Artifact ariba_2.14.7+ds-2+bd1_arm64-2024-10-18T19:03:20Z

sbuild (Debian sbuild) 0.85.11~bpo12+1 (31 August 2024) on debusine-worker-arm64-demeter-01.freexian.com

+==============================================================================+
| ariba 2.14.7+ds-2+bd1 (arm64)                Fri, 18 Oct 2024 19:03:20 +0000 |
+==============================================================================+

Package: ariba
Version: 2.14.7+ds-2+bd1
Source Version: 2.14.7+ds-2
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any

I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
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| Update chroot                                                                |
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Get:1 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ InRelease
Ign:1 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ InRelease
Get:2 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ Release [609 B]
Get:2 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ Release [609 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:4 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ Release.gpg
Ign:4 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ Release.gpg
Get:5 file:/build/ariba-mdYbfn/resolver-MbtZTV/apt_archive ./ Packages [30.4 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9921 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4904 kB]
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
  libperl5.38t64 perl-modules-5.38
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  libperl5.40 perl-modules-5.40
The following packages will be upgraded:
  apt libapt-pkg-perl libapt-pkg6.0t64 libb-hooks-op-check-perl
  libberkeleydb-perl libclass-xsaccessor-perl libclone-perl
  libcpanel-json-xs-perl libdata-messagepack-perl libdb5.3t64
  libdevel-callchecker-perl libdevel-size-perl libemail-address-xs-perl
  libhtml-parser-perl libldap-2.5-0 libmouse-perl libnet-ssleay-perl
  libnetaddr-ip-perl libparams-classify-perl libparams-util-perl
  libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl
  libsereal-decoder-perl libsereal-encoder-perl libsub-identify-perl
  libsub-name-perl libsyntax-keyword-try-perl libterm-readkey-perl
  libtext-levenshteinxs-perl libtext-markdown-discount-perl
  libtext-xslate-perl libtime-moment-perl libunicode-utf8-perl
  libvariable-magic-perl libxml-libxml-perl libxmlb2 libxs-parse-keyword-perl
  libyaml-libyaml-perl perl perl-base sysvinit-utils
42 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 14.4 MB of archives.
After this operation, 52.5 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.902.0+ds-2+b1 [33.9 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.46-1+b1 [63.6 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-5+b1 [300 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-2+b3 [20.1 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-2+b4 [72.0 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-2+b1 [172 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.16-1+b3 [13.1 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b4 [8772 B]
Get:10 http://deb.debian.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.30-1+b1 [27.1 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libsub-name-perl arm64 0.27-1+b3 [12.4 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b3 [96.7 kB]
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Get:17 http://deb.debian.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b3 [11.4 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.20-1+b4 [17.4 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b4 [97.7 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libnet-ssleay-perl arm64 1.94-1+b2 [323 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libmouse-perl arm64 2.5.11-1+b1 [141 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.05-1+b4 [28.2 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 libdevel-size-perl arm64 0.84-1+b1 [24.1 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.02-1+b4 [31.2 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.38-1+b1 [127 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 libberkeleydb-perl arm64 0.64-2+b4 [116 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40+b6 [63.8 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 perl-modules-5.40 all 5.40.0-6 [3022 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libperl5.40 arm64 5.40.0-6 [4149 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 perl arm64 5.40.0-6 [267 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 perl-base arm64 5.40.0-6 [1534 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-9 [629 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.9 [922 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.9 [1331 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 sysvinit-utils arm64 3.10-3 [32.9 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libxmlb2 arm64 0.3.21-1 [59.1 kB]
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| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

/tmp/debusine-fetch-exec-upload-rly_f7s8/ariba_2.14.7+ds-2.dsc exists in /tmp/debusine-fetch-exec-upload-rly_f7s8; copying to chroot
I: NOTICE: Log filtering will replace 'build/ariba-mdYbfn/ariba-2.14.7+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ariba-mdYbfn' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer, python3-pysam, python3-pytest, python3-bs4, python3-matplotlib, python3-tk, bowtie2, cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq, help2man, asciidoctor, build-essential, fakeroot, dumb-init
Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer, python3-pysam, python3-pytest, python3-bs4, python3-matplotlib, python3-tk, bowtie2, cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq, help2man, asciidoctor, build-essential, fakeroot, dumb-init
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
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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 packages were automatically installed and are no longer required:
  libperl5.38t64 perl-modules-5.38
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  asciidoctor autoconf automake autopoint autotools-dev blt bowtie2
  build-essential cd-hit cpp cpp-14 cpp-14-aarch64-linux-gnu
  cpp-aarch64-linux-gnu debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism dumb-init dwz fakeroot fastaq fontconfig-config
  fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14
  g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gawk gcc gcc-14
  gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu help2man libasan8 libblas3
  libc-dev-bin libc6-dev libcairo2 libcapnp-1.0.1 libcc1-0 libcrypt-dev
  libdebhelper-perl libdeflate0 libedit2 libelf1t64 libexpat1 libexpat1-dev
  libfakeroot libfile-stripnondeterminism-perl libfml-dev libfml0
  libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev
  libgfortran5 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64
  libhtscodecs2 libhwasan0 libimagequant0 libisl23 libitm1 libjbig0
  libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc
  libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4
  liblocale-gettext-perl liblsan0 libminimap-dev libminimap0 libmpc3 libmpfr6
  libmurmurhash2 libncurses6 libncursesw6 libnsl2 libopenjp2-7 libpixman-1-0
  libpng16-16t64 libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib
  libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal
  libpython3.13-stdlib libqhull-r8.0 libraqm0 libruby libruby3.1t64
  libsharpyuv0 libsigsegv2 libstdc++-14-dev libtcl8.6 libtiff6 libtirpc-common
  libtirpc3t64 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxft2 libxrender1 libxslt1.1 libxss1 linux-libc-dev m4
  mash media-types mummer po-debconf python-matplotlib-data python3
  python3-all python3-all-dev python3-appdirs python3-attr python3-autocommand
  python3-biopython python3-brotli python3-bs4 python3-cairo python3-chardet
  python3-contourpy python3-cycler python3-dateutil python3-decorator
  python3-dendropy python3-dev python3-fonttools python3-freetype python3-fs
  python3-inflect python3-iniconfig python3-jaraco.context
  python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4
  python3-matplotlib python3-minimal python3-more-itertools python3-mpmath
  python3-numpy python3-packaging python3-pil python3-pil.imagetk
  python3-pkg-resources python3-pluggy python3-pymummer python3-pyparsing
  python3-pysam python3-pytest python3-reportlab python3-rlpycairo
  python3-scipy python3-setuptools python3-six python3-soupsieve python3-sympy
  python3-tk python3-typeguard python3-typing-extensions python3-tz
  python3-ufolib2 python3-zipp python3.12 python3.12-dev python3.12-minimal
  python3.12-tk python3.13 python3.13-dev python3.13-minimal python3.13-tk
  rake rpcsvc-proto ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems
  ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools
  sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings
  xfonts-utils xml-core zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc blt-demo bowtie2-examples
  cpp-doc gcc-14-locales cpp-14-doc dh-make flit python3-build
  python3-installer python3-wheel fonts-freefont-otf | fonts-freefont-ttf
  fonts-texgyre gcc-14-doc gawk-doc gcc-multilib manpages-dev flex bison gdb
  gcc-doc gdb-aarch64-linux-gnu libc-devtools glibc-doc gsl-ref-psdoc
  | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libjs-jquery-ui-docs
  liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3-doc
  python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss
  fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb
  python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise
  python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
  fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
  python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo
  python3-gobject python3-pyqt5 python3-sip python3-tornado
  texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2
  gfortran python-numpy-doc python-pil-doc python-pyparsing-doc pdf-viewer
  python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm
  python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc
  tix python3-tk-dbg python3.12-venv python3.12-doc binfmt-support
  python3.13-venv python3.13-doc ri ruby-dev bundler cwltool sgml-base-doc
Recommended packages:
  manpages manpages-dev libarchive-cpio-perl javascript-common libgpm2
  libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+
  python3-cssselect python3-html5lib python3-olefile python3-pygments
  fonts-dejavu-extra isympy-common zip fonts-lato
The following NEW packages will be installed:
  asciidoctor autoconf automake autopoint autotools-dev blt bowtie2
  build-essential cd-hit cpp cpp-14 cpp-14-aarch64-linux-gnu
  cpp-aarch64-linux-gnu debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism dumb-init dwz fakeroot fastaq fontconfig-config
  fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14
  g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gawk gcc gcc-14
  gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu help2man libasan8 libblas3
  libc-dev-bin libc6-dev libcairo2 libcapnp-1.0.1 libcc1-0 libcrypt-dev
  libdebhelper-perl libdeflate0 libedit2 libelf1t64 libexpat1 libexpat1-dev
  libfakeroot libfile-stripnondeterminism-perl libfml-dev libfml0
  libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev
  libgfortran5 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64
  libhtscodecs2 libhwasan0 libimagequant0 libisl23 libitm1 libjbig0
  libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc
  libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4
  liblocale-gettext-perl liblsan0 libminimap-dev libminimap0 libmpc3 libmpfr6
  libmurmurhash2 libncurses6 libncursesw6 libnsl2 libopenjp2-7 libpixman-1-0
  libpng16-16t64 libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib
  libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal
  libpython3.13-stdlib libqhull-r8.0 libraqm0 libruby libruby3.1t64
  libsharpyuv0 libsigsegv2 libstdc++-14-dev libtcl8.6 libtiff6 libtirpc-common
  libtirpc3t64 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxft2 libxrender1 libxslt1.1 libxss1 linux-libc-dev m4
  mash media-types mummer po-debconf python-matplotlib-data python3
  python3-all python3-all-dev python3-appdirs python3-attr python3-autocommand
  python3-biopython python3-brotli python3-bs4 python3-cairo python3-chardet
  python3-contourpy python3-cycler python3-dateutil python3-decorator
  python3-dendropy python3-dev python3-fonttools python3-freetype python3-fs
  python3-inflect python3-iniconfig python3-jaraco.context
  python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4
  python3-matplotlib python3-minimal python3-more-itertools python3-mpmath
  python3-numpy python3-packaging python3-pil python3-pil.imagetk
  python3-pkg-resources python3-pluggy python3-pymummer python3-pyparsing
  python3-pysam python3-pytest python3-reportlab python3-rlpycairo
  python3-scipy python3-setuptools python3-six python3-soupsieve python3-sympy
  python3-tk python3-typeguard python3-typing-extensions python3-tz
  python3-ufolib2 python3-zipp python3.12 python3.12-dev python3.12-minimal
  python3.12-tk python3.13 python3.13-dev python3.13-minimal python3.13-tk
  rake rpcsvc-proto ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems
  ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools
  sbuild-build-depends-main-dummy sgml-base tk8.6-blt2.5 unicode-data
  w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev
0 upgraded, 225 newly installed, 0 to remove and 0 not upgraded.
Need to get 167 MB/181 MB of archives.
After this operation, 766 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1024 B]
Get:2 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
Get:6 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ libpython3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:7 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b1 [674 kB]
Get:8 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python-matplotlib-data 3.8.3-3+bootstrap1 [2731 kB]
Get:9 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:10 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:11 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:12 http://deb.debian.org/debian sid/main arm64 libsigsegv2 arm64 2.14-1+b1 [34.3 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 gawk arm64 1:5.2.1-2+b1 [642 kB]
Get:14 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-biopython 1.84+dfsg-3+bd1 [1643 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2 [124 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:22 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-matplotlib 3.8.3-3+bootstrap1 [5583 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0-1 [849 kB]
Get:28 file:/<<BUILDDIR>>/resolver-MbtZTV/apt_archive ./ python3-pysam 0.22.1+ds-2+debusine1 [3880 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 rubygems-integration all 1.18 [6704 B]
Get:32 http://deb.debian.org/debian sid/main arm64 rake all 13.2.1-1 [65.2 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 libncurses6 arm64 6.5-2 [95.7 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 libruby arm64 1:3.1+nmu1 [4664 B]
Get:42 http://deb.debian.org/debian sid/main arm64 ruby-rubygems all 3.4.20-1 [309 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 ruby arm64 1:3.1+nmu1 [5584 B]
Get:44 http://deb.debian.org/debian sid/main arm64 ruby-asciidoctor all 2.0.23-1 [214 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 asciidoctor all 2.0.23-1 [88.7 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:61 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2 [143 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.7-1 [328 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [533 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 blt arm64 2.5.3+dfsg-7 [6024 B]
Get:75 http://deb.debian.org/debian sid/main arm64 bowtie2 arm64 2.5.4-1 [1405 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.2-1 [2424 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1 [59.7 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b2 [50.2 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-6 [9165 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-6 [1280 B]
Get:85 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:86 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:87 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-6 [42.3 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-6 [24.1 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-6 [2578 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-6 [1162 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-6 [2386 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-6 [1039 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-6 [1442 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-6 [2364 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-6 [17.7 MB]
Get:96 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-6 [515 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:98 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:99 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-6 [2265 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-6 [10.1 MB]
Get:101 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-6 [19.9 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:103 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:104 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:105 http://deb.debian.org/debian sid/main arm64 cd-hit arm64 4.8.1-4 [506 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-7 [517 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:111 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.191-2 [188 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:121 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 74.1.2-2 [736 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20240824 [109 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 dumb-init arm64 1.2.5-3 [13.4 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 samtools arm64 1.20-3 [624 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 fastaq all 3.17.0-8 [47.7 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 help2man arm64 1.49.3 [198 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libcapnp-1.0.1 arm64 1.0.1-4 [1268 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b2 [65.9 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b2 [80.0 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-6 [361 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libgslcblas0 arm64 2.8+dfsg-3 [84.0 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 libgsl28 arm64 2.8+dfsg-3 [880 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libminimap0 arm64 0.2-8+b1 [20.8 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libminimap-dev arm64 0.2-8+b1 [32.3 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libmurmurhash2 arm64 1.6-1 [6232 B]
Get:166 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 libxslt1.1 arm64 1.1.35-1.1 [221 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 mash arm64 2.3+dfsg-6+b1 [169 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 mummer arm64 3.23+dfsg-8 [636 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 python3-attr all 24.2.0-1 [68.4 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB]
Get:188 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 python3.12-tk arm64 3.12.7-1 [110 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 python3.13-tk arm64 3.13.0-1 [101 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-tk arm64 3.12.6-1 [9428 B]
Get:192 http://deb.debian.org/debian sid/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB]
Get:193 http://deb.debian.org/debian sid/main arm64 python3-pil arm64 10.4.0-1 [480 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 python3-cairo arm64 1.26.1-2 [113 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 python3-freetype all 2.5.1-1 [89.3 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B]
Get:197 http://deb.debian.org/debian sid/main arm64 python3-reportlab all 4.2.5-1 [1117 kB]
Get:198 http://deb.debian.org/debian sid/main arm64 xml-core all 0.19 [20.1 kB]
Get:199 http://deb.debian.org/debian sid/main arm64 w3c-sgml-lib all 1.3-3 [273 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 python3-brotli arm64 1.1.0-2+b4 [301 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 python3-soupsieve all 2.6-1 [38.3 kB]
Get:202 http://deb.debian.org/debian sid/main arm64 python3-bs4 all 4.12.3-3 [133 kB]
Get:203 http://deb.debian.org/debian sid/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB]
Get:204 http://deb.debian.org/debian sid/main arm64 python3-cycler all 0.12.1-1 [9496 B]
Get:205 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:206 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:207 http://deb.debian.org/debian sid/main arm64 python3-dendropy all 4.6.1-1 [277 kB]
Get:208 http://deb.debian.org/debian sid/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB]
Get:209 http://deb.debian.org/debian sid/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:210 http://deb.debian.org/debian sid/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get:211 http://deb.debian.org/debian sid/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get:212 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.1-2 [30.9 kB]
Get:213 http://deb.debian.org/debian sid/main arm64 python3-six all 1.16.0-7 [16.4 kB]
Get:214 http://deb.debian.org/debian sid/main arm64 python3-fs all 2.4.16-4 [95.4 kB]
Get:215 http://deb.debian.org/debian sid/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB]
Get:216 http://deb.debian.org/debian sid/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b4 [25.1 kB]
Get:217 http://deb.debian.org/debian sid/main arm64 unicode-data all 15.1.0-1 [8547 kB]
Get:218 http://deb.debian.org/debian sid/main arm64 python3-fonttools arm64 4.51.0-1 [1342 kB]
Get:219 http://deb.debian.org/debian sid/main arm64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:220 http://deb.debian.org/debian sid/main arm64 python3-kiwisolver arm64 1.4.7-2 [56.7 kB]
Get:221 http://deb.debian.org/debian sid/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:222 http://deb.debian.org/debian sid/main arm64 python3-packaging all 24.1-1 [45.8 kB]
Get:223 http://deb.debian.org/debian sid/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:224 http://deb.debian.org/debian sid/main arm64 python3-pymummer all 0.11.0-4 [18.0 kB]
Get:225 http://deb.debian.org/debian sid/main arm64 python3-pytest all 8.3.3-1 [249 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 167 MB in 2s (89.8 MB/s)
Selecting previously unselected package libmpfr6:arm64.
(Reading database ... 19017 files and directories currently installed.)
Preparing to unpack .../libmpfr6_4.2.1-1+b1_arm64.deb ...
Unpacking libmpfr6:arm64 (4.2.1-1+b1) ...
Selecting previously unselected package libsigsegv2:arm64.
Preparing to unpack .../libsigsegv2_2.14-1+b1_arm64.deb ...
Unpacking libsigsegv2:arm64 (2.14-1+b1) ...
Setting up libmpfr6:arm64 (4.2.1-1+b1) ...
Setting up libsigsegv2:arm64 (2.14-1+b1) ...
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(Reading database ... 19039 files and directories currently installed.)
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Unpacking gawk (1:5.2.1-2+b1) ...
Selecting previously unselected package liblocale-gettext-perl.
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Unpacking liblocale-gettext-perl (1.07-7+b1) ...
Selecting previously unselected package libpython3.12-minimal:arm64.
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Unpacking libpython3.12-minimal:arm64 (3.12.7-1) ...
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Unpacking libexpat1:arm64 (2.6.3-1) ...
Selecting previously unselected package python3.12-minimal.
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Unpacking python3.12-minimal (3.12.7-1) ...
Setting up libpython3.12-minimal:arm64 (3.12.7-1) ...
Setting up libexpat1:arm64 (2.6.3-1) ...
Setting up python3.12-minimal (3.12.7-1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 19560 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.12.6-1+debusine1_arm64.deb ...
Unpacking python3-minimal (3.12.6-1+debusine1) ...
Selecting previously unselected package media-types.
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Unpacking media-types (10.1.0) ...
Selecting previously unselected package libncursesw6:arm64.
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Unpacking libncursesw6:arm64 (6.5-2) ...
Selecting previously unselected package libtirpc-common.
Preparing to unpack .../3-libtirpc-common_1.3.4+ds-1.3_all.deb ...
Unpacking libtirpc-common (1.3.4+ds-1.3) ...
Selecting previously unselected package libtirpc3t64:arm64.
Preparing to unpack .../4-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ...
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Setting up libtsan2:arm64 (14.2.0-6) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libisl23:arm64 (0.27-1) ...
Setting up libgsl28:arm64 (2.8+dfsg-3) ...
Setting up libc-dev-bin (2.40-3) ...
Setting up python-matplotlib-data (3.8.3-3+bootstrap1) ...
Setting up libwebpmux3:arm64 (1.4.0-0.1) ...
Setting up libpython3.13-stdlib:arm64 (3.13.0-1) ...
Setting up ruby-xmlrpc (0.3.3-2) ...
Setting up libcc1-0:arm64 (14.2.0-6) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
Setting up liblsan0:arm64 (14.2.0-6) ...
Setting up libitm1:arm64 (14.2.0-6) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up libpython3.13:arm64 (3.13.0-1) ...
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 liblapack3:arm64 (3.12.0-3) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ...
Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ...
Setting up python3.13 (3.13.0-1) ...
Setting up fontconfig-config (2.15.0-1.1) ...
Setting up libwebpdemux2:arm64 (1.4.0-0.1) ...
Setting up libxext6:arm64 (2:1.3.4-1+b2) ...
Setting up samtools (1.20-3) ...
Setting up help2man (1.49.3) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ...
Setting up mash (2.3+dfsg-6+b1) ...
Setting up libjs-sphinxdoc (7.4.7-3) ...
Setting up cpp-14-aarch64-linux-gnu (14.2.0-6) ...
Setting up xml-core (0.19) ...
Setting up libnsl2:arm64 (1.3.0-3+b2) ...
Setting up libc6-dev:arm64 (2.40-3) ...
Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
Setting up libxss1:arm64 (1:1.2.3-1+b1) ...
Setting up libfontconfig1:arm64 (2.15.0-1.1) ...
Setting up libgcc-14-dev:arm64 (14.2.0-6) ...
Setting up libstdc++-14-dev:arm64 (14.2.0-6) ...
Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ...
Setting up libxft2:arm64 (2.3.6-1+b1) ...
Setting up libpython3.12-stdlib:arm64 (3.12.7-1) ...
Setting up libtk8.6:arm64 (8.6.15-1) ...
Setting up python3.12 (3.12.7-1) ...
Setting up python3.12-tk (3.12.7-1) ...
Setting up xfonts-utils (1:7.7+7) ...
Setting up libcairo2:arm64 (1.18.2-2) ...
Setting up python3.13-tk (3.13.0-1) ...
Setting up libpython3.12t64:arm64 (3.12.7-1) ...
Setting up cpp-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up libexpat1-dev:arm64 (2.6.3-1) ...
Setting up libraqm0:arm64 (0.10.1-1+b1) ...
Setting up cpp-14 (14.2.0-6) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ...
Setting up cpp (4:14.2.0-1) ...
Setting up gcc-14-aarch64-linux-gnu (14.2.0-6) ...
Setting up libpython3-stdlib:arm64 (3.12.6-1+debusine1) ...
Setting up gcc-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ...
Setting up g++-14-aarch64-linux-gnu (14.2.0-6) ...
Setting up libfml-dev:arm64 (0.1+git20190320.b499514-1+b2) ...
Setting up blt (2.5.3+dfsg-7) ...
Setting up python3 (3.12.6-1+debusine1) ...
Setting up libpython3.12-dev:arm64 (3.12.7-1) ...
Setting up fonts-urw-base35 (20200910-8) ...
Setting up python3-zipp (3.20.2-1) ...
Setting up python3-freetype (2.5.1-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up python3-tz (2024.1-2) ...
Setting up gcc-14 (14.2.0-6) ...
Setting up bowtie2 (2.5.4-1) ...
Setting up python3-six (1.16.0-7) ...
Setting up python3-pil:arm64 (10.4.0-1) ...
Setting up python3-decorator (5.1.1-5) ...
Setting up python3-packaging (24.1-1) ...
Setting up python3-pyparsing (3.1.2-1) ...
Setting up python3-brotli (1.1.0-2+b4) ...
Setting up libpython3.13-dev:arm64 (3.13.0-1) ...
Setting up python3-cycler (0.12.1-1) ...
Setting up python3-kiwisolver (1.4.7-2) ...
Setting up python3.12-dev (3.12.7-1) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up libminimap-dev:arm64 (0.2-8+b1) ...
Setting up python3-pluggy (1.5.0-1) ...
Setting up python3-lxml:arm64 (5.3.0-1) ...
Setting up g++-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up g++-14 (14.2.0-6) ...
Setting up python3-mpmath (1.3.0-1) ...
Setting up python3-appdirs (1.4.4-4) ...
Setting up python3-soupsieve (2.6-1) ...
Setting up python3-more-itertools (10.5.0-1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.13.3-1) ...
Setting up python3-attr (24.2.0-1) ...
Setting up python3-pysam (0.22.1+ds-2+debusine1) ...
Setting up libpython3-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-cairo (1.26.1-2) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up libtool (2.4.7-7) ...
Setting up python3-lz4 (4.0.2+dfsg-1+b4) ...
Setting up python3.13-dev (3.13.0-1) ...
Setting up python3-pytest (8.3.3-1) ...
Setting up fastaq (3.17.0-8) ...
/usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
  phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
/usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
  gbk_regex = re.compile('^LOCUS\s+\S')
/usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
  phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
/usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
  gbk_regex = re.compile('^LOCUS\s+\S')
Setting up python3-typeguard (4.3.0-1) ...
Setting up python3-all (3.12.6-1+debusine1) ...
Setting up python3-tk:arm64 (3.12.6-1) ...
Setting up python3-bs4 (4.12.3-3) ...
Setting up gcc (4:14.2.0-1) ...
Setting up python3-pymummer (0.11.0-4) ...
Setting up dh-autoreconf (20) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pil.imagetk:arm64 (10.4.0-1) ...
Setting up python3-rlpycairo (0.3.0-3) ...
Setting up libpython3-all-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-dev (3.12.6-1+debusine1) ...
Setting up g++ (4:14.2.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.12) ...
Setting up python3-pkg-resources (74.1.2-2) ...
Setting up python3-all-dev (3.12.6-1+debusine1) ...
Setting up python3-setuptools (74.1.2-2) ...
Setting up debhelper (13.20) ...
Setting up python3-fs (2.4.16-4) ...
Setting up python3-chardet (5.2.0+dfsg-1) ...
Setting up python3-numpy (1:1.26.4+ds-11) ...
Setting up python3-reportlab (4.2.5-1) ...
Setting up python3-contourpy (1.3.0-2) ...
Setting up python3-dendropy (4.6.1-1) ...
Setting up dh-python (6.20240824) ...
Setting up python3-scipy (1.13.1-5) ...
Setting up python3-fonttools (4.51.0-1) ...
Setting up rake (13.2.1-1) ...
Setting up python3-ufolib2 (0.16.0+dfsg1-1) ...
Setting up ruby-sdbm:arm64 (1.0.0-5+b4) ...
Setting up python3-matplotlib (3.8.3-3+bootstrap1) ...
Setting up ruby-rubygems (3.4.20-1) ...
Setting up libruby3.1t64:arm64 (3.1.2-8.4) ...
Setting up ruby3.1 (3.1.2-8.4) ...
Setting up libruby:arm64 (1:3.1+nmu1) ...
Setting up ruby (1:3.1+nmu1) ...
Setting up ruby-asciidoctor (2.0.23-1) ...
Setting up asciidoctor (2.0.23-1) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up python3-biopython (1.84+dfsg-3+bd1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...

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

Arch check ok (arm64 included in any)

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

Kernel: Linux 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-6 gcc-14_14.2.0-6 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-6 libstdc++6_14.2.0-6 linux-libc-dev_6.11.2-1
Package versions: appstream_1.0.3-1 apt_2.9.9 asciidoctor_2.0.23-1 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 blt_2.5.3+dfsg-7 bowtie2_2.5.4-1 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 cd-hit_4.8.1-4 coreutils_9.4-3.1 cpp_4:14.2.0-1 cpp-14_14.2.0-6 cpp-14-aarch64-linux-gnu_14.2.0-6 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1 diffutils_1:3.10-1 dpkg_1.22.11 dpkg-dev_1.22.11 dumb-init_1.2.5-3 dwz_0.15-1+b1 e2fsprogs_1.47.1-1 fakeroot_1.36-1 fastaq_3.17.0-8 file_1:5.45-3 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lyx_2.4.2.1-1 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libc-dev-bin_2.40-3 libc6_2.40-3 libc6-dev_2.40-3 libcairo2_1.18.2-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcapnp-1.0.1_1.0.1-4 libcapture-tiny-perl_0.48-2 libcc1-0_14.2.0-6 libcgi-pm-perl_4.66-1 libclass-data-inheritable-perl_0.08-3 libclass-inspector-perl_1.36-3 libclass-method-modifiers-perl_2.15-1 libclass-xsaccessor-perl_1.19-4+b4 libclone-perl_0.47-1+b1 libcom-err2_1.47.1-1 libconfig-tiny-perl_2.30-1 libconst-fast-perl_0.014-2 libcpanel-json-xs-perl_4.38-1+b1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 libcurl3t64-gnutls_8.10.1-2 libdata-dpath-perl_0.60-1 libdata-messagepack-perl_1.02-1+b4 libdata-optlist-perl_0.114-1 libdata-validate-domain-perl_0.15-1 libdata-validate-ip-perl_0.31-1 libdata-validate-uri-perl_0.07-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdeflate0_1.22-1 libdevel-callchecker-perl_0.009-1+b1 libdevel-size-perl_0.84-1+b1 libdevel-stacktrace-perl_2.0500-1 libdpkg-perl_1.22.11 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libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 liblapack3_3.12.0-3 liblbfgsb0_3.0+dfsg.4-1+b1 liblcms2-2_2.16-2 libldap-2.5-0_2.5.18+dfsg-3+b1 liblerc4_4.0.0+ds-4+b1 liblist-compare-perl_0.55-2 liblist-someutils-perl_0.59-1 liblist-utilsby-perl_0.12-2 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-6 liblwp-mediatypes-perl_6.04-2 liblwp-protocol-https-perl_6.14-1 liblz1_1.15~pre1-1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 liblzo2-2_2.10-3 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmarkdown2_2.2.7-2+b1 libmd0_1.1.0-2 libminimap-dev_0.2-8+b1 libminimap0_0.2-8+b1 libmldbm-perl_2.05-4 libmodule-implementation-perl_0.09-2 libmodule-runtime-perl_0.016-2 libmoo-perl_2.005005-1 libmoox-aliases-perl_0.001006-2 libmount1_2.40.2-9 libmouse-perl_2.5.11-1+b1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libmurmurhash2_1.6-1 libnamespace-clean-perl_0.27-2 libncurses6_6.5-2 libncursesw6_6.5-2 libnet-domain-tld-perl_1.75-4 libnet-http-perl_6.23-1 libnet-ipv6addr-perl_1.02-1 libnet-netmask-perl_2.0002-2 libnet-ssleay-perl_1.94-1+b2 libnetaddr-ip-perl_4.079+dfsg-2+b4 libnettle8t64_3.10-1 libnghttp2-14_1.63.0-1 libnghttp3-9_1.4.0-1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libnsl2_1.3.0-3+b2 libnumber-compare-perl_0.03-3 libopenjp2-7_2.5.0-2+b3 libp11-kit0_0.25.5-2 libpackage-stash-perl_0.40-1 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libparams-classify-perl_0.015-2+b4 libparams-util-perl_1.102-3+b1 libpath-tiny-perl_0.146-1 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-6 libperlio-gzip-perl_0.20-1+b4 libperlio-utf8-strict-perl_0.010-1+b3 libpipeline1_1.5.8-1 libpixman-1-0_0.42.2-1+b1 libpng16-16t64_1.6.44-2 libproc-processtable-perl_0.636-1+b3 libpsl5t64_0.21.2-1.1 libpython3-all-dev_3.12.6-1+debusine1 libpython3-dev_3.12.6-1+debusine1 libpython3-stdlib_3.12.6-1+debusine1 libpython3.12-dev_3.12.7-1 libpython3.12-minimal_3.12.7-1 libpython3.12-stdlib_3.12.7-1 libpython3.12t64_3.12.7-1 libpython3.13_3.13.0-1 libpython3.13-dev_3.13.0-1 libpython3.13-minimal_3.13.0-1 libpython3.13-stdlib_3.13.0-1 libqhull-r8.0_2020.2-6+b1 libraqm0_0.10.1-1+b1 libreadline8t64_8.2-5 libregexp-wildcards-perl_1.05-3 librole-tiny-perl_2.002004-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libruby_1:3.1+nmu1 libruby3.1t64_3.1.2-8.4 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsereal-decoder-perl_5.004+ds-1+b3 libsereal-encoder-perl_5.004+ds-1+b3 libsframe1_2.43.1-5 libsharpyuv0_1.4.0-0.1 libsigsegv2_2.14-1+b1 libsmartcols1_2.40.2-9 libsort-versions-perl_1.62-3 libsqlite3-0_3.46.1-1 libss2_1.47.1-1 libssh2-1t64_1.11.0-7 libssl3t64_3.3.2-1 libstdc++-14-dev_14.2.0-6 libstdc++6_14.2.0-6 libstemmer0d_2.2.0-4+b1 libstrictures-perl_2.000006-1 libsub-exporter-perl_0.990-1 libsub-exporter-progressive-perl_0.001013-3 libsub-identify-perl_0.14-3+b3 libsub-install-perl_0.929-1 libsub-name-perl_0.27-1+b3 libsub-quote-perl_2.006008-1 libsyntax-keyword-try-perl_0.30-1+b1 libsystemd0_256.7-1 libtasn1-6_4.19.0-3+b2 libtcl8.6_8.6.15+dfsg-2 libterm-readkey-perl_2.38-2+b4 libtext-glob-perl_0.11-3 libtext-levenshteinxs-perl_0.03-5+b4 libtext-markdown-discount-perl_0.16-1+b3 libtext-xslate-perl_3.5.9-2+b1 libtiff6_4.5.1+git230720-5 libtime-duration-perl_1.21-2 libtime-moment-perl_0.44-2+b4 libtimedate-perl_2.3300-2 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtk8.6_8.6.15-1 libtool_2.4.7-7 libtry-tiny-perl_0.32-1 libtsan2_14.2.0-6 libubsan1_14.2.0-6 libuchardet0_0.0.8-1+b1 libudev1_256.7-1 libunicode-utf8-perl_0.62-2+b3 libunistring5_1.2-1 liburi-perl_5.30-1 libuuid1_2.40.2-9 libvariable-magic-perl_0.64-1+b1 libwebp7_1.4.0-0.1 libwebpdemux2_1.4.0-0.1 libwebpmux3_1.4.0-0.1 libwww-mechanize-perl_2.19-1 libwww-perl_6.77-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxcb-render0_1.17.0-2 libxcb-shm0_1.17.0-2 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxext6_2:1.3.4-1+b2 libxft2_2.3.6-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-5+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml2_2.12.7+dfsg+really2.9.14-0.1 libxmlb2_0.3.21-1 libxrender1_1:0.9.10-1.1+b1 libxs-parse-keyword-perl_0.46-1+b1 libxslt1.1_1.1.35-1.1 libxss1_1:1.2.3-1+b1 libxxhash0_0.8.2-2+b1 libyaml-0-2_0.2.5-1+b1 libyaml-libyaml-perl_0.902.0+ds-2+b1 libzstd1_1.5.6+dfsg-1 lintian_2.119.0 linux-libc-dev_6.11.2-1 login_1:4.16.0-2+really2.40.2-9 login.defs_1:4.16.0-4 logsave_1.47.1-1 lzop_1.04-2 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mash_2.3+dfsg-6+b1 mawk_1.3.4.20240905-1 media-types_10.1.0 mount_2.40.2-9 mummer_3.23+dfsg-8 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openssl_3.3.2-1 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 patchutils_0.4.2-1 perl_5.40.0-6 perl-base_5.40.0-6 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-6 perl-openssl-defaults_7+b2 plzip_1.11-2 po-debconf_1.0.21+nmu1 python-matplotlib-data_3.8.3-3+bootstrap1 python3_3.12.6-1+debusine1 python3-all_3.12.6-1+debusine1 python3-all-dev_3.12.6-1+debusine1 python3-appdirs_1.4.4-4 python3-attr_24.2.0-1 python3-autocommand_2.2.2-3 python3-biopython_1.84+dfsg-3+bd1 python3-brotli_1.1.0-2+b4 python3-bs4_4.12.3-3 python3-cairo_1.26.1-2 python3-chardet_5.2.0+dfsg-1 python3-contourpy_1.3.0-2 python3-cycler_0.12.1-1 python3-dateutil_2.9.0-3 python3-decorator_5.1.1-5 python3-dendropy_4.6.1-1 python3-dev_3.12.6-1+debusine1 python3-fonttools_4.51.0-1 python3-freetype_2.5.1-1 python3-fs_2.4.16-4 python3-inflect_7.3.1-2 python3-iniconfig_1.1.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-kiwisolver_1.4.7-2 python3-lxml_5.3.0-1 python3-lz4_4.0.2+dfsg-1+b4 python3-matplotlib_3.8.3-3+bootstrap1 python3-minimal_3.12.6-1+debusine1 python3-more-itertools_10.5.0-1 python3-mpmath_1.3.0-1 python3-numpy_1:1.26.4+ds-11 python3-packaging_24.1-1 python3-pil_10.4.0-1 python3-pil.imagetk_10.4.0-1 python3-pkg-resources_74.1.2-2 python3-pluggy_1.5.0-1 python3-pymummer_0.11.0-4 python3-pyparsing_3.1.2-1 python3-pysam_0.22.1+ds-2+debusine1 python3-pytest_8.3.3-1 python3-reportlab_4.2.5-1 python3-rlpycairo_0.3.0-3 python3-scipy_1.13.1-5 python3-setuptools_74.1.2-2 python3-six_1.16.0-7 python3-soupsieve_2.6-1 python3-sympy_1.13.3-1 python3-tk_3.12.6-1 python3-typeguard_4.3.0-1 python3-typing-extensions_4.12.2-2 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-zipp_3.20.2-1 python3.12_3.12.7-1 python3.12-dev_3.12.7-1 python3.12-minimal_3.12.7-1 python3.12-tk_3.12.7-1 python3.13_3.13.0-1 python3.13-dev_3.13.0-1 python3.13-minimal_3.13.0-1 python3.13-tk_3.13.0-1 rake_13.2.1-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 ruby_1:3.1+nmu1 ruby-asciidoctor_2.0.23-1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.4.20-1 ruby-sdbm_1.0.0-5+b4 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.3-2 ruby3.1_3.1.2-8.4 rubygems-integration_1.18 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 shared-mime-info_2.4-5+b1 sysvinit-utils_3.10-3 t1utils_1.41-4 tar_1.35+dfsg-3 tk8.6-blt2.5_2.5.3+dfsg-7 tzdata_2024b-3 ucf_3.0043+nmu1 unicode-data_15.1.0-1 unzip_6.0-28 util-linux_2.40.2-9 w3c-sgml-lib_1.3-3 x11-common_1:7.7+23.1 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+7 xml-core_0.19 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1

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


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

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

Format: 3.0 (quilt)
Source: ariba
Binary: ariba
Architecture: any
Version: 2.14.7+ds-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/sanger-pathogens/ariba
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ariba
Vcs-Git: https://salsa.debian.org/med-team/ariba.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer, python3-pysam, python3-pytest, python3-bs4, python3-matplotlib, python3-tk, bowtie2, cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq, help2man, asciidoctor, spades [amd64] <!nocheck>
Package-List:
 ariba deb science optional arch=any
Checksums-Sha1:
 9dbd8c5a23a1dc7349406f1b692b6f648f704674 1919824 ariba_2.14.7+ds.orig.tar.xz
 c758bdde968ae77d1027af334565af4b4361d842 10460 ariba_2.14.7+ds-2.debian.tar.xz
Checksums-Sha256:
 17cab969952233e110a58515cb9b2752d58c9a8edc9e930891d07a1a3c2f3fbb 1919824 ariba_2.14.7+ds.orig.tar.xz
 ad9c8fdb2efa678ba63f83a6e0866489126b98168dfed13d8ba81e66b2b150bd 10460 ariba_2.14.7+ds-2.debian.tar.xz
Files:
 36818f9fdc447f1c7064089115d41417 1919824 ariba_2.14.7+ds.orig.tar.xz
 3a92ec7a86f45564213687a01268b250 10460 ariba_2.14.7+ds-2.debian.tar.xz

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gpgv: Signature made Thu Feb  1 11:28:39 2024 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-2.dsc: no acceptable signature found
dpkg-source: info: extracting ariba in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ariba_2.14.7+ds.orig.tar.xz
dpkg-source: info: unpacking ariba_2.14.7+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch
dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch
dpkg-source: info: applying add-testdata.patch
dpkg-source: info: applying disable-tests-with-internet-access.patch
dpkg-source: info: applying support-pymummer-0.11.patch
dpkg-source: info: applying run-debian-spades-wrapper.patch
dpkg-source: info: applying python3.12.patch

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

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 2.14.7+ds-2+bd1

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

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=debusine-worker

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

Command: dpkg-buildpackage --sanitize-env -us -uc -mDebusine Rebuild <debusine@example.net> -B -rfakeroot
dpkg-buildpackage: info: source package ariba
dpkg-buildpackage: info: source version 2.14.7+ds-2+bd1
dpkg-buildpackage: info: source distribution sid
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf /<<PKGBUILDDIR>>/debian/man
dh_auto_clean --
I: pybuild base:311: python3.13 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
I: pybuild base:311: python3.12 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary-arch
dh binary-arch --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running config
I: pybuild base:311: python3.12 setup.py config 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.13 setup.py build 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/vfdb_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/assembly_compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/mlst_profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/summary_cluster_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/sequence_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/assembly.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/faidx.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/link.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/mlst_reporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/summary_cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/sequence_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/external_progs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/cdhit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/ref_seq_chooser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/scaffold_graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/samtools_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/aln_to_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/read_store.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
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copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
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copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
running build_ext
building 'minimap_ariba' extension
creating build
creating build/temp.linux-aarch64-cpython-313
creating build/temp.linux-aarch64-cpython-313/ariba
creating build/temp.linux-aarch64-cpython-313/ariba/ext
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.13 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-aarch64-cpython-313/ariba/ext/minimap_ariba.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/ariba/ext/minimap_ariba.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/minimap_ariba.cpython-313-aarch64-linux-gnu.so -lz -lminimap
building 'fermilite_ariba' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-aarch64-cpython-313/ariba/ext/fml-asm_ariba.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/ariba/ext/fml-asm_ariba.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/fermilite_ariba.cpython-313-aarch64-linux-gnu.so -lz -lfml
building 'vcfcall_ariba' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-aarch64-cpython-313/ariba/ext/vcfcall_ariba.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/ariba/ext/vcfcall_ariba.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/vcfcall_ariba.cpython-313-aarch64-linux-gnu.so
running build_scripts
creating build/scripts-3.13
copying and adjusting scripts/ariba -> build/scripts-3.13
changing mode of build/scripts-3.13/ariba from 644 to 755
I: pybuild base:311: /usr/bin/python3 setup.py build 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/vfdb_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/assembly_compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/mlst_profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary_cluster_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/sequence_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/assembly.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/faidx.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/link.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/mlst_reporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary_cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/sequence_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/external_progs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/cdhit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/ref_seq_chooser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/scaffold_graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/samtools_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/aln_to_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/read_store.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/pubmlst_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/read_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/ref_genes_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/megares_data_finder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/versions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/report_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/card_record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/bam_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/pubmlst_ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary_sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/report_flag_expander.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/clusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/megares_zip_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/mic_plotter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/mapping.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/histogram.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/assembly_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/reference_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/aln2meta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/pubmlstspecies.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/getref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/micplot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/prepareref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/reportfilter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/refquery.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/expandflag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/pubmlstget.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
copying ariba/tasks/prepareref_tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/megares_zip_parser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/histogram_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/versions_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/bam_parse_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/sequence_metadata_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/summary_sample_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/pubmlst_ref_preparer_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/mic_plotter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/samtools_variants_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/ref_genes_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/sequence_variant_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/mlst_reporter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/flag_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/mapping_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/read_store_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/summary_cluster_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/report_flag_expander_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/ref_seq_chooser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/common_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/clusters_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/cdhit_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/vfdb_parser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/assembly_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/aln_to_metadata_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/assembly_variants_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/tb_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/reference_data_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/faidx_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/link_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/ncbi_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/assembly_compare_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/summary_cluster_variant_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/report_filter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/read_filter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/scaffold_graph_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/card_record_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/summary_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/test_refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/pubmlst_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/ref_preparer_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/cluster_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/megares_data_finder_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/mlst_profile_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
copying ariba/tests/external_progs_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
copying ariba/test_run_data/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
copying ariba/test_run_data/ref_seqs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
copying ariba/test_run_data/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
copying ariba/test_run_data/metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20190102.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/NC_000962.3.fa.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/NC_000962.3.gb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181221.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20190102.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181221.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181115.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181115.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/reference_data_load_fasta_file.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
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copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
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copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
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copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
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copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
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copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
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copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
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copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
running build_ext
building 'minimap_ariba' extension
creating build/temp.linux-aarch64-cpython-312
creating build/temp.linux-aarch64-cpython-312/ariba
creating build/temp.linux-aarch64-cpython-312/ariba/ext
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.12 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-aarch64-cpython-312/ariba/ext/minimap_ariba.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/ariba/ext/minimap_ariba.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/minimap_ariba.cpython-312-aarch64-linux-gnu.so -lz -lminimap
building 'fermilite_ariba' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-aarch64-cpython-312/ariba/ext/fml-asm_ariba.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/ariba/ext/fml-asm_ariba.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/fermilite_ariba.cpython-312-aarch64-linux-gnu.so -lz -lfml
building 'vcfcall_ariba' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-aarch64-cpython-312/ariba/ext/vcfcall_ariba.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/ariba/ext/vcfcall_ariba.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/vcfcall_ariba.cpython-312-aarch64-linux-gnu.so
running build_scripts
creating build/scripts-3.12
copying and adjusting scripts/ariba -> build/scripts-3.12
changing mode of build/scripts-3.12/ariba from 644 to 755
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build; python3.13 -m pytest 
============================= test session starts ==============================
platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: typeguard-4.3.0
collected 0 items / 44 errors

==================================== ERRORS ====================================
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/aln_to_metadata_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/aln_to_metadata_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_compare_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_compare_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_variants_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_variants_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/bam_parse_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/bam_parse_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/card_record_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/card_record_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/cdhit_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/cdhit_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/cluster_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/cluster_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/clusters_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/clusters_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/common_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/common_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/external_progs_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/external_progs_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/faidx_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/faidx_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/flag_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/flag_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/histogram_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/histogram_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/link_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/link_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/mapping_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mapping_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_data_finder_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_data_finder_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_zip_parser_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_zip_parser_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_profile_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_profile_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_reporter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_reporter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/ncbi_getter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ncbi_getter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_getter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_getter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/read_filter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/read_filter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/read_store_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/read_store_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_genes_getter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_genes_getter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_preparer_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_preparer_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_seq_chooser_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_seq_chooser_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/reference_data_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/reference_data_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/report_filter_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/report_filter_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/report_flag_expander_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/report_flag_expander_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/samtools_variants_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/samtools_variants_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/scaffold_graph_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/scaffold_graph_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_metadata_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_metadata_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_variant_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_variant_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_variant_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_variant_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_sample_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_sample_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
__ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/tb_test.py __
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/tb_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/test_refdata_query.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/test_refdata_query.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/versions_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/versions_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
_ ERROR collecting .pybuild/cpython3_3.13_ariba/build/ariba/tests/vfdb_parser_test.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/vfdb_parser_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ariba/__init__.py:57: in <module>
    from ariba import *
ariba/clusters.py:13: in <module>
    from ariba import cluster, common, histogram, mlst_reporter, read_store, report, report_filter, reference_data, tb
ariba/tb.py:8: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in <module>
    from Bio.SeqIO import TwoBitIO
/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in <module>
    raise MissingPythonDependencyError(
E   Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/
=============================== warnings summary ===============================
ariba/__init__.py:1
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import get_distribution

../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
    __version__ = Distribution().from_name('pyfastaq').version

ariba/external_progs.py:34
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.'
    'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')),

ariba/external_progs.py:35
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.'
    'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')),

ariba/external_progs.py:36
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.'
    'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)'))

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR ariba/tests/aln_to_metadata_test.py
ERROR ariba/tests/assembly_compare_test.py
ERROR ariba/tests/assembly_test.py
ERROR ariba/tests/assembly_variants_test.py
ERROR ariba/tests/bam_parse_test.py
ERROR ariba/tests/card_record_test.py
ERROR ariba/tests/cdhit_test.py
ERROR ariba/tests/cluster_test.py
ERROR ariba/tests/clusters_test.py
ERROR ariba/tests/common_test.py
ERROR ariba/tests/external_progs_test.py
ERROR ariba/tests/faidx_test.py
ERROR ariba/tests/flag_test.py
ERROR ariba/tests/histogram_test.py
ERROR ariba/tests/link_test.py
ERROR ariba/tests/mapping_test.py
ERROR ariba/tests/megares_data_finder_test.py
ERROR ariba/tests/megares_zip_parser_test.py
ERROR ariba/tests/mic_plotter_test.py
ERROR ariba/tests/mlst_profile_test.py
ERROR ariba/tests/mlst_reporter_test.py
ERROR ariba/tests/ncbi_getter_test.py
ERROR ariba/tests/pubmlst_getter_test.py
ERROR ariba/tests/pubmlst_ref_preparer_test.py
ERROR ariba/tests/read_filter_test.py
ERROR ariba/tests/read_store_test.py
ERROR ariba/tests/ref_genes_getter_test.py
ERROR ariba/tests/ref_preparer_test.py
ERROR ariba/tests/ref_seq_chooser_test.py
ERROR ariba/tests/reference_data_test.py
ERROR ariba/tests/report_filter_test.py
ERROR ariba/tests/report_flag_expander_test.py
ERROR ariba/tests/samtools_variants_test.py
ERROR ariba/tests/scaffold_graph_test.py
ERROR ariba/tests/sequence_metadata_test.py
ERROR ariba/tests/sequence_variant_test.py
ERROR ariba/tests/summary_cluster_test.py
ERROR ariba/tests/summary_cluster_variant_test.py
ERROR ariba/tests/summary_sample_test.py
ERROR ariba/tests/summary_test.py
ERROR ariba/tests/tb_test.py
ERROR ariba/tests/test_refdata_query.py
ERROR ariba/tests/versions_test.py
ERROR ariba/tests/vfdb_parser_test.py
!!!!!!!!!!!!!!!!!!! Interrupted: 44 errors during collection !!!!!!!!!!!!!!!!!!!
======================== 5 warnings, 44 errors in 1.97s ========================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build; python3.13 -m pytest 
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build; python3.12 -m pytest 
============================= test session starts ==============================
platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: typeguard-4.3.0
collected 356 items

ariba/tests/aln_to_metadata_test.py ....................                 [  5%]
ariba/tests/assembly_compare_test.py ................                    [ 10%]
ariba/tests/assembly_test.py ..ss.....                                   [ 12%]
ariba/tests/assembly_variants_test.py ...........                        [ 15%]
ariba/tests/bam_parse_test.py ......                                     [ 17%]
ariba/tests/card_record_test.py ........                                 [ 19%]
ariba/tests/cdhit_test.py ................                               [ 24%]
ariba/tests/cluster_test.py .............................                [ 32%]
ariba/tests/clusters_test.py ................                            [ 36%]
ariba/tests/common_test.py ..                                            [ 37%]
ariba/tests/external_progs_test.py .                                     [ 37%]
ariba/tests/faidx_test.py .                                              [ 37%]
ariba/tests/flag_test.py .......                                         [ 39%]
ariba/tests/histogram_test.py ....                                       [ 41%]
ariba/tests/link_test.py .........                                       [ 43%]
ariba/tests/mapping_test.py .......                                      [ 45%]
ariba/tests/megares_data_finder_test.py ..                               [ 46%]
ariba/tests/megares_zip_parser_test.py .....                             [ 47%]
ariba/tests/mic_plotter_test.py .............                            [ 51%]
ariba/tests/mlst_profile_test.py ....                                    [ 52%]
ariba/tests/mlst_reporter_test.py .....                                  [ 53%]
ariba/tests/pubmlst_getter_test.py ...                                   [ 54%]
ariba/tests/pubmlst_ref_preparer_test.py ..                              [ 55%]
ariba/tests/read_filter_test.py .                                        [ 55%]
ariba/tests/read_store_test.py .......                                   [ 57%]
ariba/tests/ref_genes_getter_test.py .                                   [ 57%]
ariba/tests/ref_preparer_test.py .....                                   [ 58%]
ariba/tests/ref_seq_chooser_test.py .......                              [ 60%]
ariba/tests/reference_data_test.py ..............................        [ 69%]
ariba/tests/report_filter_test.py .................                      [ 74%]
ariba/tests/report_flag_expander_test.py .                               [ 74%]
ariba/tests/samtools_variants_test.py .......                            [ 76%]
ariba/tests/scaffold_graph_test.py .....                                 [ 77%]
ariba/tests/sequence_metadata_test.py .....                              [ 79%]
ariba/tests/sequence_variant_test.py .......                             [ 81%]
ariba/tests/summary_cluster_test.py .......................              [ 87%]
ariba/tests/summary_cluster_variant_test.py ....                         [ 88%]
ariba/tests/summary_sample_test.py ....                                  [ 89%]
ariba/tests/summary_test.py ....................                         [ 95%]
ariba/tests/tb_test.py .......                                           [ 97%]
ariba/tests/test_refdata_query.py .....                                  [ 98%]
ariba/tests/versions_test.py .                                           [ 99%]
ariba/tests/vfdb_parser_test.py ...                                      [100%]

=============================== warnings summary ===============================
ariba/__init__.py:1
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import get_distribution

../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
    __version__ = Distribution().from_name('pyfastaq').version

ariba/external_progs.py:34
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.'
    'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')),

ariba/external_progs.py:35
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.'
    'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')),

ariba/external_progs.py:36
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.'
    'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)'))

.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/mic_plotter.py:222: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.
    cmap = cmx.get_cmap(colormap)

.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/mic_plotter.py:206: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.
    cmap = cmx.get_cmap(colormap)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============ 354 passed, 2 skipped, 9 warnings in 83.06s (0:01:23) =============
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13
make: *** [debian/rules:10: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-10-18T19:08:27Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Type: any
Build-Space: 78312
Build-Time: 104
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 157
Job: /tmp/debusine-fetch-exec-upload-rly_f7s8/ariba_2.14.7+ds-2.dsc
Machine Architecture: arm64
Package: ariba
Package-Time: 307
Source-Version: 2.14.7+ds-2
Space: 78312
Status: attempted
Version: 2.14.7+ds-2+bd1
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Finished at 2024-10-18T19:08:27Z
Build needed 00:05:07, 78312k disk space