge
ne.CoreGene prop-
Underfull \hbox (badness 10000) in paragraph at lines 613--614
[]\T1/txtt/m/n/10 ModelConfParser \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in mac-
[191]
Underfull \hbox (badness 10000) in paragraph at lines 638--639
[]\T1/txtt/m/n/10 multi_system \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.gene.Mo
delGene prop-erty\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 639--641
[]\T1/txtt/m/n/10 multi_system \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.hit.Abs
tractCounterpartHit
Underfull \hbox (badness 10000) in paragraph at lines 644--646
[]\T1/txtt/m/n/10 multisystems_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 651--653
[]\T1/txtt/m/n/10 neutral_hits \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.
AbstractUnordered
Underfull \hbox (badness 10000) in paragraph at lines 666--668
[]\T1/txtt/m/n/10 parse() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.definition_p
arser.DefinitionParser
Underfull \hbox (badness 10000) in paragraph at lines 670--672
[]\T1/txtt/m/n/10 parse() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.macs
yprofile.HmmProfile
Underfull \hbox (badness 10000) in paragraph at lines 674--675
[]\T1/txtt/m/n/10 parse_args() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 675--677
[]\T1/txtt/m/n/10 parse_filtering() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 675--677
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 678--680
[]\T1/txtt/m/n/10 parse_weights() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 678--680
\T1/qtm/m/it/10 sypy.model_conf_parser.ModelConfParser
Underfull \hbox (badness 10000) in paragraph at lines 681--682
[]\T1/txtt/m/n/10 present_genes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.syst
em.MatchMaker
Underfull \hbox (badness 6188) in paragraph at lines 693--695
[]\T1/txtt/m/n/10 rejected_candidates_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10
in mod-ule mac-
Underfull \hbox (badness 6188) in paragraph at lines 695--697
[]\T1/txtt/m/n/10 rejected_candidates_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10
in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 698--700
[]\T1/txtt/m/n/10 remote_exists() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 698--700
\T1/qtm/m/it/10 sypy.package.RemoteModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 702--703
[]\T1/txtt/m/n/10 replicon_infos() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.dat
abase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 704--706
[]\T1/txtt/m/n/10 replicon_name \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system
.AbstractSetOfHits
Underfull \hbox (badness 10000) in paragraph at lines 706--707
[]\T1/txtt/m/n/10 replicon_names() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.dat
abase.RepliconDB
Underfull \hbox (badness 10000) in paragraph at lines 709--711
[]\T1/txtt/m/n/10 root_name() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 715--716
[]\T1/txtt/m/n/10 save_extract() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.repor
t.HMMReport
[192]
Underfull \hbox (badness 10000) in paragraph at lines 721--723
[]\T1/txtt/m/n/10 search_systems() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Overfull \hbox (25.85234pt too wide) in paragraph at lines 724--726
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvLikelySystemSerializer
Overfull \hbox (53.63235pt too wide) in paragraph at lines 726--728
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvRejectedCandidatesSerializer
Overfull \hbox (7.43233pt too wide) in paragraph at lines 728--730
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSolutionSerializer
Overfull \hbox (16.31233pt too wide) in paragraph at lines 730--732
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSpecialHitSerializer
Overfull \hbox (1.41234pt too wide) in paragraph at lines 732--734
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TsvSystemSerializer
Overfull \hbox (25.49234pt too wide) in paragraph at lines 734--736
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TxtLikelySystemSerializer
Overfull \hbox (1.05234pt too wide) in paragraph at lines 736--738
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TxtSystemSerializer
Overfull \hbox (31.85233pt too wide) in paragraph at lines 738--740
[]\T1/txtt/m/n/10 serialize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.serializ
ation.TxtUnikelySystemSerializer
Underfull \hbox (badness 10000) in paragraph at lines 740--742
[]\T1/txtt/m/n/10 set_base_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 742--744
[]\T1/txtt/m/n/10 set_general_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-
ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 744--746
[]\T1/txtt/m/n/10 set_hmmer_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul
e mac-
Underfull \hbox (badness 10000) in paragraph at lines 746--748
[]\T1/txtt/m/n/10 set_path_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 748--750
[]\T1/txtt/m/n/10 set_score_options() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul
e mac-
Underfull \hbox (badness 10000) in paragraph at lines 750--751
[]\T1/txtt/m/n/10 set_section() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 756--758
[]\T1/txtt/m/n/10 solutions_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule
mac-
Underfull \hbox (badness 10000) in paragraph at lines 758--760
[]\T1/txtt/m/n/10 sort_hits_by_status() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 762--764
[]\T1/txtt/m/n/10 split_fqn() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.registri
es.DefinitionLocation
Underfull \hbox (badness 10000) in paragraph at lines 766--768
[]\T1/txtt/m/n/10 summary_best_solution() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo
d-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 772--774
[]\T1/txtt/m/n/10 systems_to_tsv() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 774--776
[]\T1/txtt/m/n/10 systems_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule m
ac-
Underfull \hbox (badness 10000) in paragraph at lines 784--785
[]\T1/txtt/m/n/10 topology \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.database.Re
pliconInfo at-tribute\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 785--787
[]\T1/txtt/m/n/10 TsvLikelySystemSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 cla
ss in mac-
Underfull \hbox (badness 10000) in paragraph at lines 789--790
[]\T1/txtt/m/n/10 TsvSolutionSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class i
n mac-
Underfull \hbox (badness 10000) in paragraph at lines 790--792
[]\T1/txtt/m/n/10 TsvSpecialHitSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class
in mac-
Underfull \hbox (badness 10000) in paragraph at lines 793--795
[]\T1/txtt/m/n/10 TxtLikelySystemSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 cla
ss in mac-
Underfull \hbox (badness 10000) in paragraph at lines 796--798
[]\T1/txtt/m/n/10 TxtUnikelySystemSerializer \T1/qtm/m/n/10 (\T1/qtm/m/it/10 cl
ass in mac-
Underfull \hbox (badness 10000) in paragraph at lines 801--803
[]\T1/txtt/m/n/10 unarchive_package() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-
Underfull \hbox (badness 10000) in paragraph at lines 801--803
\T1/qtm/m/it/10 sypy.package.AbstractModelIndex method\T1/qtm/m/n/10 ),
Underfull \hbox (badness 10000) in paragraph at lines 803--805
[]\T1/txtt/m/n/10 unlikely_systems_to_txt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in
mod-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 811--813
[]\T1/txtt/m/n/10 verbosity_to_log_level() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 813--815
[]\T1/txtt/m/n/10 verbosity_to_log_level() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m
od-ule mac-
Underfull \hbox (badness 10000) in paragraph at lines 819--820
[]\T1/txtt/m/n/10 wholeness \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.system.Abs
tractSetOfHits prop-
Overfull \hbox (43.15242pt too wide) in paragraph at lines 822--824
[]\T1/txtt/m/n/10 write() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 mac-sypy.scripts.macs
yconfig.ConfigParserWithComments
[193]
[194]) (./macsyfinder.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/q
hvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvbi.pfb></usr/share/tex
mf/fonts/type1/public/tex-gyre/qhvr.pfb></usr/share/texmf/fonts/type1/public/te
x-gyre/qtmb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmbi.pfb></usr/s
hare/texmf/fonts/type1/public/tex-gyre/qtmr.pfb></usr/share/texmf/fonts/type1/p
ublic/tex-gyre/qtmri.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfo
nts/t1xbtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/txfonts/tcxbtt.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/txfonts/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb>
Output written on macsyfinder.pdf (198 pages, 2637543 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: 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/3899812 and its subdirectories
I: Current time: Tue Jan 21 11:20:09 -12 2025
I: pbuilder-time-stamp: 1737501609