[Debian-med-packaging] Bug#1028774: Bug#1028774: macsyfinder: FTBFS: RuntimeError: cannot join current thread

Sun Jan 15 10:35:42 GMT 2023

Control: tags -1 + moreinfo

Hi Lucas, Hi Nilesh,

Lucas Nussbaum, on 2023-01-15:
> On 15/01/23 at 12:20 +0530, Nilesh Patra wrote:
> > It passes for me in a clean unstable chroot. Could you please check if this
> > is still persistent or was just a on-off thing?
> 
> I can still reproduce

I didn't manage to reproduce the problem, see the build log
attached.  Having a close look at the test, I was under the
impression at some point that when having less than five cores
could eventually trigger an issue, but tests on low profile
virtual machine didn't raise any issue to me neither.  The build
log is attached for comparison, but nothing jumps at me as of
what could trigger the error.

Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/1, please excuse my verbosity.
On air: Steve Hughes - 50,50 Zone
-------------- next part --------------
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on fusion

+==============================================================================+
| macsyfinder (amd64)                          Sun, 15 Jan 2023 09:47:57 +0000 |
+==============================================================================+

Package: macsyfinder
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: full

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-440f7a4e-9994-4b39-ad45-fc3b12bcdb50' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/macsyfinder-9Wp3g0/resolver-9l3Jsd' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Hit:1 http://localhost:3142/deb.debian.org/debian sid InRelease
Hit:2 http://localhost/~emollier/repos experimental InRelease
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+

Check APT
---------

Use of uninitialized value in numeric gt (>) at /usr/share/perl5/Sbuild/Build.pm line 1178.
Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'macsyfinder' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/macsyfinder.git
Please use:
git clone https://salsa.debian.org/med-team/macsyfinder.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 33.9 MB of source archives.
Get:1 http://localhost:3142/deb.debian.org/debian sid/main macsyfinder 2.0-1 (dsc) [2420 B]
Get:2 http://localhost:3142/deb.debian.org/debian sid/main macsyfinder 2.0-1 (tar) [33.8 MB]
Get:3 http://localhost:3142/deb.debian.org/debian sid/main macsyfinder 2.0-1 (diff) [9732 B]
Fetched 33.9 MB in 1s (36.7 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/macsyfinder-9Wp3g0/macsyfinder-2.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/macsyfinder-9Wp3g0' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+

Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-sphinx, python3-networkx, python3-yaml, python3-colorlog, python3-colorama, python3-pandas, python3-sphinx-rtd-theme, tex-gyre, texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer, debhelper, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-sphinx, python3-networkx, python3-yaml, python3-colorlog, python3-colorama, python3-pandas, python3-sphinx-rtd-theme, tex-gyre, texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer, debhelper, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [990 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [961 B]
Fetched 2560 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils binutils-common
  binutils-x86-64-linux-gnu bsdextrautils build-essential bzip2
  ca-certificates cpp cpp-12 debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism docutils-common dpkg-dev dwz fakeroot file
  fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato
  fonts-lmodern g++ g++-12 gcc gcc-12 gettext gettext-base graphviz groff-base
  hmmer intltool-debian latexmk libabsl20220623 libann0 libaom3
  libapache-pom-java libarchive-zip-perl libasan8 libatomic1 libavif15
  libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0
  libcdt5 libcgraph6 libcommons-logging-java libcommons-parent-java
  libcrypt-dev libctf-nobfd0 libctf0 libdatrie1 libdav1d6 libde265-0
  libdebhelper-perl libdeflate0 libdivsufsort3 libdpkg-perl libexpat1
  libfakeroot libfile-stripnondeterminism-perl libfontbox-java libfontconfig1
  libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgcc-12-dev libgd3
  libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgts-0.7-5
  libgvc6 libgvpr2 libharfbuzz0b libheif1 libice6 libicu72 libisl23 libitm1
  libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore
  libjson-perl libkpathsea6 liblab-gamut1 liblapack3 liblerc4 liblsan0
  libltdl7 libmagic-mgc libmagic1 libmpc3 libmpdec3 libmpfr6 libnsl-dev
  libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
  libpaper1 libpathplan4 libpdfbox-java libpipeline1 libpixman-1-0 libpng16-16
  libptexenc1 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
  libpython3.11-minimal libpython3.11-stdlib libquadmath0 librav1e0 libsm6
  libsqlite3-0 libstdc++-12-dev libsub-override-perl libsvtav1enc1 libsynctex2
  libteckit0 libtexlua53-5 libtexluajit2 libthai-data libthai0 libtiff6
  libtirpc-dev libtool libtsan2 libubsan1 libuchardet0 libwebp7 libx11-6
  libx11-data libx265-199 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6
  libyaml-0-2 libyuv0 libzzip-0-13 linux-libc-dev m4 make man-db media-types
  openssl patch po-debconf preview-latex-style python-babel-localedata python3
  python3-alabaster python3-babel python3-certifi python3-chardet
  python3-charset-normalizer python3-colorama python3-colorlog
  python3-dateutil python3-distutils python3-docutils python3-idna
  python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe
  python3-minimal python3-networkx python3-numpy python3-packaging
  python3-pandas python3-pandas-lib python3-pkg-resources python3-pygments
  python3-requests python3-roman python3-setuptools python3-six
  python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme python3-tz
  python3-urllib3 python3-yaml python3.10 python3.10-minimal python3.11
  python3.11-minimal rpcsvc-proto sgml-base sphinx-common
  sphinx-rtd-theme-common t1utils tex-common tex-gyre texlive-base
  texlive-binaries texlive-fonts-recommended texlive-latex-base
  texlive-latex-extra texlive-latex-recommended texlive-pictures
  texlive-plain-generic ucf x11-common xdg-utils xfonts-encodings xfonts-utils
  xml-core xz-utils
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc bzip2-doc cpp-doc
  gcc-12-locales cpp-12-doc dh-make flit python3-build python3-tomli
  python3-installer debian-keyring g++-multilib g++-12-multilib gcc-12-doc
  gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-12-multilib gettext-doc
  libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff hmmer-doc
  ghostscript glibc-doc libavalon-framework-java libcommons-logging-java-doc
  libexcalibur-logkit-java liblog4j1.2-java gnupg | sq | sqop | pgpainless-cli
  git bzr libgd-tools low-memory-monitor libstdc++-12-doc libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc make-doc apparmor www-browser ed
  diffutils-doc libmail-box-perl python3-doc python3-tk python3-venv
  docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
  python-jinja2-doc gfortran python3-dev python3-pytest python-pandas-doc
  python3-statsmodels python-pygments-doc ttf-bitstream-vera
  python3-cryptography python3-openssl python3-socks python-requests-doc
  python-setuptools-doc python3-stemmer dvipng fonts-freefont-otf
  imagemagick-6.q16 libjs-mathjax sphinx-doc python3-brotli python3.10-venv
  python3.10-doc binfmt-support python3.11-venv python3.11-doc sgml-base-doc
  gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec
  texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex icc-profiles
  libfile-which-perl texlive-latex-extra-doc texlive-science
  texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex
  texlive-pictures-doc vprerex default-jre-headless
Recommended packages:
  gnupg | sq | sqop | pgpainless-cli libalgorithm-merge-perl curl | wget
  | lynx fonts-liberation2 xpdf | pdf-viewer gv | postscript-viewer manpages
  manpages-dev libc-devtools libfile-fcntllock-perl libarchive-cpio-perl
  libglib2.0-data shared-mime-info xdg-user-dirs libgts-bin javascript-common
  libjson-xs-perl libltdl-dev libmail-sendmail-perl python3-pil python3-gdal
  python3-matplotlib python3-pydot python3-pygraphviz python3-scipy
  python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4
  python3-html5lib python3-lxml python3-tables python3-numba fonts-texgyre
  fonts-texgyre-math lmodern dvisvgm tipa default-jre
  libspreadsheet-parseexcel-perl ruby tk libfile-mimeinfo-perl
  libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils binutils-common
  binutils-x86-64-linux-gnu bsdextrautils build-essential bzip2
  ca-certificates cpp cpp-12 debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism docutils-common dpkg-dev dwz fakeroot file
  fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato
  fonts-lmodern g++ g++-12 gcc gcc-12 gettext gettext-base graphviz groff-base
  hmmer intltool-debian latexmk libabsl20220623 libann0 libaom3
  libapache-pom-java libarchive-zip-perl libasan8 libatomic1 libavif15
  libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0
  libcdt5 libcgraph6 libcommons-logging-java libcommons-parent-java
  libcrypt-dev libctf-nobfd0 libctf0 libdatrie1 libdav1d6 libde265-0
  libdebhelper-perl libdeflate0 libdivsufsort3 libdpkg-perl libexpat1
  libfakeroot libfile-stripnondeterminism-perl libfontbox-java libfontconfig1
  libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgcc-12-dev libgd3
  libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgts-0.7-5
  libgvc6 libgvpr2 libharfbuzz0b libheif1 libice6 libicu72 libisl23 libitm1
  libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore
  libjson-perl libkpathsea6 liblab-gamut1 liblapack3 liblerc4 liblsan0
  libltdl7 libmagic-mgc libmagic1 libmpc3 libmpdec3 libmpfr6 libnsl-dev
  libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
  libpaper1 libpathplan4 libpdfbox-java libpipeline1 libpixman-1-0 libpng16-16
  libptexenc1 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
  libpython3.11-minimal libpython3.11-stdlib libquadmath0 librav1e0 libsm6
  libsqlite3-0 libstdc++-12-dev libsub-override-perl libsvtav1enc1 libsynctex2
  libteckit0 libtexlua53-5 libtexluajit2 libthai-data libthai0 libtiff6
  libtirpc-dev libtool libtsan2 libubsan1 libuchardet0 libwebp7 libx11-6
  libx11-data libx265-199 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6
  libyaml-0-2 libyuv0 libzzip-0-13 linux-libc-dev m4 make man-db media-types
  openssl patch po-debconf preview-latex-style python-babel-localedata python3
  python3-alabaster python3-babel python3-certifi python3-chardet
  python3-charset-normalizer python3-colorama python3-colorlog
  python3-dateutil python3-distutils python3-docutils python3-idna
  python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe
  python3-minimal python3-networkx python3-numpy python3-packaging
  python3-pandas python3-pandas-lib python3-pkg-resources python3-pygments
  python3-requests python3-roman python3-setuptools python3-six
  python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme python3-tz
  python3-urllib3 python3-yaml python3.10 python3.10-minimal python3.11
  python3.11-minimal rpcsvc-proto sbuild-build-depends-main-dummy sgml-base
  sphinx-common sphinx-rtd-theme-common t1utils tex-common tex-gyre
  texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base
  texlive-latex-extra texlive-latex-recommended texlive-pictures
  texlive-plain-generic ucf x11-common xdg-utils xfonts-encodings xfonts-utils
  xml-core xz-utils
0 upgraded, 238 newly installed, 0 to remove and 0 not upgraded.
Need to get 285 MB of archives.
After this operation, 1081 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1008 B]
Get:2 http://localhost:3142/deb.debian.org/debian sid/main amd64 fonts-lato all 2.0-2.1 [2696 kB]
Get:3 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.1-2 [812 kB]
Get:4 http://localhost:3142/deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get:5 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.1-2 [2065 kB]
Get:6 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.1-1 [25.5 kB]
Get:7 http://localhost:3142/deb.debian.org/debian sid/main amd64 media-types all 8.0.0 [33.4 kB]
Get:8 http://localhost:3142/deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB]
Get:9 http://localhost:3142/deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.40.1-1 [838 kB]
Get:10 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.1-2 [1712 kB]
Get:11 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.1-2 [567 kB]
Get:12 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.1-1 [8580 B]
Get:13 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3 amd64 3.11.1-1 [25.2 kB]
Get:14 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpython3.10-minimal amd64 3.10.9-1 [784 kB]
Get:15 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3.10-minimal amd64 3.10.9-1 [1951 kB]
Get:16 http://localhost:3142/deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB]
Get:17 http://localhost:3142/deb.debian.org/debian sid/main amd64 bzip2 amd64 1.0.8-5+b1 [49.8 kB]
Get:18 http://localhost:3142/deb.debian.org/debian sid/main amd64 openssl amd64 3.0.7-1 [1400 kB]
Get:19 http://localhost:3142/deb.debian.org/debian sid/main amd64 ca-certificates all 20211016 [156 kB]
Get:20 http://localhost:3142/deb.debian.org/debian sid/main amd64 libmagic-mgc amd64 1:5.44-1 [303 kB]
Get:21 http://localhost:3142/deb.debian.org/debian sid/main amd64 libmagic1 amd64 1:5.44-1 [104 kB]
Get:22 http://localhost:3142/deb.debian.org/debian sid/main amd64 file amd64 1:5.44-1 [42.4 kB]
Get:23 http://localhost:3142/deb.debian.org/debian sid/main amd64 gettext-base amd64 0.21-10 [160 kB]
Get:24 http://localhost:3142/deb.debian.org/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:25 http://localhost:3142/deb.debian.org/debian sid/main amd64 groff-base amd64 1.22.4-9 [916 kB]
Get:26 http://localhost:3142/deb.debian.org/debian sid/main amd64 bsdextrautils amd64 2.38.1-4 [86.2 kB]
Get:27 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get:28 http://localhost:3142/deb.debian.org/debian sid/main amd64 man-db amd64 2.11.2-1 [1386 kB]
Get:29 http://localhost:3142/deb.debian.org/debian sid/main amd64 ucf all 3.0043 [74.0 kB]
Get:30 http://localhost:3142/deb.debian.org/debian sid/main amd64 xz-utils amd64 5.4.1-0.0 [440 kB]
Get:31 http://localhost:3142/deb.debian.org/debian sid/main amd64 m4 amd64 1.4.19-2 [287 kB]
Get:32 http://localhost:3142/deb.debian.org/debian sid/main amd64 autoconf all 2.71-3 [332 kB]
Get:33 http://localhost:3142/deb.debian.org/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:34 http://localhost:3142/deb.debian.org/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:35 http://localhost:3142/deb.debian.org/debian sid/main amd64 autopoint all 0.21-10 [495 kB]
Get:36 http://localhost:3142/deb.debian.org/debian sid/main amd64 binutils-common amd64 2.40-1 [2485 kB]
Get:37 http://localhost:3142/deb.debian.org/debian sid/main amd64 libbinutils amd64 2.40-1 [573 kB]
Get:38 http://localhost:3142/deb.debian.org/debian sid/main amd64 libctf-nobfd0 amd64 2.40-1 [153 kB]
Get:39 http://localhost:3142/deb.debian.org/debian sid/main amd64 libctf0 amd64 2.40-1 [89.8 kB]
Get:40 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgprofng0 amd64 2.40-1 [812 kB]
Get:41 http://localhost:3142/deb.debian.org/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.40-1 [2245 kB]
Get:42 http://localhost:3142/deb.debian.org/debian sid/main amd64 binutils amd64 2.40-1 [65.0 kB]
Get:43 http://localhost:3142/deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.36-8 [43.8 kB]
Get:44 http://localhost:3142/deb.debian.org/debian sid/main amd64 linux-libc-dev amd64 6.1.4-1 [1709 kB]
Get:45 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB]
Get:46 http://localhost:3142/deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB]
Get:47 http://localhost:3142/deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB]
Get:48 http://localhost:3142/deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB]
Get:49 http://localhost:3142/deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.36-8 [1897 kB]
Get:50 http://localhost:3142/deb.debian.org/debian sid/main amd64 libisl23 amd64 0.25-1 [690 kB]
Get:51 http://localhost:3142/deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB]
Get:52 http://localhost:3142/deb.debian.org/debian sid/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB]
Get:53 http://localhost:3142/deb.debian.org/debian sid/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB]
Get:54 http://localhost:3142/deb.debian.org/debian sid/main amd64 cpp amd64 4:12.2.0-3 [6836 B]
Get:55 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB]
Get:56 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgomp1 amd64 12.2.0-14 [116 kB]
Get:57 http://localhost:3142/deb.debian.org/debian sid/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB]
Get:58 http://localhost:3142/deb.debian.org/debian sid/main amd64 libatomic1 amd64 12.2.0-14 [9328 B]
Get:59 http://localhost:3142/deb.debian.org/debian sid/main amd64 libasan8 amd64 12.2.0-14 [2195 kB]
Get:60 http://localhost:3142/deb.debian.org/debian sid/main amd64 liblsan0 amd64 12.2.0-14 [969 kB]
Get:61 http://localhost:3142/deb.debian.org/debian sid/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB]
Get:62 http://localhost:3142/deb.debian.org/debian sid/main amd64 libubsan1 amd64 12.2.0-14 [883 kB]
Get:63 http://localhost:3142/deb.debian.org/debian sid/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB]
Get:64 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB]
Get:65 http://localhost:3142/deb.debian.org/debian sid/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB]
Get:66 http://localhost:3142/deb.debian.org/debian sid/main amd64 gcc amd64 4:12.2.0-3 [5216 B]
Get:67 http://localhost:3142/deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB]
Get:68 http://localhost:3142/deb.debian.org/debian sid/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB]
Get:69 http://localhost:3142/deb.debian.org/debian sid/main amd64 g++ amd64 4:12.2.0-3 [1356 B]
Get:70 http://localhost:3142/deb.debian.org/debian sid/main amd64 make amd64 4.3-4.1 [396 kB]
Get:71 http://localhost:3142/deb.debian.org/debian sid/main amd64 libdpkg-perl all 1.21.18 [576 kB]
Get:72 http://localhost:3142/deb.debian.org/debian sid/main amd64 patch amd64 2.7.6-7 [128 kB]
Get:73 http://localhost:3142/deb.debian.org/debian sid/main amd64 dpkg-dev all 1.21.18 [1301 kB]
Get:74 http://localhost:3142/deb.debian.org/debian sid/main amd64 build-essential amd64 12.9 [7704 B]
Get:75 http://localhost:3142/deb.debian.org/debian sid/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get:76 http://localhost:3142/deb.debian.org/debian sid/main amd64 libtool all 2.4.7-5 [517 kB]
Get:77 http://localhost:3142/deb.debian.org/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:78 http://localhost:3142/deb.debian.org/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:79 http://localhost:3142/deb.debian.org/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get:80 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:81 http://localhost:3142/deb.debian.org/debian sid/main amd64 dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:82 http://localhost:3142/deb.debian.org/debian sid/main amd64 dwz amd64 0.15-1 [109 kB]
Get:83 http://localhost:3142/deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get:84 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b2 [687 kB]
Get:85 http://localhost:3142/deb.debian.org/debian sid/main amd64 gettext amd64 0.21-10 [1300 kB]
Get:86 http://localhost:3142/deb.debian.org/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:87 http://localhost:3142/deb.debian.org/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:88 http://localhost:3142/deb.debian.org/debian sid/main amd64 debhelper all 13.11.4 [942 kB]
Get:89 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:90 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-distutils all 3.10.8-1 [139 kB]
Get:91 http://localhost:3142/deb.debian.org/debian sid/main amd64 dh-python all 5.20230109 [103 kB]
Get:92 http://localhost:3142/deb.debian.org/debian sid/main amd64 xml-core all 0.18+nmu1 [23.8 kB]
Get:93 http://localhost:3142/deb.debian.org/debian sid/main amd64 docutils-common all 0.17.1+dfsg-3 [113 kB]
Get:94 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfakeroot amd64 1.30.1-1.1 [28.1 kB]
Get:95 http://localhost:3142/deb.debian.org/debian sid/main amd64 fakeroot amd64 1.30.1-1.1 [66.7 kB]
Get:96 http://localhost:3142/deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b5 [279 kB]
Get:97 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get:98 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB]
Get:99 http://localhost:3142/deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB]
Get:100 http://localhost:3142/deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.14.1-3 [315 kB]
Get:101 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.14.1-3 [386 kB]
Get:102 http://localhost:3142/deb.debian.org/debian sid/main amd64 fontconfig amd64 2.14.1-3 [449 kB]
Get:103 http://localhost:3142/deb.debian.org/debian sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get:104 http://localhost:3142/deb.debian.org/debian sid/main amd64 fonts-lmodern all 2.005-1 [4540 kB]
Get:105 http://localhost:3142/deb.debian.org/debian sid/main amd64 libann0 amd64 1.1.2+doc-9 [24.2 kB]
Get:106 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcdt5 amd64 2.42.2-7+b3 [39.8 kB]
Get:107 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcgraph6 amd64 2.42.2-7+b3 [63.2 kB]
Get:108 http://localhost:3142/deb.debian.org/debian sid/main amd64 libaom3 amd64 3.5.0-1 [1796 kB]
Get:109 http://localhost:3142/deb.debian.org/debian sid/main amd64 libdav1d6 amd64 1.0.0-2 [495 kB]
Get:110 http://localhost:3142/deb.debian.org/debian sid/main amd64 libabsl20220623 amd64 20220623.1-1 [391 kB]
Get:111 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgav1-1 amd64 0.18.0-1+b1 [332 kB]
Get:112 http://localhost:3142/deb.debian.org/debian sid/main amd64 librav1e0 amd64 0.5.1-6 [763 kB]
Get:113 http://localhost:3142/deb.debian.org/debian sid/main amd64 libsvtav1enc1 amd64 1.4.1+dfsg-1 [2121 kB]
Get:114 http://localhost:3142/deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.2-1+b1 [169 kB]
Get:115 http://localhost:3142/deb.debian.org/debian sid/main amd64 libyuv0 amd64 0.0~git20230104.6e4b0ac-1 [167 kB]
Get:116 http://localhost:3142/deb.debian.org/debian sid/main amd64 libavif15 amd64 0.11.1-1 [93.8 kB]
Get:117 http://localhost:3142/deb.debian.org/debian sid/main amd64 libde265-0 amd64 1.0.9-1 [247 kB]
Get:118 http://localhost:3142/deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB]
Get:119 http://localhost:3142/deb.debian.org/debian sid/main amd64 libx265-199 amd64 3.5-2+b1 [1150 kB]
Get:120 http://localhost:3142/deb.debian.org/debian sid/main amd64 libheif1 amd64 1.13.0-1 [203 kB]
Get:121 http://localhost:3142/deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get:122 http://localhost:3142/deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get:123 http://localhost:3142/deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get:124 http://localhost:3142/deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.2.2-2+b3 [279 kB]
Get:125 http://localhost:3142/deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.0-3 [315 kB]
Get:126 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get:127 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get:128 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get:129 http://localhost:3142/deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.3-3 [292 kB]
Get:130 http://localhost:3142/deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.3-3 [759 kB]
Get:131 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB]
Get:132 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgd3 amd64 2.3.3-7+b1 [124 kB]
Get:133 http://localhost:3142/deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.74.4-1 [1396 kB]
Get:134 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-5+b1 [160 kB]
Get:135 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB]
Get:136 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB]
Get:137 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB]
Get:138 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get:139 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB]
Get:140 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.16.0-7 [575 kB]
Get:141 http://localhost:3142/deb.debian.org/debian sid/main amd64 libltdl7 amd64 2.4.7-5 [393 kB]
Get:142 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get:143 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get:144 http://localhost:3142/deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 6.0.0-1 [1938 kB]
Get:145 http://localhost:3142/deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-1 [176 kB]
Get:146 http://localhost:3142/deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB]
Get:147 http://localhost:3142/deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB]
Get:148 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB]
Get:149 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB]
Get:150 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB]
Get:151 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpathplan4 amd64 2.42.2-7+b3 [42.2 kB]
Get:152 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgvc6 amd64 2.42.2-7+b3 [678 kB]
Get:153 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgvpr2 amd64 2.42.2-7+b3 [189 kB]
Get:154 http://localhost:3142/deb.debian.org/debian sid/main amd64 liblab-gamut1 amd64 2.42.2-7+b3 [198 kB]
Get:155 http://localhost:3142/deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB]
Get:156 http://localhost:3142/deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get:157 http://localhost:3142/deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get:158 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxt6 amd64 1:1.2.1-1 [189 kB]
Get:159 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB]
Get:160 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB]
Get:161 http://localhost:3142/deb.debian.org/debian sid/main amd64 graphviz amd64 2.42.2-7+b3 [611 kB]
Get:162 http://localhost:3142/deb.debian.org/debian sid/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB]
Get:163 http://localhost:3142/deb.debian.org/debian sid/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB]
Get:164 http://localhost:3142/deb.debian.org/debian sid/main amd64 tex-common all 6.18 [32.5 kB]
Get:165 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB]
Get:166 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB]
Get:167 http://localhost:3142/deb.debian.org/debian sid/main amd64 libkpathsea6 amd64 2022.20220321.62855-5 [152 kB]
Get:168 http://localhost:3142/deb.debian.org/debian sid/main amd64 libptexenc1 amd64 2022.20220321.62855-5 [43.5 kB]
Get:169 http://localhost:3142/deb.debian.org/debian sid/main amd64 libsynctex2 amd64 2022.20220321.62855-5 [59.6 kB]
Get:170 http://localhost:3142/deb.debian.org/debian sid/main amd64 libtexlua53-5 amd64 2022.20220321.62855-5 [111 kB]
Get:171 http://localhost:3142/deb.debian.org/debian sid/main amd64 libtexluajit2 amd64 2022.20220321.62855-5 [246 kB]
Get:172 http://localhost:3142/deb.debian.org/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:173 http://localhost:3142/deb.debian.org/debian sid/main amd64 libteckit0 amd64 2.5.11+ds1-1+b1 [335 kB]
Get:174 http://localhost:3142/deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB]
Get:175 http://localhost:3142/deb.debian.org/debian sid/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB]
Get:176 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-binaries amd64 2022.20220321.62855-5 [10.5 MB]
Get:177 http://localhost:3142/deb.debian.org/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:178 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-base all 2022.20221123-1 [21.9 MB]
Get:179 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-latex-base all 2022.20221123-1 [1175 kB]
Get:180 http://localhost:3142/deb.debian.org/debian sid/main amd64 latexmk all 1:4.79-1 [198 kB]
Get:181 http://localhost:3142/deb.debian.org/debian sid/main amd64 libapache-pom-java all 29-2 [5276 B]
Get:182 http://localhost:3142/deb.debian.org/debian sid/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get:183 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get:184 http://localhost:3142/deb.debian.org/debian sid/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB]
Get:185 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfontbox-java all 1:1.8.16-2 [211 kB]
Get:186 http://localhost:3142/deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB]
Get:187 http://localhost:3142/deb.debian.org/debian sid/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get:188 http://localhost:3142/deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:189 http://localhost:3142/deb.debian.org/debian sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:190 http://localhost:3142/deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 5.3.0-3 [130 kB]
Get:191 http://localhost:3142/deb.debian.org/debian sid/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get:192 http://localhost:3142/deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get:193 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpdfbox-java all 1:1.8.16-2 [5205 kB]
Get:194 http://localhost:3142/deb.debian.org/debian sid/main amd64 libpython3.10-stdlib amd64 3.10.9-1 [1684 kB]
Get:195 http://localhost:3142/deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get:196 http://localhost:3142/deb.debian.org/debian sid/main amd64 preview-latex-style all 12.2-1 [201 kB]
Get:197 http://localhost:3142/deb.debian.org/debian sid/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB]
Get:198 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB]
Get:199 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-pkg-resources all 65.6.3-1 [278 kB]
Get:200 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-tz all 2022.7-1 [32.1 kB]
Get:201 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-babel all 2.10.3-1 [103 kB]
Get:202 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-certifi all 2022.9.24-1 [153 kB]
Get:203 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get:204 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get:205 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-colorama all 0.4.6-2 [36.8 kB]
Get:206 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-colorlog all 6.7.0-1 [26.5 kB]
Get:207 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-six all 1.16.0-4 [17.5 kB]
Get:208 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-dateutil all 2.8.2-1 [78.2 kB]
Get:209 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-roman all 3.3-3 [9880 B]
Get:210 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-docutils all 0.17.1+dfsg-3 [380 kB]
Get:211 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-idna all 3.3-1 [39.4 kB]
Get:212 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get:213 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-markupsafe amd64 2.1.1-1+b1 [13.7 kB]
Get:214 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-jinja2 all 3.0.3-2 [121 kB]
Get:215 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-networkx all 2.8.8-1 [1425 kB]
Get:216 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3.10 amd64 3.10.9-1 [509 kB]
Get:217 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.1-2 [5966 kB]
Get:218 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-packaging all 23.0-1 [32.5 kB]
Get:219 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 1.5.2+dfsg-6 [6269 kB]
Get:220 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-pandas all 1.5.2+dfsg-6 [2882 kB]
Get:221 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB]
Get:222 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-urllib3 all 1.26.12-1 [117 kB]
Get:223 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get:224 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-setuptools all 65.6.3-1 [520 kB]
Get:225 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB]
Get:226 http://localhost:3142/deb.debian.org/debian sid/main amd64 sphinx-common all 5.3.0-3 [652 kB]
Get:227 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-sphinx all 5.3.0-3 [549 kB]
Get:228 http://localhost:3142/deb.debian.org/debian sid/main amd64 sphinx-rtd-theme-common all 1.2.0~rc1+dfsg-1 [996 kB]
Get:229 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-sphinx-rtd-theme all 1.2.0~rc1+dfsg-1 [26.4 kB]
Get:230 http://localhost:3142/deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0-3+b1 [159 kB]
Get:231 http://localhost:3142/deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.1 [573 kB]
Get:232 http://localhost:3142/deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB]
Get:233 http://localhost:3142/deb.debian.org/debian sid/main amd64 tex-gyre all 20180621-6 [6209 kB]
Get:234 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-fonts-recommended all 2022.20221123-1 [4988 kB]
Get:235 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-latex-recommended all 2022.20221123-1 [8882 kB]
Get:236 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-pictures all 2022.20221123-1 [15.8 MB]
Get:237 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-latex-extra all 2022.20221123-2 [19.2 MB]
Get:238 http://localhost:3142/deb.debian.org/debian sid/main amd64 texlive-plain-generic all 2022.20221123-2 [28.6 MB]
Preconfiguring packages ...
Fetched 285 MB in 2s (122 MB/s)
Selecting previously unselected package fonts-lato.
(Reading database ... 10901 files and directories currently installed.)
Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ...
Unpacking fonts-lato (2.0-2.1) ...
Selecting previously unselected package libpython3.11-minimal:amd64.
Preparing to unpack .../libpython3.11-minimal_3.11.1-2_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.1-2) ...
Selecting previously unselected package libexpat1:amd64.
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Setting up libsqlite3-0:amd64 (3.40.1-1) ...
Setting up liblab-gamut1:amd64 (2.42.2-7+b3) ...
Setting up binutils-common:amd64 (2.40-1) ...
Setting up x11-common (1:7.7+23) ...
Running in chroot, ignoring request.
Setting up libmagic1:amd64 (1:5.44-1) ...
Setting up libdeflate0:amd64 (1.14-1) ...
Setting up linux-libc-dev:amd64 (6.1.4-1) ...
Setting up libctf-nobfd0:amd64 (2.40-1) ...
Setting up gettext-base (0.21-10) ...
Setting up m4 (1.4.19-2) ...
Setting up libxcb-shm0:amd64 (1.15-1) ...
Setting up libzzip-0-13:amd64 (0.13.72+dfsg.1-1.1) ...
Setting up file (1:5.44-1) ...
Setting up libsvtav1enc1:amd64 (1.4.1+dfsg-1) ...
Setting up libgomp1:amd64 (12.2.0-14) ...
Setting up bzip2 (1.0.8-5+b1) ...
Setting up libjbig0:amd64 (2.1-6.1) ...
Setting up librav1e0:amd64 (0.5.1-6) ...
Setting up libfakeroot:amd64 (1.30.1-1.1) ...
Setting up python-babel-localedata (2.10.3-1) ...
Setting up fakeroot (1.30.1-1.1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-5+b1) ...
Setting up libfontenc1:amd64 (1:1.1.4-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:amd64 (3.11.0-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ...
Setting up rpcsvc-proto (1.4.3-1) ...
Setting up libjpeg62-turbo:amd64 (1:2.1.2-1+b1) ...
Setting up libx11-data (2:1.8.3-3) ...
Setting up make (4.3-4.1) ...
Setting up libmpfr6:amd64 (4.2.0-1) ...
Setting up libteckit0:amd64 (2.5.11+ds1-1+b1) ...
Setting up libpathplan4:amd64 (2.42.2-7+b3) ...
Setting up libapache-pom-java (29-2) ...
Setting up libann0 (1.1.2+doc-9) ...
Setting up xz-utils (5.4.1-0.0) ...
update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
Setting up xfonts-encodings (1:1.0.4-2.1) ...
Setting up libfribidi0:amd64 (1.0.8-2.1) ...
Setting up t1utils (1.41-4) ...
Setting up libquadmath0:amd64 (12.2.0-14) ...
Setting up libtexlua53-5:amd64 (2022.20220321.62855-5) ...
Setting up libpng16-16:amd64 (1.6.39-2) ...
Setting up libmpc3:amd64 (1.3.1-1) ...
Setting up libatomic1:amd64 (12.2.0-14) ...
Setting up patch (2.7.6-7) ...
Setting up libpython3.10-minimal:amd64 (3.10.9-1) ...
Setting up autopoint (0.21-10) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libgav1-1:amd64 (0.18.0-1+b1) ...
Setting up ucf (3.0043) ...
Setting up libdav1d6:amd64 (1.0.0-2) ...
Setting up libltdl7:amd64 (2.4.7-5) ...
Setting up libdpkg-perl (1.21.18) ...
Setting up libkpathsea6:amd64 (2022.20220321.62855-5) ...
Setting up libgfortran5:amd64 (12.2.0-14) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:amd64 (1.2.2-2+b3) ...
Setting up libubsan1:amd64 (12.2.0-14) ...
Setting up libnuma1:amd64 (2.0.16-1) ...
Setting up dwz (0.15-1) ...
Setting up libnsl-dev:amd64 (1.3.0-2) ...
Setting up libcrypt-dev:amd64 (1:4.4.33-2) ...
Setting up libtiff6:amd64 (4.5.0-3) ...
Setting up libasan8:amd64 (12.2.0-14) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libjson-perl (4.10000-1) ...
Setting up libmpdec3:amd64 (2.5.1-2) ...
Setting up fonts-lmodern (2.005-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libx11-6:amd64 (2:1.8.3-3) ...
Setting up libthai-data (0.1.29-1) ...
Setting up sgml-base (1.31) ...
Setting up libcdt5:amd64 (2.42.2-7+b3) ...
Setting up libcgraph6:amd64 (2.42.2-7+b3) ...
Setting up libtsan2:amd64 (12.2.0-14) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libbinutils:amd64 (2.40-1) ...
Setting up libisl23:amd64 (0.25-1) ...
Setting up libde265-0:amd64 (1.0.9-1) ...
Setting up libc-dev-bin (2.36-8) ...
Setting up libdivsufsort3:amd64 (2.0.1-5) ...
Setting up openssl (3.0.7-1) ...
Setting up libyuv0:amd64 (0.0~git20230104.6e4b0ac-1) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b2) ...
Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
Setting up sphinx-rtd-theme-common (1.2.0~rc1+dfsg-1) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libcc1-0:amd64 (12.2.0-14) ...
Setting up liblsan0:amd64 (12.2.0-14) ...
Setting up libitm1:amd64 (12.2.0-14) ...
Setting up libsynctex2:amd64 (2022.20220321.62855-5) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up libctf0:amd64 (2.40-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-2) ...
Setting up libpaper1:amd64 (1.1.28+b1) ...

Creating config file /etc/papersize with new version
Setting up libice6:amd64 (2:1.0.10-1) ...
Setting up liblapack3:amd64 (3.11.0-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up cpp-12 (12.2.0-14) ...
Setting up gettext (0.21-10) ...
Setting up libpdfbox-java (1:1.8.16-2) ...
Setting up libxpm4:amd64 (1:3.5.12-1) ...
Setting up libavif15:amd64 (0.11.1-1) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
Setting up fontconfig-config (2.14.1-3) ...
Setting up libpython3.11-stdlib:amd64 (3.11.1-2) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libcommons-logging-java (1.2-3) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up libpaper-utils (1.1.28+b1) ...
Setting up python3.10-minimal (3.10.9-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libpython3.10-stdlib:amd64 (3.10.9-1) ...
Setting up tex-common (6.18) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libthai0:amd64 (0.1.29-1) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libgprofng0:amd64 (2.40-1) ...
Setting up libptexenc1:amd64 (2022.20220321.62855-5) ...
Setting up libfreetype6:amd64 (2.12.1+dfsg-4) ...
Setting up libgcc-12-dev:amd64 (12.2.0-14) ...
Setting up libjs-sphinxdoc (5.3.0-3) ...
Setting up libx265-199:amd64 (3.5-2+b1) ...
Setting up dh-strip-nondeterminism (1.13.0-2) ...
Setting up libgvpr2:amd64 (2.42.2-7+b3) ...
Setting up groff-base (1.22.4-9) ...
Setting up cpp (4:12.2.0-3) ...
Setting up xml-core (0.18+nmu1) ...
Setting up hmmer (3.3.2+dfsg-1) ...
Setting up libc6-dev:amd64 (2.36-8) ...
Setting up libharfbuzz0b:amd64 (6.0.0-1) ...
Setting up libfontconfig1:amd64 (2.14.1-3) ...
Setting up libsm6:amd64 (2:1.2.3-1) ...
Setting up libpython3-stdlib:amd64 (3.11.1-1) ...
Setting up binutils-x86-64-linux-gnu (2.40-1) ...
Setting up python3.11 (3.11.1-2) ...
Setting up fontconfig (2.14.1-3) ...
Regenerating fonts cache... done.
Setting up python3.10 (3.10.9-1) ...
Setting up libxi6:amd64 (2:1.8-1+b1) ...
Setting up libstdc++-12-dev:amd64 (12.2.0-14) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up preview-latex-style (12.2-1) ...
Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ...
Setting up libheif1:amd64 (1.13.0-1) ...
Setting up python3 (3.11.1-1) ...
Setting up binutils (2.40-1) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.11.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer.
Setting up python3-markupsafe (2.1.1-1+b1) ...
Setting up libcairo2:amd64 (1.16.0-7) ...
Setting up python3-tz (2022.7-1) ...
Setting up dpkg-dev (1.21.18) ...
Setting up python3-six (1.16.0-4) ...
Setting up python3-roman (3.3-3) ...
Setting up python3-jinja2 (3.0.3-2) ...
Setting up python3-packaging (23.0-1) ...
Setting up python3-certifi (2022.9.24-1) ...
Setting up gcc-12 (12.2.0-14) ...
Setting up python3-snowballstemmer (2.2.0-2) ...
Setting up sphinx-common (5.3.0-3) ...
Setting up libgd3:amd64 (2.3.3-7+b1) ...
Setting up python3-idna (3.3-1) ...
Setting up libxt6:amd64 (1:1.2.1-1) ...
Setting up python3-urllib3 (1.26.12-1) ...
Setting up python3-dateutil (2.8.2-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up tex-gyre (20180621-6) ...
Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ...
Setting up python3-imagesize (1.4.1-1) ...
Setting up g++-12 (12.2.0-14) ...
Setting up python3-pkg-resources (65.6.3-1) ...
Setting up python3-distutils (3.10.8-1) ...
Setting up dh-python (5.20230109) ...
Setting up libxmu6:amd64 (2:1.1.3-3) ...
Setting up python3-setuptools (65.6.3-1) ...
Setting up libtool (2.4.7-5) ...
Setting up python3-babel (2.10.3-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-colorama (0.4.6-2) ...
Setting up python3-colorlog (6.7.0-1) ...
Setting up python3-charset-normalizer (3.0.1-2) ...
Setting up python3-alabaster (0.7.12-1) ...
Setting up python3-yaml (6.0-3+b1) ...
Setting up libxaw7:amd64 (2:1.0.14-1) ...
Setting up python3-networkx (2.8.8-1) ...
Setting up gcc (4:12.2.0-3) ...
Setting up dh-autoreconf (20) ...
Setting up python3-pygments (2.14.0+dfsg-1) ...
Setting up python3-chardet (5.1.0+dfsg-2) ...
Setting up python3-requests (2.28.1+dfsg-1) ...
Setting up libgvc6 (2.42.2-7+b3) ...
Setting up python3-numpy (1:1.24.1-2) ...
Setting up g++ (4:12.2.0-3) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up texlive-binaries (2022.20220321.62855-5) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up build-essential (12.9) ...
Setting up texlive-base (2022.20221123-1) ...
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 graphviz (2.42.2-7+b3) ...
Setting up python3-pandas-lib:amd64 (1.5.2+dfsg-6) ...
Setting up texlive-plain-generic (2022.20221123-2) ...
Setting up debhelper (13.11.4) ...
Setting up python3-pandas (1.5.2+dfsg-6) ...
Setting up texlive-latex-base (2022.20221123-1) ...
Setting up texlive-latex-recommended (2022.20221123-1) ...
Setting up texlive-pictures (2022.20221123-1) ...
Setting up texlive-fonts-recommended (2022.20221123-1) ...
Setting up latexmk (1:4.79-1) ...
Setting up texlive-latex-extra (2022.20221123-2) ...
Processing triggers for libc-bin (2.36-8) ...
Processing triggers for systemd (252.4-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.17.1+dfsg-3) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.17.1+dfsg-3) ...
Setting up python3-sphinx (5.3.0-3) ...
Setting up python3-sphinx-rtd-theme (1.2.0~rc1+dfsg-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
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.

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in amd64 i386)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.1.0-1-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.4-1 (2023-01-07) amd64 (x86_64)
Toolchain package versions: binutils_2.40-1 dpkg-dev_1.21.18 g++-12_12.2.0-14 gcc-12_12.2.0-14 libc6-dev_2.36-8 libstdc++-12-dev_12.2.0-14 libstdc++6_12.2.0-14 linux-libc-dev_6.1.4-1
Package versions: adduser_3.130 apt_2.5.4 apt-utils_2.5.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-1 binutils-common_2.40-1 binutils-x86-64-linux-gnu_2.40-1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b1 ca-certificates_20211016 coreutils_9.1-1 cpio_2.13+dfsg-7.1 cpp_4:12.2.0-3 cpp-12_12.2.0-14 cron_3.0pl1-156 cron-daemon-common_3.0pl1-156 dash_0.5.12-2 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.4 debian-archive-keyring_2021.1.1 debianutils_5.7-0.4 dh-autoreconf_20 dh-python_5.20230109 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-3 dmidecode_3.4-1 dmsetup_2:1.02.185-2 docutils-common_0.17.1+dfsg-3 dpkg_1.21.18 dpkg-dev_1.21.18 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1.1 fakeroot_1.30.1-1.1 fdisk_2.38.1-4 file_1:5.44-1 findutils_4.9.0-4 fontconfig_2.14.1-3 fontconfig-config_2.14.1-3 fonts-dejavu-core_2.37-2 fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1 fonts-lato_2.0-2.1 fonts-lmodern_2.005-1 g++_4:12.2.0-3 g++-12_12.2.0-14 gcc_4:12.2.0-3 gcc-10-base_10.4.0-7 gcc-11-base_11.3.0-11 gcc-12_12.2.0-14 gcc-12-base_12.2.0-14 gcc-9-base_9.5.0-2+b3 gettext_0.21-10 gettext-base_0.21-10 gpgv_2.2.40-1 graphviz_2.42.2-7+b3 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hmmer_3.3.2+dfsg-1 hostname_3.23+nmu1 ifupdown_0.8.39+b1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iproute2_6.1.0-1 iputils-ping_3:20221126-1 isc-dhcp-client_4.4.3-P1-1.1 isc-dhcp-common_4.4.3-P1-1.1 kmod_30+20221128-1 latexmk_1:4.79-1 less_590-1.1 libabsl20220623_20220623.1-1 libacl1_2.3.1-2 libann0_1.1.2+doc-9 libaom3_3.5.0-1 libapache-pom-java_29-2 libapparmor1_3.0.8-1 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-14 libatomic1_12.2.0-14 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1+b2 libavif15_0.11.1-1 libbinutils_2.40-1 libblas3_3.11.0-2 libblkid1_2.38.1-4 libbpf0_1:0.8.0-1 libbpf1_1:1.1.0-1 libbrotli1_1.0.9-2+b5 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-8 libc-dev-bin_2.36-8 libc6_2.36-8 libc6-dev_2.36-8 libcairo2_1.16.0-7 libcap-ng0_0.8.3-1+b2 libcap2_1:2.66-3 libcap2-bin_1:2.66-3 libcc1-0_12.2.0-14 libcdt5_2.42.2-7+b3 libcgraph6_2.42.2-7+b3 libcom-err2_1.46.6~rc1-1.1 libcommons-logging-java_1.2-3 libcommons-parent-java_56-1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.6.0-2 libctf-nobfd0_2.40-1 libctf0_2.40-1 libdatrie1_0.2.13-2+b1 libdav1d6_1.0.0-2 libdb5.3_5.3.28+dfsg1-0.10 libde265-0_1.0.9-1 libdebconfclient0_0.266 libdebhelper-perl_13.11.4 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-2 libdivsufsort3_2.0.1-5 libdns-export1110_1:9.11.19+dfsg-2.1+b1 libdpkg-perl_1.21.18 libedit2_3.1-20221030-2 libelf1_0.188-2.1 libestr0_0.1.11-1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1.1 libfakeroot_1.30.1-1.1 libfastjson4_0.99.9-2 libfdisk1_2.38.1-4 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.0-2 libfontbox-java_1:1.8.16-2 libfontconfig1_2.14.1-3 libfontenc1_1:1.1.4-1 libfreetype6_2.12.1+dfsg-4 libfribidi0_1.0.8-2.1 libgav1-1_0.18.0-1+b1 libgcc-12-dev_12.2.0-14 libgcc-s1_12.2.0-14 libgcrypt20_1.10.1-3 libgd3_2.3.3-7+b1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14 libglib2.0-0_2.74.4-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-14 libgpg-error0_1.46-1 libgprofng0_2.40-1 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20.1-1 libgts-0.7-5_0.7.6+darcs121130-5+b1 libgvc6_2.42.2-7+b3 libgvpr2_2.42.2-7+b3 libharfbuzz0b_6.0.0-1 libheif1_1.13.0-1 libhogweed6_3.8.1-2 libice6_2:1.0.10-1 libicu72_72.1-3 libidn2-0_2.3.3-1+b1 libip4tc2_1.8.8-1 libisc-export1105_1:9.11.19+dfsg-2.1+b1 libisl23_0.25-1 libitm1_12.2.0-14 libjansson4_2.14-2 libjbig0_2.1-6.1 libjpeg62-turbo_1:2.1.2-1+b1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_5.3.0-3 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-c5_0.16-2 libjson-perl_4.10000-1 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1 libkpathsea6_2022.20220321.62855-5 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 liblab-gamut1_2.42.2-7+b3 liblapack3_3.11.0-2 liblerc4_4.0.0+ds-2 liblocale-gettext-perl_1.07-5 liblognorm5_2.0.6-4 liblsan0_12.2.0-14 libltdl7_2.4.7-5 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.0 libmagic-mgc_1:5.44-1 libmagic1_1:5.44-1 libmd0_1.0.4-2 libmnl0_1.0.4-3 libmount1_2.38.1-4 libmpc3_1.3.1-1 libmpdec3_2.5.1-2 libmpfr6_4.2.0-1 libncurses6_6.4-1 libncursesw6_6.4-1 libnettle8_3.8.1-2 libnewt0.52_0.52.23-1 libnftables1_1.0.6-1 libnftnl11_1.2.4-2 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma1_2.0.16-1 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-2 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-6 libpam0g_1.5.2-6 libpango-1.0-0_1.50.12+ds-1 libpangocairo-1.0-0_1.50.12+ds-1 libpangoft2-1.0-0_1.50.12+ds-1 libpaper-utils_1.1.28+b1 libpaper1_1.1.28+b1 libpathplan4_2.42.2-7+b3 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libpdfbox-java_1:1.8.16-2 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.39-2 libpopt0_1.19+dfsg-1 libproc2-0_2:4.0.2-3 libprocps8_2:3.3.17-7.1 libptexenc1_2022.20220321.62855-5 libpython3-stdlib_3.11.1-1 libpython3.10-minimal_3.10.9-1 libpython3.10-stdlib_3.10.9-1 libpython3.11-minimal_3.11.1-2 libpython3.11-stdlib_3.11.1-2 libquadmath0_12.2.0-14 librav1e0_0.5.1-6 libreadline8_8.2-1.3 libseccomp2_2.5.4-1+b2 libselinux1_3.4-1+b4 libsemanage-common_3.4-1 libsemanage2_3.4-1+b4 libsepol2_3.4-2 libslang2_2.3.3-2 libsm6_2:1.2.3-1 libsmartcols1_2.38.1-4 libsqlite3-0_3.40.1-1 libss2_1.46.6~rc1-1.1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-14 libstdc++6_12.2.0-14 libsub-override-perl_0.09-4 libsvtav1enc1_1.4.1+dfsg-1 libsynctex2_2022.20220321.62855-5 libsystemd-shared_252.4-1 libsystemd0_252.4-1 libtasn1-6_4.19.0-2 libteckit0_2.5.11+ds1-1+b1 libtexlua53-5_2022.20220321.62855-5 libtexluajit2_2022.20220321.62855-5 libtext-charwidth-perl_0.04-11 libtext-glob-perl_0.11-3 libtext-iconv-perl_1.7-8 libtext-wrapi18n-perl_0.06-10 libthai-data_0.1.29-1 libthai0_0.1.29-1 libtiff6_4.5.0-3 libtinfo6_6.4-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_12.2.0-14 libubsan1_12.2.0-14 libuchardet0_0.0.7-1 libudev1_252.4-1 libunistring2_1.0-2 libuuid1_2.38.1-4 libwebp7_1.2.2-2+b3 libx11-6_2:1.8.3-3 libx11-data_2:1.8.3-3 libx265-199_3.5-2+b1 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1+b1 libxi6_2:1.8-1+b1 libxml2_2.9.14+dfsg-1.1+b2 libxmu6_2:1.1.3-3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1.1 libxt6_1:1.2.1-1 libxtables12_1.8.8-1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libyuv0_0.0~git20230104.6e4b0ac-1 libzstd1_1.5.2+dfsg2-3 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_6.1.4-1 login_1:4.13+dfsg1-1 logrotate_3.21.0-1 logsave_1.46.6~rc1-1.1 m4_1.4.19-2 make_4.3-4.1 man-db_2.11.2-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-4 nano_7.1-1 ncurses-base_6.4-1 ncurses-bin_6.4-1 netbase_6.4 nftables_1.0.6-1 openssl_3.0.7-1 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 po-debconf_1.0.21+nmu1 preview-latex-style_12.2-1 procps_2:4.0.2-3 python-babel-localedata_2.10.3-1 python3_3.11.1-1 python3-alabaster_0.7.12-1 python3-babel_2.10.3-1 python3-certifi_2022.9.24-1 python3-chardet_5.1.0+dfsg-2 python3-charset-normalizer_3.0.1-2 python3-colorama_0.4.6-2 python3-colorlog_6.7.0-1 python3-dateutil_2.8.2-1 python3-distutils_3.10.8-1 python3-docutils_0.17.1+dfsg-3 python3-idna_3.3-1 python3-imagesize_1.4.1-1 python3-jinja2_3.0.3-2 python3-lib2to3_3.10.8-1 python3-markupsafe_2.1.1-1+b1 python3-minimal_3.11.1-1 python3-networkx_2.8.8-1 python3-numpy_1:1.24.1-2 python3-packaging_23.0-1 python3-pandas_1.5.2+dfsg-6 python3-pandas-lib_1.5.2+dfsg-6 python3-pkg-resources_65.6.3-1 python3-pygments_2.14.0+dfsg-1 python3-requests_2.28.1+dfsg-1 python3-roman_3.3-3 python3-setuptools_65.6.3-1 python3-six_1.16.0-4 python3-snowballstemmer_2.2.0-2 python3-sphinx_5.3.0-3 python3-sphinx-rtd-theme_1.2.0~rc1+dfsg-1 python3-tz_2022.7-1 python3-urllib3_1.26.12-1 python3-yaml_6.0-3+b1 python3.10_3.10.9-1 python3.10-minimal_3.10.9-1 python3.11_3.11.1-2 python3.11-minimal_3.11.1-2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 rsyslog_8.2212.0-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 sphinx-common_5.3.0-3 sphinx-rtd-theme-common_1.2.0~rc1+dfsg-1 systemd_252.4-1 systemd-sysv_252.4-1 sysvinit-utils_3.06-2 t1utils_1.41-4 tar_1.34+dfsg-1.1 tasksel_3.71 tasksel-data_3.71 tex-common_6.18 tex-gyre_20180621-6 texlive-base_2022.20221123-1 texlive-binaries_2022.20220321.62855-5 texlive-fonts-recommended_2022.20221123-1 texlive-latex-base_2022.20221123-1 texlive-latex-extra_2022.20221123-2 texlive-latex-recommended_2022.20221123-1 texlive-pictures_2022.20221123-1 texlive-plain-generic_2022.20221123-2 tzdata_2022g-2 ucf_3.0043 udev_252.4-1 usrmerge_35 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 vim-common_2:9.0.1000-4 vim-tiny_2:9.0.1000-4 whiptail_0.52.23-1 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.1 xfonts-utils_1:7.7+6 xml-core_0.18+nmu1 xxd_2:9.0.1000-4 xz-utils_5.4.1-0.0 zlib1g_1:1.2.13.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+

Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: macsyfinder
Binary: macsyfinder
Architecture: amd64 i386
Version: 2.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: bertrand Neron <bneron at pasteur.fr>
Homepage: https://github.com/gem-pasteur/macsyfinder
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/macsyfinder
Vcs-Git: https://salsa.debian.org/med-team/macsyfinder.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-setuptools
Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-sphinx, python3-networkx <!nocheck>, python3-yaml <!nocheck>, python3-colorlog <!nocheck>, python3-colorama, python3-pandas <!nocheck>, python3-sphinx-rtd-theme <!nodoc>, tex-gyre <!nodoc>, texlive-latex-recommended, texlive-plain-generic, texlive-latex-extra, texlive-fonts-recommended, latexmk, graphviz, hmmer, debhelper
Package-List:
 macsyfinder deb science optional arch=amd64,i386
Checksums-Sha1:
 821238d282eeb6ae5bfd8e23a87b640c825a9e10 33849432 macsyfinder_2.0.orig.tar.gz
 671922f64e776e86729a0126289b4d35febf99eb 9732 macsyfinder_2.0-1.debian.tar.xz
Checksums-Sha256:
 a290075f0a280298cd123185ff47f5a2193d780c491c3cd1d72b36dd75342d8b 33849432 macsyfinder_2.0.orig.tar.gz
 1c7132f89b0960ab159132a749ecd8dc7d190275c7003c8af2970ad58026518c 9732 macsyfinder_2.0-1.debian.tar.xz
Files:
 9a695b339b23062305c72a7959b49fe7 33849432 macsyfinder_2.0.orig.tar.gz
 92960bed4f58fce912fd1d216bf1c0d6 9732 macsyfinder_2.0-1.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-gpg-verify.ia06PnZt/trustedkeys.kbx': General error
gpgv: Signature made Mon Sep 19 15:25:42 2022 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille at debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.0-1.dsc: no acceptable signature found
dpkg-source: info: extracting macsyfinder in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking macsyfinder_2.0.orig.tar.gz
dpkg-source: info: unpacking macsyfinder_2.0-1.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 privacy
dpkg-source: info: applying fix-test-parse.patch
dpkg-source: info: applying do_not_test_parse_model_old_syntax.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=emollier
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-amd64-sbuild
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=emollier
SCHROOT_SESSION_ID=sid-amd64-sbuild-440f7a4e-9994-4b39-ad45-fc3b12bcdb50
SCHROOT_UID=1000
SCHROOT_USER=emollier
SHELL=/bin/sh
USER=emollier

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot
dpkg-buildpackage: info: source package macsyfinder
dpkg-buildpackage: info: source version 2.0-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 dpkg-source -b .
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building macsyfinder using existing ./macsyfinder_2.0.orig.tar.gz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building macsyfinder in macsyfinder_2.0-1.debian.tar.xz
dpkg-source: info: building macsyfinder in macsyfinder_2.0-1.dsc
 debian/rules binary
dh binary --with python3,sphinxdoc --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py config 
running config
   dh_auto_build -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/system.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/solution.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/serialization.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/search_genes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/registries.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/package.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/model_conf_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/hit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/gene.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/error.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/definition_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/database.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
copying macsypy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/macsyprofile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/macsyfinder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/macsydata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/macsyconfig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/macsy_merge_results.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/macsy_gembase_split.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
copying macsypy/scripts/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py test 
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
running egg_info
creating MacSyFinder.egg-info
writing MacSyFinder.egg-info/PKG-INFO
writing dependency_links to MacSyFinder.egg-info/dependency_links.txt
writing entry points to MacSyFinder.egg-info/entry_points.txt
writing requirements to MacSyFinder.egg-info/requires.txt
writing top-level names to MacSyFinder.egg-info/top_level.txt
writing manifest file 'MacSyFinder.egg-info/SOURCES.txt'
reading manifest file 'MacSyFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*' under directory 'doc/build/html'
warning: no files found matching 'doc/build/latex/macsyfinder.pdf'
warning: no files found matching 'etc/macsyfinder.conf'
warning: no previously-included files matching '*' found under directory 'tests/__pycache__/'
warning: no previously-included files found matching 'tests/__init__.pyc'
warning: no previously-included files found matching '.coverage'
warning: no previously-included files found matching 'coverage_html/'
warning: no previously-included files found matching '.gitignore'
warning: no previously-included files found matching '.travis.yml'
warning: no previously-included files found matching '.github/'
warning: no files found matching 'CONTRIBUTORS'
warning: no files found matching 'NEWS'
adding license file 'COPYING'
writing manifest file 'MacSyFinder.egg-info/SOURCES.txt'
running build_ext
test_Config (test_Config.TestConfig.test_Config) ... ok
test_Config_args (test_Config.TestConfig.test_Config_args) ... ok
test_Config_conf_file_virtualenv (test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok
test_Config_default_conf_file (test_Config.TestConfig.test_Config_default_conf_file) ... ok
test_Config_file_bad_values (test_Config.TestConfig.test_Config_file_bad_values) ... ok
test_Config_file_n_args (test_Config.TestConfig.test_Config_file_n_args) ... ok
test_bad_db_type (test_Config.TestConfig.test_bad_db_type) ... ok
test_bad_models_dir (test_Config.TestConfig.test_bad_models_dir) ... ok
test_bad_sequence_db (test_Config.TestConfig.test_bad_sequence_db) ... ok
test_bad_topology (test_Config.TestConfig.test_bad_topology) ... ok
test_bad_topology_file (test_Config.TestConfig.test_bad_topology_file) ... ok
test_bad_values (test_Config.TestConfig.test_bad_values) ... ok
test_cmd_config_file (test_Config.TestConfig.test_cmd_config_file) ... ok
test_config_file_2_dict (test_Config.TestConfig.test_config_file_2_dict) ... ok
test_e_value_search (test_Config.TestConfig.test_e_value_search) ... ok
test_hit_weights (test_Config.TestConfig.test_hit_weights) ... ok
test_model_conf (test_Config.TestConfig.test_model_conf) ... ok
test_models_dir (test_Config.TestConfig.test_models_dir) ... ok
test_no_cut_ga (test_Config.TestConfig.test_no_cut_ga) ... ok
test_out_dir (test_Config.TestConfig.test_out_dir) ... ok
test_previous_n_sequence_db (test_Config.TestConfig.test_previous_n_sequence_db) ... ignore sequence_db '/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta' use sequence_db from previous_run '/<<PKGBUILDDIR>>/tests/data/data_set/results_1'.
ok
test_previous_wo_cfg (test_Config.TestConfig.test_previous_wo_cfg) ... ok
test_project_config_file (test_Config.TestConfig.test_project_config_file) ... ok
test_save (test_Config.TestConfig.test_save) ... ok
test_set_log_level (test_Config.TestConfig.test_set_log_level) ... ok
test_set_option (test_Config.TestConfig.test_set_option) ... ok
test_str_2_tuple (test_Config.TestConfig.test_str_2_tuple) ... ok
test_working_dir (test_Config.TestConfig.test_working_dir) ... ok
test_NoneConfig (test_Config.TestNoneConfig.test_NoneConfig) ... ok
test_bad_exchangeable_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... Models Parsing
Invalid model definition 'foo/bad_exchangeable_inter_gene_max_space': inter_gene_max_space must be an integer: 1.5
ok
test_bad_gene_inter_gene_max_space_2 (test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) ... Models Parsing
Invalid model definition 'foo/bad_inter_gene_max_space_2': inter_gene_max_space must be an integer: 2.5
ok
test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... Models Parsing
Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_inter_gene_max_space.xml): inter_gene_max_space must be an integer: 12.5
ok
test_bad_max_nb_genes (test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... Models Parsing
Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_max_nb_genes.xml): max_nb_genes must be an integer: HOHOHO
ok
test_bad_min_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... Models Parsing
model 'bad_min_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6
ok
test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... Models Parsing
Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_min_genes_required_2.xml): min_genes_required must be an integer: 16.5
ok
test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... Models Parsing
model 'bad_min_mandatory_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6
ok
test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... Models Parsing
ok
test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... Models Parsing
Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_min_mandatory_genes_required_4.xml): min_mandatory_genes_required must be an integer: 12.5
ok
test_exchangeable_inheritance (test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... Models Parsing
ok
test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... Models Parsing
ok
test_gene_no_name (test_DefinitionParser.TestModelParser.test_gene_no_name) ... Models Parsing
Invalid model definition 'foo/gene_no_name': gene without name
ok
test_gene_w_unkown_attr (test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... Models Parsing
unable to parse model definition 'foo/gene_w_unknown_attribute' : The model definition gene_w_unknown_attribute.xml has an unknown attribute 'multi-system' for a gene. Please fix the definition.
ok
test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... Models Parsing
ok
test_invalid_homolog (test_DefinitionParser.TestModelParser.test_invalid_homolog) ... Models Parsing
ok
test_invalid_homolog_2 (test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... Models Parsing
Invalid model definition 'foo/invalid_homolog_2': gene without name
ok
test_invalid_presence (test_DefinitionParser.TestModelParser.test_invalid_presence) ... Models Parsing
Invalid model 'foo/fail_invalid_presence' definition: presence value must be either: 'mandatory', 'accessory', 'neutral', 'forbidden' not foo_bar
ok
test_loner (test_DefinitionParser.TestModelParser.test_loner) ... Models Parsing
Models Parsing
ok
test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... Models Parsing
Models Parsing
ok
test_min_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... Models Parsing
ok
test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... Models Parsing
ok
test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... Models Parsing
model 'bad_min_mandatory_genes_required_3' is not consistent: 'min_mandatory_genes_required': 6 must be lesser or equal than the number of 'mandatory' components in the model: 5
ok
test_model_w_unkown_attr (test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... Models Parsing
unable to parse model definition 'foo/model_w_unknown_attribute' : The model definition model_w_unknown_attribute.xml has an unknow attribute 'multi-loci'. Please fix the definition.
ok
test_multi_loci_cfg (test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... Models Parsing
ok
test_multi_model (test_DefinitionParser.TestModelParser.test_multi_model) ... Models Parsing
ok
test_multi_system (test_DefinitionParser.TestModelParser.test_multi_system) ... Models Parsing
ok
test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... Models Parsing
Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/no_inter_gene_max_space.xml): inter_gene_max_space must be defined
ok
test_only_one_accessory (test_DefinitionParser.TestModelParser.test_only_one_accessory) ... Models Parsing
model 'only_one_accessory' is not consistent: there is only one gene in your model. So its status should be 'mandatory'.
ok
test_parse_model_old_syntax (test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails'
test_parse_with_exchangeable (test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... Models Parsing
ok
test_wo_presence (test_DefinitionParser.TestModelParser.test_wo_presence) ... Models Parsing
Invalid model definition 'foo/fail_wo_presence': gene 'sctN_FLG' without presence
ok
test_add_exchangeable (test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok
test_alternate_of (test_Exchangeable.TestExchangeable.test_alternate_of) ... ok
test_is_exchangeable (test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok
test_loner (test_Exchangeable.TestExchangeable.test_loner) ... ok
test_model (test_Exchangeable.TestExchangeable.test_model) ... ok
test_multi_system (test_Exchangeable.TestExchangeable.test_multi_system) ... ok
test_add_get_gene (test_GeneBank.Test.test_add_get_gene) ... ok
test_contains (test_GeneBank.Test.test_contains) ... ok
test_genes_fqn (test_GeneBank.Test.test_genes_fqn) ... ok
test_get_uniq_object (test_GeneBank.Test.test_get_uniq_object) ... ok
test_iter (test_GeneBank.Test.test_iter) ... ok
test_build_force (test_Indexes.TestIndex.test_build_force) ... ok
test_build_my_indexes (test_Indexes.TestIndex.test_build_my_indexes) ... unable to index the sequence dataset: /tmp/test_macsyfinder_indexes/test_base_with_errors.fa : list index out of range
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/macsypy/database.py", line 192, in _build_my_indexes
    for seq_id, comment, length in f_iter:
  File "/<<PKGBUILDDIR>>/macsypy/database.py", line 53, in fasta_iter
    _id = header[0]
          ~~~~~~^^^
IndexError: list index out of range
ok
test_build_no_idx (test_Indexes.TestIndex.test_build_no_idx) ... ok
test_build_not_writable (test_Indexes.TestIndex.test_build_not_writable) ... The '/tmp/test_macsyfinder_indexes' dir is not writable.
ok
test_build_with_idx (test_Indexes.TestIndex.test_build_with_idx) ... The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building.
The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building.
ok
test_find_my_indexes (test_Indexes.TestIndex.test_find_my_indexes) ... ok
test_index_dir (test_Indexes.TestIndex.test_index_dir) ... ok
test_iter (test_Indexes.TestIndex.test_iter) ... ok
test_allowed_hits (test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok
test_forbidden_hits (test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok
test_hits (test_LikelySystem.LikelySystemTest.test_hits) ... ok
test_init (test_LikelySystem.LikelySystemTest.test_init) ... ok
test_str (test_LikelySystem.LikelySystemTest.test_str) ... ok
test_hits (test_LikelySystem.UnlikelySystemTest.test_hits) ... ok
test_init (test_LikelySystem.UnlikelySystemTest.test_init) ... ok
test_reason (test_LikelySystem.UnlikelySystemTest.test_reason) ... ok
test_str (test_LikelySystem.UnlikelySystemTest.test_str) ... ok
test_MacsyDefaults_no_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok
test_MacsyDefaults_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok
test_ordered_match (test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok
test_sort_hits_by_status (test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... Gene 'fliE' not found in model 'foo/model_B'
ok
test_unordered_match (test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok
test_accessor_mutator (test_Model.TestModel.test_accessor_mutator) ... ok
test_eq (test_Model.TestModel.test_eq) ... ok
test_filter (test_Model.TestModel.test_filter) ... ok
test_fqn (test_Model.TestModel.test_fqn) ... ok
test_get_gene (test_Model.TestModel.test_get_gene) ... ok
test_gt (test_Model.TestModel.test_gt) ... ok
test_hash (test_Model.TestModel.test_hash) ... ok
test_inter_gene_max_space (test_Model.TestModel.test_inter_gene_max_space) ... ok
test_lt (test_Model.TestModel.test_lt) ... ok
test_max_nb_genes (test_Model.TestModel.test_max_nb_genes) ... ok
test_min_genes_required (test_Model.TestModel.test_min_genes_required) ... ok
test_min_mandatory_genes_required (test_Model.TestModel.test_min_mandatory_genes_required) ... ok
test_multi_loci (test_Model.TestModel.test_multi_loci) ... ok
test_str (test_Model.TestModel.test_str) ... ok
test_add_get_model (test_ModelBank.Test.test_add_get_model) ... ok
test_contains (test_ModelBank.Test.test_contains) ... ok
test_get_uniq_object (test_ModelBank.Test.test_get_uniq_object) ... ok
test_iter (test_ModelBank.Test.test_iter) ... ok
test_execute_hmm_protected_path (test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok
test_execute_hmm_w_GA_n_nocutga (test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok
test_execute_hmm_with_GA (test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping'
test_execute_hmm_wo_GA (test_Profile.TestProfile.test_execute_hmm_wo_GA) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000)
ok
test_execute_hmmer_failed (test_Profile.TestProfile.test_execute_hmmer_failed) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000)
an error occurred during Hmmer execution: command = "/tmp/hmmer_failed" --cpu 1 -o "/tmp/macsyfinder-20230115_09-49-02/hmmer_results/abc.search_hmm.out" -E 0.100000 "/<<PKGBUILDDIR>>/tests/data/models/foo/profiles/abc.hmm" "/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta"  : return code = 127 check /tmp/macsyfinder-20230115_09-49-02/hmmer_results/abc.search_hmm.err
ok
test_execute_unknown_binary (test_Profile.TestProfile.test_execute_unknown_binary) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000)
an error occurred during Hmmer execution: command = "Nimportnaoik" --cpu 1 -o "/tmp/macsyfinder-20230115_09-49-02/hmmer_results/abc.search_hmm.out" -E 0.100000 "/<<PKGBUILDDIR>>/tests/data/models/foo/profiles/abc.hmm" "/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta"  : return code = 127 check /tmp/macsyfinder-20230115_09-49-02/hmmer_results/abc.search_hmm.err
ok
test_ga_threshold (test_Profile.TestProfile.test_ga_threshold) ... bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''.
GA score will not used for gene 'bad_GA'.
bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''.
GA score will not used for gene 'bad_GA'.
bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA    22.00'.
GA score will not used for gene 'bad_GA_2'.
bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA    22.00'.
GA score will not used for gene 'bad_GA_2'.
ok
test_len (test_Profile.TestProfile.test_len) ... ok
test_str (test_Profile.TestProfile.test_str) ... ok
test_get_profile (test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok
test_get_uniq_object (test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok
test_unknow_profile (test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok
test_hits (test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok
test_init (test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok
test_str (test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok
test_fill_gembase_min_max_default_topology (test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok
test_fill_gembase_min_max_with_topology (test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok
test_fill_ordered_replicon_min_max (test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok
test_fill_topology (test_RepliconDB.Test.test_fill_topology) ... ok
test_get (test_RepliconDB.Test.test_get) ... ok
test_getitem (test_RepliconDB.Test.test_getitem) ... ok
test_guess_if_really_gembase (test_RepliconDB.Test.test_guess_if_really_gembase) ... ok
test_in (test_RepliconDB.Test.test_in) ... ok
test_items (test_RepliconDB.Test.test_items) ... ok
test_iteritems (test_RepliconDB.Test.test_iteritems) ... ok
test_names (test_RepliconDB.Test.test_names) ... ok
test_replicon_infos (test_RepliconDB.Test.test_replicon_infos) ... ok
test_extract (test_Report.TestGembaseHMMReport.test_extract) ... ok
test_extract_concurent (test_Report.TestGembaseHMMReport.test_extract_concurent) ... /<<PKGBUILDDIR>>/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead
  main_thread = threading.currentThread()
ok
test_extract (test_Report.TestGeneralHMMReport.test_extract) ... ok
test_extract_concurent (test_Report.TestGeneralHMMReport.test_extract_concurent) ... /<<PKGBUILDDIR>>/tests/test_Report.py:539: DeprecationWarning: currentThread() is deprecated, use current_thread() instead
  main_thread = threading.currentThread()
ok
test_HMMReport (test_Report.TestHMMReport.test_HMMReport) ... ok
test_best_hit (test_Report.TestHMMReport.test_best_hit) ... ok
test_build_my_db (test_Report.TestHMMReport.test_build_my_db) ... ok
test_fill_my_db (test_Report.TestHMMReport.test_fill_my_db) ... ok
test_hit_start (test_Report.TestHMMReport.test_hit_start) ... ok
test_parse_hmm_body (test_Report.TestHMMReport.test_parse_hmm_body) ... ok
test_parse_hmm_header (test_Report.TestHMMReport.test_parse_hmm_header) ... ok
test_save_extract (test_Report.TestHMMReport.test_save_extract) ... ok
test_str (test_Report.TestHMMReport.test_str) ... ok
test_extract (test_Report.TestOrderedHMMReport.test_extract) ... hit id 'NC_xxxxx_xx_056141' was not indexed, rebuild sequence 'test_base.fa' index
ok
test_extract_concurent (test_Report.TestOrderedHMMReport.test_extract_concurent) ... /<<PKGBUILDDIR>>/tests/test_Report.py:460: DeprecationWarning: currentThread() is deprecated, use current_thread() instead
  main_thread = threading.currentThread()
ok
test_HitSystemTracker (test_System.SystemTest.test_HitSystemTracker) ... ok
test_count (test_System.SystemTest.test_count) ... ok
test_fulfilled_function (test_System.SystemTest.test_fulfilled_function) ... ok
test_get_hits_encoding_multisystem (test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok
test_get_loners (test_System.SystemTest.test_get_loners) ... ok
test_get_multisystems (test_System.SystemTest.test_get_multisystems) ... ok
test_hits (test_System.SystemTest.test_hits) ... ok
test_init (test_System.SystemTest.test_init) ... ok
test_is_compatible (test_System.SystemTest.test_is_compatible) ... ok
test_loci_nb (test_System.SystemTest.test_loci_nb) ... ok
test_loci_num (test_System.SystemTest.test_loci_num) ... ok
test_multi_loci (test_System.SystemTest.test_multi_loci) ... ok
test_occurrence (test_System.SystemTest.test_occurrence) ... ok
test_position (test_System.SystemTest.test_position) ... ok
test_score (test_System.SystemTest.test_score) ... ok
test_wholeness (test_System.SystemTest.test_wholeness) ... ok
test_build_clusters (test_cluster.TestBuildCluster.test_build_clusters) ... ok
test_clusterize (test_cluster.TestBuildCluster.test_clusterize) ... ok
test_colocates (test_cluster.TestBuildCluster.test_colocates) ... ok
test_get_true_loners (test_cluster.TestBuildCluster.test_get_true_loners) ... ok
test_contains (test_cluster.TestCluster.test_contains) ... ok
test_fulfilled_function (test_cluster.TestCluster.test_fulfilled_function) ... ok
test_init (test_cluster.TestCluster.test_init) ... Cannot build a cluster from hits coming from different replicons
ok
test_len (test_cluster.TestCluster.test_len) ... ok
test_loner (test_cluster.TestCluster.test_loner) ... ok
test_merge (test_cluster.TestCluster.test_merge) ... ok
test_multi_system (test_cluster.TestCluster.test_multi_system) ... ok
test_replace (test_cluster.TestCluster.test_replace) ... ok
test_replicon_name (test_cluster.TestCluster.test_replicon_name) ... ok
test_score (test_cluster.TestCluster.test_score) ... ok
test_str (test_cluster.TestCluster.test_str) ... ok
test_2_systems_not_compatible (test_functional_test.Test.test_2_systems_not_compatible) ... ok
test_cfg_n_previous_run (test_functional_test.Test.test_cfg_n_previous_run) ... ok
test_degenerated_systems (test_functional_test.Test.test_degenerated_systems) ... ok
test_gembase (test_functional_test.Test.test_gembase) ... ok
test_index_dir (test_functional_test.Test.test_index_dir) ... ok
test_model_unknown (test_functional_test.Test.test_model_unknown) ... ok
test_no_db_type (test_functional_test.Test.test_no_db_type) ... ok
test_no_models (test_functional_test.Test.test_no_models) ... ok
test_no_seq_db (test_functional_test.Test.test_no_seq_db) ... ok
test_only_loners (test_functional_test.Test.test_only_loners) ... ok
test_ordered_1_cluster_3_loners (test_functional_test.Test.test_ordered_1_cluster_3_loners) ... ok
test_ordered_1_clusters_3_loners_w_exchangeable (test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) ... ok
test_ordered_1_loner_exch_in_clust (test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... ok
test_ordered_1_loner_in_clust (test_functional_test.Test.test_ordered_1_loner_in_clust) ... ok
test_ordered_2_clusters_1_loner (test_functional_test.Test.test_ordered_2_clusters_1_loner) ... ok
test_ordered_2_clusters_3_loners (test_functional_test.Test.test_ordered_2_clusters_3_loners) ... ok
test_ordered_circular (test_functional_test.Test.test_ordered_circular) ... ok
test_ordered_linear (test_functional_test.Test.test_ordered_linear) ... ok
test_ordered_multi_loci (test_functional_test.Test.test_ordered_multi_loci) ... ok
test_ordered_multi_model (test_functional_test.Test.test_ordered_multi_model) ... ok
test_ordered_multi_system (test_functional_test.Test.test_ordered_multi_system) ... ok
test_ordered_multi_system_out_system (test_functional_test.Test.test_ordered_multi_system_out_system) ... ok
test_ordered_only_one_multi_model (test_functional_test.Test.test_ordered_only_one_multi_model) ... ok
test_ordered_single_loci (test_functional_test.Test.test_ordered_single_loci) ... ok
test_uncomplete_degenerated_systems (test_functional_test.Test.test_uncomplete_degenerated_systems) ... ok
test_unordered (test_functional_test.Test.test_unordered) ... ok
test_unordered_no_hits (test_functional_test.Test.test_unordered_no_hits) ... ok
test_unordered_only_forbidden (test_functional_test.Test.test_unordered_only_forbidden) ... ok
test_working_dir_exists (test_functional_test.Test.test_working_dir_exists) ... ok
test_working_dir_exists_and_not_dir (test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok
test_core_gene (test_gene.TestCoreGene.test_core_gene) ... ok
test_str (test_gene.TestGeneStatus.test_str) ... ok
test_add_exchangeable (test_gene.TestModelGene.test_add_exchangeable) ... ok
test_alternate_of (test_gene.TestModelGene.test_alternate_of) ... ok
test_core_gene (test_gene.TestModelGene.test_core_gene)
test getter/setter for core_gene property ... ok
test_exhangeables (test_gene.TestModelGene.test_exhangeables) ... ok
test_hash (test_gene.TestModelGene.test_hash) ... ok
test_init (test_gene.TestModelGene.test_init) ... ok
test_inter_gene_max_space (test_gene.TestModelGene.test_inter_gene_max_space)
test getter for inter_gene_max_space property ... ok
test_is_Forbidden (test_gene.TestModelGene.test_is_Forbidden)
test if gene belong to model mandatory genes ... ok
test_is_accessory (test_gene.TestModelGene.test_is_accessory)
test if gene belong to model mandatory genes ... ok
test_is_exchangeable (test_gene.TestModelGene.test_is_exchangeable) ... ok
test_is_mandatory (test_gene.TestModelGene.test_is_mandatory)
test if gene belong to model mandatory genes ... ok
test_loner (test_gene.TestModelGene.test_loner)
test getter for loner property ... ok
test_model (test_gene.TestModelGene.test_model)
test getter/setter for model property ... ok
test_multi_model (test_gene.TestModelGene.test_multi_model)
test getter for multi_modelproperty ... ok
test_multi_system (test_gene.TestModelGene.test_multi_system)
test getter for multi_system property ... ok
test_str (test_gene.TestModelGene.test_str) ... ok
test_unknown_attribute (test_gene.TestModelGene.test_unknown_attribute) ... ok
test_cmp (test_hit.CoreHitTest.test_cmp) ... ok
test_eq (test_hit.CoreHitTest.test_eq) ... ok
test_get_position (test_hit.CoreHitTest.test_get_position) ... ok
test_hash (test_hit.CoreHitTest.test_hash) ... ok
test_str (test_hit.CoreHitTest.test_str) ... ok
test_compute_best_MSHit (test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok
test_get_best_hits (test_hit.GetBestHitTest.test_get_best_hits) ... ok
test_get_best_hits_4_func (test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok
test_sort_multisystem_hits (test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok
test_hit_weight_default (test_hit.HitWeightTest.test_hit_weight_default) ... ok
test_hit_weight_not_default (test_hit.HitWeightTest.test_hit_weight_not_default) ... ok
test_counterpart (test_hit.LonerMultiSystemTest.test_counterpart) ... Try to set counterpart for hit 'gspD' with non compatible hits: ['gspD', 'sctJ']
ok
test_init (test_hit.LonerMultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system
ok
test_loner (test_hit.LonerMultiSystemTest.test_loner) ... ok
test_multi_system (test_hit.LonerMultiSystemTest.test_multi_system) ... ok
test_str (test_hit.LonerMultiSystemTest.test_str) ... ok
test_counterpart (test_hit.LonerTest.test_counterpart) ... ok
test_init (test_hit.LonerTest.test_init) ... hit_2 cannot be a loner gene_ref 'sctJ' not tag as loner
ok
test_len (test_hit.LonerTest.test_len) ... ok
test_loner (test_hit.LonerTest.test_loner) ... ok
test_multi_system (test_hit.LonerTest.test_multi_system) ... ok
test_str (test_hit.LonerTest.test_str) ... ok
test_delegation (test_hit.ModelHitTest.test_delegation) ... ok
test_eq (test_hit.ModelHitTest.test_eq) ... ok
test_hash (test_hit.ModelHitTest.test_hash) ... ok
test_init (test_hit.ModelHitTest.test_init) ... ok
test_loner (test_hit.ModelHitTest.test_loner) ... ok
test_multi_model (test_hit.ModelHitTest.test_multi_model) ... ok
test_multi_system (test_hit.ModelHitTest.test_multi_system) ... ok
test_counterpart (test_hit.MultiSystemTest.test_counterpart) ... ok
test_init (test_hit.MultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system
ok
test_len (test_hit.MultiSystemTest.test_len) ... ok
test_loner (test_hit.MultiSystemTest.test_loner) ... ok
test_multi_system (test_hit.MultiSystemTest.test_multi_system) ... ok
test_str (test_hit.MultiSystemTest.test_str) ... ok
test_functional_split (test_macsy_gembase_split.TestSplit.test_functional_split) ... /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='UTF-8'>
  for h in logger.handlers[:]:
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp3lqbye8_/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='UTF-8'>
  self.tearDown()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_functional_split_out_error (test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... /tmp/tmp1fnjse06/macsyfinder_test_split/base is not a directory
ok
test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... /tmp/tmpyktr94up/macsyfinder_test_split/base is not writable
Cannot create /tmp/tmpyktr94up/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmpyktr94up/macsyfinder_test_split/base'
ok
test_functional_merge (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv'
Merging 'best_solution.tsv' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_best_solution.tsv'
Merging 'all_systems.tsv' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_all_systems.tsv'
Merging 'best_solution_multisystems.tsv' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv'
Merging 'best_solution_loners.tsv' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv'
Merging 'rejected_candidates.tsv' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv'
Merging 'all_systems.txt' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_all_systems.txt'
Merging 'rejected_candidates.txt' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt'
Merging 'best_solution_summary' in to '/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv'
/usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp6n9hh9eq/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'>
  self.tearDown()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_functional_merge_one_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpn4mhl_mw/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'>
  self.tearDown()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_functional_merge_out_error (test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... /tmp/tmpjmwr4gid/macsyfinder_test_merge/merged_results is not a directory
ok
test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... /tmp/tmp3_xcpopj/macsyfinder_test_merge/merged_results is not writable
Cannot create /tmp/tmp3_xcpopj/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmp3_xcpopj/macsyfinder_test_merge/merged_results'
ok
test_functional_merge_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpxh3idq71/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'>
  self.tearDown()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_merge_and_reindex_invalid_solid (test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... Cannot reindex int(GCF_000006845) + 1: invalid literal for int() with base 10: 'GCF_000006845'
ok
test_add_comment (test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok
test_write (test_macsyconfig.TestConfigParserWithComment.test_write) ... ok
test_ask (test_macsyconfig.TestMacsyconfig.test_ask) ... ok
test_ask_bad_value (test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok
test_ask_default_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok
test_ask_use_default (test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok
test_ask_value_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok
test_check_bool (test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok
test_check_choice (test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok
test_check_dir (test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok
test_check_exe (test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok
test_check_file (test_macsyconfig.TestMacsyconfig.test_check_file) ... ok
test_check_float (test_macsyconfig.TestMacsyconfig.test_check_float) ... ok
test_check_positive_int (test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok
test_check_str (test_macsyconfig.TestMacsyconfig.test_check_str) ... ok
test_functional_dark_theme (test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok
test_functional_file_already_exists (test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok
test_parse_args (test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok
test_set_base_options (test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok
test_set_general_options (test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok
test_set_hmmer_options (test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok
test_set_path_options (test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok
test_set_path_options_with_system_models_dir (test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok
test_set_score_options (test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok
test_set_section (test_macsyconfig.TestMacsyconfig.test_set_section) ... ok
test_set_section_use_defaults (test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok
test_available (test_macsydata.TestMacsydata.test_available) ... ok
test_build_argparser (test_macsydata.TestMacsydata.test_build_argparser) ... ok
test_check (test_macsydata.TestMacsydata.test_check) ... If everyone were like you, I'd be out of business
To push the models in organization:
	cd /tmp/tmpxan2notu/fake_1
Transform the models into a git repository
	git init .
	git add .
	git commit -m 'initial commit'
add a remote repository to host the models
for instance if you want to add the models to 'macsy-models'
	git remote add origin https://github.com/macsy-models/
	git tag 0.0b2
	git push origin 0.0b2
ok
test_check_with_errors (test_macsydata.TestMacsydata.test_check_with_errors) ... The package 'fake_1' have no 'definitions' directory.
The package 'fake_1' have no 'profiles' directory.
Please fix issues above, before publishing these models.
ok
test_check_with_warnings (test_macsydata.TestMacsydata.test_check_with_warnings) ... The package 'fake_1' have not any LICENSE file. May be you have not right to use it.
The package 'fake_1' have not any README file.

macsydata says: You're only giving me a partial QA payment?
I'll take it this time, but I'm not happy.
I'll be really happy, if you fix warnings above, before to publish these models.
ok
test_cite (test_macsydata.TestMacsydata.test_cite) ... Models 'nimportnaoik' not found locally.
ok
test_cmd_name (test_macsydata.TestMacsydata.test_cmd_name) ... ok
test_definition_all_def (test_macsydata.TestMacsydata.test_definition_all_def) ... /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp5218r4jc/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
/<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp5218r4jc/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'>
  return open(path, 'r').read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_definition_bad_def (test_macsydata.TestMacsydata.test_definition_bad_def) ... Model 'fake_1/niportnaoik' not found.
ok
test_definition_bad_pack (test_macsydata.TestMacsydata.test_definition_bad_pack) ... Package 'nimportnaoik' not found.
ok
test_definition_bad_subfamily (test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... 'niportnaoik' not found in package 'fake_1'.
ok
test_definition_models_dir (test_macsydata.TestMacsydata.test_definition_models_dir) ... /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp269wq68c/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
/<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp269wq68c/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'>
  return open(path, 'r').read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_definition_one_def (test_macsydata.TestMacsydata.test_definition_one_def) ... /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpxcc5t0nf/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
/<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpxcc5t0nf/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'>
  return open(path, 'r').read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_download (test_macsydata.TestMacsydata.test_download) ... Downloading fake_1 1.0
Successfully downloaded packaging fake_1 in /tmp/tmp92oqdkp5/fake_1-1.0.tar.gz
No version that satisfy requirements '>2.0' for 'fake_1'.
Available versions: 1.0
Downloading fake_1 1.0
github limit error
ok
test_freeze (test_macsydata.TestMacsydata.test_freeze) ... ok
test_help (test_macsydata.TestMacsydata.test_help) ... Models 'nimportnaoik' not found locally.
ok
test_info (test_macsydata.TestMacsydata.test_info) ... Models 'nimportnaoik' not found locally.
ok
test_install_bad_target (test_macsydata.TestMacsydata.test_install_bad_target) ... ok
test_install_installed_package_corrupted (test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmpznde2ail/models
Cleaning.
The models fake_pack (0.0b2) have been installed successfully.
fake_pack locally installed is corrupted.
You can fix it by removing '/tmp/tmpznde2ail/models/fake_pack'.
ok
test_install_local (test_macsydata.TestMacsydata.test_install_local) ... Extracting fake_pack (3.0).
Installing fake_pack (3.0) in /tmp/tmpwb5wpr2e/models
Cleaning.
The models fake_pack (3.0) have been installed successfully.
ok
test_install_local_already_installed (test_macsydata.TestMacsydata.test_install_local_already_installed) ... Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmpiq4av9bn/models
Cleaning.
The models fake_pack (0.0b2) have been installed successfully.
Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmpiq4av9bn/models/fake_pack.
To force installation use option -f --force-reinstall.
ok
test_install_local_already_installed_force (test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmphklpxv62/models
Cleaning.
The models fake_pack (0.0b2) have been installed successfully.
Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmphklpxv62/models
Cleaning.
The models fake_pack (0.0b2) have been installed successfully.
ok
test_install_remote (test_macsydata.TestMacsydata.test_install_remote) ... Downloading fake_pack (0.0b2).
Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmp4lzob1av/models
Cleaning.
The models fake_pack (0.0b2) have been installed successfully.
ok
test_install_remote_already_in_local (test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmpylwuuh14/models/fake_pack.
To force installation use option -f --force-reinstall.
ok
test_install_remote_already_in_local_force (test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... Downloading fake_pack (0.0b2).
Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmpf_xmarzt/models
Cleaning.
The models fake_pack (0.0b2) have been installed successfully.
ok
test_install_remote_lower_in_local (test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... fake_pack (0.0b2) is already installed but 1.0 version is available.
To install it please run 'macsydata install --upgrade fake_pack'
ok
test_install_remote_permision_error (test_macsydata.TestMacsydata.test_install_remote_permision_error) ... /tmp/tmp8l3vxqnb/models is not readable: [Errno 13] Permission denied: '/tmp/tmp8l3vxqnb/models' : skip it.
Downloading fake_pack (0.0b2).
Extracting fake_pack (0.0b2).
Installing fake_pack (0.0b2) in /tmp/tmp8l3vxqnb/models
/tmp/tmp8l3vxqnb/models is not writable: [Errno 13] Permission denied: '/tmp/tmp8l3vxqnb/models/fake_pack'
Maybe you can use --user option to install in your HOME.
ok
test_install_remote_spec_not_found (test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... Could not find version that satisfied 'fake_pack>0.0b2'
ok
test_install_remote_upper_in_local (test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... fake_pack (0.0b2) is already installed.
To downgrade to 0.0b1 use option -f --force-reinstall.
ok
test_install_target (test_macsydata.TestMacsydata.test_install_target) ... Extracting fake_pack (3.0).
Installing fake_pack (3.0) in /tmp/tmp1fqm3mt5/target
Cleaning.
The models fake_pack (3.0) have been installed successfully.
ok
test_list (test_macsydata.TestMacsydata.test_list) ... ok
test_list_outdated (test_macsydata.TestMacsydata.test_list_outdated) ... ok
test_list_uptodate (test_macsydata.TestMacsydata.test_list_uptodate) ... ok
test_list_verbose (test_macsydata.TestMacsydata.test_list_verbose) ... [Errno 2] No such file or directory: '/tmp/tmpxy4te3_t/models/fake_1/metadata.yml'
ok
test_no_subcommand (test_macsydata.TestMacsydata.test_no_subcommand) ... ok
test_search_in_pack_desc (test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok
test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok
test_search_in_pack_name (test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok
test_search_in_pack_name_match_case (test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok
test_search_reach_limit (test_macsydata.TestMacsydata.test_search_reach_limit) ... bla
ok
test_uninstall (test_macsydata.TestMacsydata.test_uninstall) ... models 'fake_1' in /tmp/tmpx0pomhjf/models/fake_1 uninstalled.
Models 'foo' not found locally.
ok
test_verbosity_to_log_level (test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok
test_db_type_set_to_gembase (test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... GA bit thresholds unavailable on profile T2SS_gspO. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilB. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilQ. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilD. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilX. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilC. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile MSH_mshM. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilA. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_fimT. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilT. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilO. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilP. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilW. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilM. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilU. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilE. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilN. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilY. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile T4P_pilV. Switch to e-value threshold (-E 0.100000)
GA bit thresholds unavailable on profile ComM_comC. Switch to e-value threshold (-E 0.100000)
Most of replicons contains only ONE sequence are you sure that '/<<PKGBUILDDIR>>/tests/data/base/ordered_replicon_base.fasta' is a 'gembase'.
ok
test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok
test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok
test_list_models (test_macsyfinder.TestMacsyfinder.test_list_models) ... ok
test_loners_to_tsv (test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok
test_multisystem_to_tsv (test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok
test_parse_args (test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok
test_rejected_candidates_to_tsv (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok
test_rejected_candidates_to_txt (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok
test_search_systems (test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok
test_search_systems_unordered (test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok
test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok
test_summary_best_solution (test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok
test_summary_best_solution_empty (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok
test_summary_best_solution_lack_models (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok
test_summary_best_solution_lack_models_replicons (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok
test_summary_best_solution_lack_replicon (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok
test_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok
test_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok
test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok
test_LightHit (test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok
test_build_my_db (test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok
test_fill_my_db (test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok
test_functional (test_macsyprofile.TestMacsyprofile.test_functional) ... ok
test_functional_best_score (test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok
test_functional_coverage (test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok
test_functional_evalue (test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok
test_functional_no_hits (test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok
test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... nimportnaoik: No such directory.
ok
test_functional_out_exists (test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... The file /tmp/tmp0w4cne6b already exists. Remove it or specify a new output name --out or use --force option
ok
test_functional_pattern (test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok
test_getProfile_len (test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok
test_get_gene_name (test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok
test_header (test_macsyprofile.TestMacsyprofile.test_header) ... ok
test_hit_start (test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok
test_parse (test_macsyprofile.TestMacsyprofile.test_parse) ... ok
test_parse_hmm_body (test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok
test_parse_hmm_header (test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok
test_pasre_args (test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok
test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok
test_init_logger_default (test_macsypy.Test.test_init_logger_default) ... ok
test_init_logger_logfile (test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpz7o6970n' mode='a' encoding='UTF-8'>
  self.tearDown()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
test_init_logger_no_out (test_macsypy.Test.test_init_logger_no_out) ... ok
test_logger_set_level_bad_level (test_macsypy.Test.test_logger_set_level_bad_level) ... ok
test_logger_set_level_default (test_macsypy.Test.test_logger_set_level_default) ... ok
test_logger_set_level_error (test_macsypy.Test.test_logger_set_level_error) ... ok
test_logger_set_level_handlers (test_macsypy.Test.test_logger_set_level_handlers) ... ok
test_parse (test_model_conf_parser.TestModelConfParser.test_parse) ... ok
test_parse_bad_file (test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... unable to parse model configuration '/<<PKGBUILDDIR>>/tests/data/conf_files/project.conf' : syntax error: line 2, column 0
ok
test_parse_filtering (test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... cannot parse 'cut_ga' element in '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' expect True, 1, False, 0 got : 'FOO'
ok
test_parse_w_bad_value (test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... The model configuration file '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO'
ok
test_parse_w_unkown_tag (test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... unknown element 'nimportnaoik' in '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' ignore it.
ok
test_parse_weights (test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok
test_parse_wo_filtering (test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok
test_parse_wo_weights (test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok
test_init (test_package.TestLocalModelIndex.test_init) ... ok
test_init (test_package.TestModelIndex.test_init) ... ok
test_check (test_package.TestPackage.test_check) ... ok
test_check_metadata (test_package.TestPackage.test_check_metadata) ... ok
test_check_model_conf (test_package.TestPackage.test_check_model_conf) ... ok
test_check_model_conf_bad_conf (test_package.TestPackage.test_check_model_conf_bad_conf) ... The model configuration file '/tmp/macsy_test_package/fake_model/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO'
ok
test_check_model_conf_no_conf (test_package.TestPackage.test_check_model_conf_no_conf) ... ok
test_check_model_consistency (test_package.TestPackage.test_check_model_consistency) ... ok
test_check_model_consistency_bad_definitions (test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok
test_check_model_consistency_extra_profile (test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok
test_check_model_consistency_lack_one_profile (test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok
test_check_no_readme_n_no_license (test_package.TestPackage.test_check_no_readme_n_no_license) ... ok
test_check_structure (test_package.TestPackage.test_check_structure) ... ok
test_check_structure_bad_path (test_package.TestPackage.test_check_structure_bad_path) ... ok
test_check_structure_no_def (test_package.TestPackage.test_check_structure_no_def) ... ok
test_check_structure_no_license (test_package.TestPackage.test_check_structure_no_license) ... ok
test_check_structure_no_metadata (test_package.TestPackage.test_check_structure_no_metadata) ... ok
test_check_structure_no_profiles (test_package.TestPackage.test_check_structure_no_profiles) ... ok
test_check_structure_no_readme (test_package.TestPackage.test_check_structure_no_readme) ... ok
test_find_readme (test_package.TestPackage.test_find_readme) ... ok
test_help (test_package.TestPackage.test_help) ... ok
test_info (test_package.TestPackage.test_info) ... ok
test_init (test_package.TestPackage.test_init) ... ok
test_metadata (test_package.TestPackage.test_metadata) ... ok
test_parse_arch_path (test_package.TestPackageFunc.test_parse_arch_path) ... ok
test_download (test_package.TestRemoteModelIndex.test_download) ... ok
test_get_metadata (test_package.TestRemoteModelIndex.test_get_metadata) ... ok
test_init (test_package.TestRemoteModelIndex.test_init) ... ok
test_list_package_vers (test_package.TestRemoteModelIndex.test_list_package_vers) ... ok
test_list_packages (test_package.TestRemoteModelIndex.test_list_packages) ... ok
test_remote_exists (test_package.TestRemoteModelIndex.test_remote_exists) ... ok
test_unarchive (test_package.TestRemoteModelIndex.test_unarchive) ... ok
test_url_json (test_package.TestRemoteModelIndex.test_url_json) ... ok
test_url_json_reach_limit (test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok
test_DefinitionLocationn (test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok
test_add_submodel (test_registries.DefinitionLocationTest.test_add_submodel) ... ok
test_all (test_registries.DefinitionLocationTest.test_all) ... ok
test_eq (test_registries.DefinitionLocationTest.test_eq) ... ok
test_family_name (test_registries.DefinitionLocationTest.test_family_name) ... ok
test_greater (test_registries.DefinitionLocationTest.test_greater) ... ok
test_hash (test_registries.DefinitionLocationTest.test_hash) ... ok
test_lesser (test_registries.DefinitionLocationTest.test_lesser) ... ok
test_root_name (test_registries.DefinitionLocationTest.test_root_name) ... ok
test_separator (test_registries.DefinitionLocationTest.test_separator) ... ok
test_split_fqn (test_registries.DefinitionLocationTest.test_split_fqn) ... ok
test_str (test_registries.DefinitionLocationTest.test_str) ... ok
test_ModelLocation (test_registries.ModelLocationTest.test_ModelLocation) ... ok
test_get_all_definitions (test_registries.ModelLocationTest.test_get_all_definitions) ... ok
test_get_definition (test_registries.ModelLocationTest.test_get_definition) ... ok
test_get_definitions (test_registries.ModelLocationTest.test_get_definitions) ... ok
test_get_profile (test_registries.ModelLocationTest.test_get_profile) ... ok
test_get_profiles_names (test_registries.ModelLocationTest.test_get_profiles_names) ... ok
test_str (test_registries.ModelLocationTest.test_str) ... ok
test_version (test_registries.ModelLocationTest.test_version) ... ok
test_version_no_metadata (test_registries.ModelLocationTest.test_version_no_metadata) ... The models package 'simple' is not versioned contact the package manager to fix it.
ok
test_add_get (test_registries.ModelRegistryTest.test_add_get) ... ok
test_models (test_registries.ModelRegistryTest.test_models) ... ok
test_scan_models_dir (test_registries.ModelRegistryTest.test_scan_models_dir) ... ok
test_str (test_registries.ModelRegistryTest.test_str) ... ok
test_join_def_path (test_registries.RegitriesUtilsTest.test_join_def_path) ... ok
test_split_def_name (test_registries.RegitriesUtilsTest.test_split_def_name) ... ok
test_search (test_search_genes.TestSearchGenes.test_search) ... ok
test_search_fail (test_search_genes.TestSearchGenes.test_search_fail) ... ok
test_search_recover (test_search_genes.TestSearchGenes.test_search_recover) ... ok
test_LikelySystemSerializer_txt (test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok
test_RejectedClusters_tsv (test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok
test_SolutionSerializer_tsv (test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok
test_SpecialHitSerializer_tsv (test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok
test_SystemSerializer_str (test_serialization.SerializationTest.test_SystemSerializer_str) ... ok
test_SystemSerializer_tsv (test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok
test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok
test_combine_clusters (test_solution.SolutionExplorerTest.test_combine_clusters) ... ok
test_combine_multisystems (test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok
test_find_best_solution (test_solution.SolutionExplorerTest.test_find_best_solution) ... ok
test_average_wholeness (test_solution.SolutionTest.test_average_wholeness) ... ok
test_gt (test_solution.SolutionTest.test_gt) ... ok
test_hits_number (test_solution.SolutionTest.test_hits_number) ... ok
test_hits_positions (test_solution.SolutionTest.test_hits_positions) ... ok
test_iteration (test_solution.SolutionTest.test_iteration) ... ok
test_lt (test_solution.SolutionTest.test_lt) ... ok
test_score (test_solution.SolutionTest.test_score) ... ok
test_sorting (test_solution.SolutionTest.test_sorting) ... ok
test_systems (test_solution.SolutionTest.test_systems) ... ok
test_get_def_to_detect (test_utils.TestUtils.test_get_def_to_detect) ... ok
test_get_replicon_names (test_utils.TestUtils.test_get_replicon_names) ... ok
test_threads_available (test_utils.TestUtils.test_threads_available) ... ok

----------------------------------------------------------------------
Ran 486 tests in 8.850s

OK (skipped=2)
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   dh_auto_install --destdir=debian/macsyfinder/ -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/macsyfinder 
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running build
running build_py
running install_lib
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/__init__.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/macsy_gembase_split.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/macsy_merge_results.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/macsyconfig.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/macsydata.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/macsyfinder.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts/macsyprofile.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/__init__.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/cluster.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/config.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/database.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/definition_parser.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/error.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/gene.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/hit.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/model.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/model_conf_parser.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/package.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/profile.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/registries.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/report.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/search_genes.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/serialization.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/solution.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/system.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/utils.py -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsy_gembase_split.py to macsy_gembase_split.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsy_merge_results.py to macsy_merge_results.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsyconfig.py to macsyconfig.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsydata.py to macsydata.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsyfinder.py to macsyfinder.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/scripts/macsyprofile.py to macsyprofile.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/cluster.py to cluster.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/config.py to config.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/database.py to database.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/definition_parser.py to definition_parser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/error.py to error.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/gene.py to gene.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/hit.py to hit.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/model.py to model.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/model_conf_parser.py to model_conf_parser.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/package.py to package.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/profile.py to profile.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/registries.py to registries.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/report.py to report.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/search_genes.py to search_genes.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/serialization.py to serialization.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/solution.py to solution.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/system.py to system.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/macsypy/utils.py to utils.cpython-311.pyc
running install_data
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/share
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/share/macsyfinder
creating /<<PKGBUILDDIR>>/debian/macsyfinder/usr/share/macsyfinder/models
copying data/models/README -> /<<PKGBUILDDIR>>/debian/macsyfinder/usr/share/macsyfinder/models
running install_egg_info
running egg_info
writing MacSyFinder.egg-info/PKG-INFO
writing dependency_links to MacSyFinder.egg-info/dependency_links.txt
writing entry points to MacSyFinder.egg-info/entry_points.txt
writing requirements to MacSyFinder.egg-info/requires.txt
writing top-level names to MacSyFinder.egg-info/top_level.txt
reading manifest file 'MacSyFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*' under directory 'doc/build/html'
warning: no files found matching 'doc/build/latex/macsyfinder.pdf'
warning: no files found matching 'etc/macsyfinder.conf'
warning: no previously-included files found matching 'tests/__init__.pyc'
warning: no previously-included files found matching '.coverage'
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warning: no files found matching 'CONTRIBUTORS'
warning: no files found matching 'NEWS'
adding license file 'COPYING'
writing manifest file 'MacSyFinder.egg-info/SOURCES.txt'
Copying MacSyFinder.egg-info to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/lib/python3.11/dist-packages/MacSyFinder-2.0.egg-info
Skipping SOURCES.txt
running install_scripts
Installing macsyconfig script to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/bin
Installing macsydata script to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/bin
Installing macsyfinder script to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/bin
Installing macsymerge script to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/bin
Installing macsyprofile script to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/bin
Installing macsysplit script to /<<PKGBUILDDIR>>/debian/macsyfinder/usr/bin
I: pybuild pybuild:333: cp -a /<<PKGBUILDDIR>>/debian/etc /<<PKGBUILDDIR>>/debian/macsyfinder/etc && cd /<<PKGBUILDDIR>>/doc && make html latexpdf
make[1]: Entering directory '/<<PKGBUILDDIR>>/doc'
Running Sphinx v5.3.0
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 42 source files that are out of date
updating environment: [new config] 42 added, 0 changed, 0 removed
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reading sources... [100%] user_guide/quickstart

/<<PKGBUILDDIR>>/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: ERROR: Unexpected indentation.
/<<PKGBUILDDIR>>/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer:1: WARNING: Block quote ends without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/macsypy/serialization.py:docstring of macsypy.serialization.TsvLikelySystemSerializer:1: WARNING: Definition list ends without a blank line; unexpected unindent.
/<<PKGBUILDDIR>>/macsypy/serialization.py:docstring of macsypy.serialization.TxtLikelySystemSerializer:1: WARNING: Definition list ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
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writing output... [100%] user_guide/quickstart

/<<PKGBUILDDIR>>/doc/source/user_guide/functioning.rst:109: WARNING: undefined label: 'rejected_candidates_file'
generating indices... genindex py-modindex done
highlighting module code... [  4%] macsypy.cluster
highlighting module code... [  9%] macsypy.config
highlighting module code... [ 13%] macsypy.database
highlighting module code... [ 18%] macsypy.definition_parser
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highlighting module code... [ 45%] macsypy.package
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highlighting module code... [ 54%] macsypy.registries
highlighting module code... [ 59%] macsypy.report
highlighting module code... [ 63%] macsypy.scripts.macsyconfig
highlighting module code... [ 68%] macsypy.scripts.macsydata
highlighting module code... [ 72%] macsypy.scripts.macsyfinder
highlighting module code... [ 77%] macsypy.scripts.macsyprofile
highlighting module code... [ 81%] macsypy.search_genes
highlighting module code... [ 86%] macsypy.serialization
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writing additional pages... search done
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copying images... [ 18%] _static/logo_macsyfinder.png
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copying downloadable files... [ 50%] _static/code/pre-push
copying downloadable files... [100%] _static/msf_summary.py

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 5 warnings.

The HTML pages are in build/html.
Running Sphinx v5.3.0
making output directory... done
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing macsyfinder.tex... index user_guide/index user_guide/new_v2 user_guide/installation user_guide/quickstart user_guide/input user_guide/gembase_convention user_guide/outputs user_guide/big_data user_guide/model_definition user_guide/functioning user_guide/FAQ modeler_guide/index modeler_guide/package modeler_guide/modeling modeler_guide/helper_tools modeler_guide/publish_package modeler_guide/gallery modeler_guide/models_V1ToV2 modeler_guide/FAQ_modeler developer_guide/index developer_guide/overview developer_guide/api/index developer_guide/api/config developer_guide/api/model_conf_parser developer_guide/api/registries developer_guide/api/definition_parser developer_guide/api/model developer_guide/api/gene developer_guide/api/profile developer_guide/api/hit developer_guide/api/cluster developer_guide/api/system developer_guide/api/report developer_guide/api/search_genes developer_guide/api/solution developer_guide/api/serialization developer_guide/api/database developer_guide/api/error developer_guide/api/utils developer_guide/api/package developer_guide/api/scripts 
resolving references...
/<<PKGBUILDDIR>>/doc/source/user_guide/functioning.rst:109: WARNING: undefined label: 'rejected_candidates_file'
done
writing... done
copying images... [  6%] _static/logo_macsyfinder.png
copying images... [ 12%] _static/figure_main-2.png
copying images... [ 18%] _static/msf_functionning_step1.pdf
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copying images... [100%] _static/gene_obj_interaction.pdf

copying TeX support files... copying TeX support files...
done
build succeeded, 1 warning.

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 '/<<PKGBUILDDIR>>/doc/build/latex'
latexmk -pdf -dvi- -ps-  'macsyfinder.tex'
Rc files read:
  /etc/LatexMk
  latexmkrc
Latexmk: This is Latexmk, John Collins, 7 Jan. 2023. Version 4.79.
No existing .aux file, so I'll make a simple one, and require run of *latex.
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex':  Reasons for rerun
Category 'other':
  Rerun of 'pdflatex' forced or previously required

------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex   -recorder  "macsyfinder.tex"'
------------
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./macsyfinder.tex
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