sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-09.freexian.com
+==============================================================================+
| ariba 2.14.7+ds-3+bd1 (arm64) Mon, 04 Nov 2024 14:48:53 +0000 |
+==============================================================================+
Package: ariba
Version: 2.14.7+ds-3+bd1
Source Version: 2.14.7+ds-3
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any
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Get:5 http://deb.debian.org/debian sid InRelease [202 kB]
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The following packages will be upgraded:
bsdextrautils bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 login
mount util-linux
9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
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Get:9 http://deb.debian.org/debian sid/main arm64 login arm64 1:4.16.0-2+really2.40.2-10 [79.8 kB]
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Local sources
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| Install package build dependencies |
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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
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
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
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Install main build dependencies (apt-based resolver)
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Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
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 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-jaraco.text 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 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-jaraco.text 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 163 MB/182 MB of archives.
After this operation, 776 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1016 B]
Get:2 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
Get:6 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ libpython3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:7 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python-matplotlib-data 3.8.3-3+bootstrap1 [2731 kB]
Get:8 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:9 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:10 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:11 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b2 [680 kB]
Get:12 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-numpy 1:1.26.4+ds-11+bd1 [3816 kB]
Get:13 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-pil.imagetk 10.4.0-1+debusine1 [79.9 kB]
Get:14 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-pil 10.4.0-1+debusine1 [498 kB]
Get:15 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-biopython 1.84+dfsg-4+bd1 [1644 kB]
Get:16 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-kiwisolver 1.4.7-2+bd1 [71.6 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB]
Get:19 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-matplotlib 3.8.3-3+bootstrap1 [5583 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-2 [90.1 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2+b1 [125 kB]
Get:26 file:/<<BUILDDIR>>/resolver-g7IUbP/apt_archive ./ python3-pysam 0.22.1+ds-2+debusine1 [3880 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0-1 [849 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 rubygems-integration all 1.18 [6704 B]
Get:36 http://deb.debian.org/debian sid/main arm64 rake all 13.2.1-1 [65.2 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 libruby arm64 1:3.1+nmu1 [4664 B]
Get:41 http://deb.debian.org/debian sid/main arm64 ruby-sdbm arm64 1.0.0-5+b5 [14.6 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 ruby-rubygems all 3.4.20-1 [309 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 ruby arm64 1:3.1+nmu1 [5584 B]
Get:48 http://deb.debian.org/debian sid/main arm64 ruby-asciidoctor all 2.0.23-1 [214 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 asciidoctor all 2.0.23-1 [88.7 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:65 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.10-1 [337 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.10-1 [788 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B]
Get:79 http://deb.debian.org/debian sid/main arm64 bowtie2 arm64 2.5.4-1 [1405 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.5-1 [2443 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b3 [50.5 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8 [9166 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-8 [1284 B]
Get:89 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:90 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:91 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-8 [42.2 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:100 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:102 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:103 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB]
Get:105 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:107 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:108 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:109 http://deb.debian.org/debian sid/main arm64 cd-hit arm64 4.8.1-4+b1 [509 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:115 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.4.0-1 [36.9 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:125 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 75.2.0-1 [731 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20241024 [109 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 samtools arm64 1.20-3+b1 [629 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 fastaq all 3.17.0-8 [47.7 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 help2man arm64 1.49.3+b1 [198 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libcapnp-1.0.1 arm64 1.0.1-4+b1 [1296 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-2 [142 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b2 [65.9 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b2 [80.0 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 libgslcblas0 arm64 2.8+dfsg-4 [84.1 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libgsl28 arm64 2.8+dfsg-4 [881 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-4+b2 [154 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libminimap0 arm64 0.2-8+b2 [21.1 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 libminimap-dev arm64 0.2-8+b2 [32.5 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 libmurmurhash2 arm64 1.6-1+b1 [6592 B]
Get:170 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 mash arm64 2.3+dfsg-6+b1 [169 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:188 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 python3-attr all 24.2.0-1 [68.4 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:192 http://deb.debian.org/debian sid/main arm64 python3.12-tk arm64 3.12.7-1 [110 kB]
Get:193 http://deb.debian.org/debian sid/main arm64 python3.13-tk arm64 3.13.0-1 [101 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 python3-tk arm64 3.12.6-1 [9428 B]
Get:195 http://deb.debian.org/debian sid/main arm64 python3-cairo arm64 1.26.1-2 [113 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 python3-freetype all 2.5.1-1 [89.3 kB]
Get:197 http://deb.debian.org/debian sid/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B]
Get:198 http://deb.debian.org/debian sid/main arm64 python3-reportlab all 4.2.5-1 [1117 kB]
Get:199 http://deb.debian.org/debian sid/main arm64 xml-core all 0.19 [20.1 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 w3c-sgml-lib all 1.3-3 [273 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 python3-brotli arm64 1.1.0-2+b5 [307 kB]
Get:202 http://deb.debian.org/debian sid/main arm64 python3-soupsieve all 2.6-1 [38.3 kB]
Get:203 http://deb.debian.org/debian sid/main arm64 python3-bs4 all 4.12.3-3 [133 kB]
Get:204 http://deb.debian.org/debian sid/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB]
Get:205 http://deb.debian.org/debian sid/main arm64 python3-cycler all 0.12.1-1 [9496 B]
Get:206 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:207 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:208 http://deb.debian.org/debian sid/main arm64 python3-dendropy all 4.6.1-1 [277 kB]
Get:209 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.1-2 [30.9 kB]
Get:210 http://deb.debian.org/debian sid/main arm64 python3-six all 1.16.0-7 [16.4 kB]
Get:211 http://deb.debian.org/debian sid/main arm64 python3-fs all 2.4.16-4 [95.4 kB]
Get:212 http://deb.debian.org/debian sid/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB]
Get:213 http://deb.debian.org/debian sid/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b5 [25.3 kB]
Get:214 http://deb.debian.org/debian sid/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB]
Get:215 http://deb.debian.org/debian sid/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get:216 http://deb.debian.org/debian sid/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get:217 http://deb.debian.org/debian sid/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:218 http://deb.debian.org/debian sid/main arm64 unicode-data all 15.1.0-1 [8547 kB]
Get:219 http://deb.debian.org/debian sid/main arm64 python3-fonttools arm64 4.54.1-4 [1356 kB]
Get:220 http://deb.debian.org/debian sid/main arm64 python3-iniconfig all 1.1.1-2 [6396 B]
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
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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 python3-minimal (3.12.6-1+debusine1) ...
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/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')
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+------------------------------------------------------------------------------+
| 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_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.5-1
Package versions: appstream_1.0.3-1+b1 apt_2.9.10 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_3.6.5 bash_5.2.32-1+b2 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+b1 bowtie2_2.5.4-1 bsdextrautils_2.40.2-10 bsdutils_1:2.40.2-10 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 cd-hit_4.8.1-4+b1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-aarch64-linux-gnu_14.2.0-8 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9+b1 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20+b1 dh-autoreconf_20 dh-python_6.20241024 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1+b1 diffutils_1:3.10-1+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 fastaq_3.17.0-8 file_1:5.45-3+b1 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1+b1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: ariba
Binary: ariba
Architecture: any
Version: 2.14.7+ds-3
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
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Dgit: 14d74f5fd85ac851917305f9e0860e1cbadd0de7 debian archive/debian/2.14.7+ds-3 https://git.dgit.debian.org/ariba
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gpgv: Signature made Sun Nov 3 19:29:27 2024 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-3.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-3.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-3+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
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
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-3+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/samtools_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/assembly.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/ref_genes_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/faidx.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/megares_data_finder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/mic_plotter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/reference_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/bam_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/histogram.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/summary_sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/link.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/mlst_profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/scaffold_graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/card_record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/vfdb_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/clusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/summary_cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/megares_zip_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/pubmlst_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/assembly_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/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/read_store.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/versions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/pubmlst_ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/assembly_compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/read_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/mapping.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/cdhit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/sequence_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/report_filter.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/mlst_reporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/sequence_metadata.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/ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/external_progs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
copying ariba/report_flag_expander.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/refquery.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/prepareref_tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/expandflag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/aln2meta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/getref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/micplot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/pubmlstget.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/pubmlstspecies.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/reportfilter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
copying ariba/tasks/prepareref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/mic_plotter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/cdhit_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/mlst_profile_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/assembly_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/report_filter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/read_filter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/pubmlst_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/summary_sample_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/reference_data_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/sequence_variant_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/link_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/aln_to_metadata_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/scaffold_graph_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/mapping_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/summary_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/ref_preparer_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/clusters_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/ref_genes_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/cluster_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/bam_parse_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/megares_zip_parser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/tb_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/pubmlst_ref_preparer_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/report_flag_expander_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/ref_seq_chooser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/flag_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/mlst_reporter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/versions_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/external_progs_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/assembly_variants_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/histogram_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/summary_cluster_variant_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/common_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/megares_data_finder_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/assembly_compare_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/ncbi_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/samtools_variants_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/faidx_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/vfdb_parser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/read_store_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/summary_cluster_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/test_refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/sequence_metadata_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
copying ariba/tests/card_record_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
copying ariba/test_run_data/ref_seqs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
copying ariba/test_run_data/metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
copying ariba/test_run_data/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
copying ariba/test_run_data/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/NC_000962.3.gb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181221.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20190102.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181115.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/NC_000962.3.fa.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181221.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20190102.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
copying ariba/tb_data/panel.20181115.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
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copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
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copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
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copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
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copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_2.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_test_full_run_multiple_vars/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
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copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_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_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_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_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
creating /<<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
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/reads_2.fq -> /<<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/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/samtools_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/assembly.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/tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/faidx.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/mic_plotter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/reference_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/bam_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/histogram.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary_sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/link.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/mlst_profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/scaffold_graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/card_record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/vfdb_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/clusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/summary_cluster.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/pubmlst_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/assembly_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/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/read_store.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/versions.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/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/assembly_compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/read_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/mapping.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/cdhit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/sequence_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/report_filter.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/mlst_reporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/sequence_metadata.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/ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/external_progs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
copying ariba/report_flag_expander.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba
creating /<<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/prepareref_tb.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/expandflag.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/version.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/run.py -> /<<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/__init__.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/micplot.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/pubmlstspecies.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/prepareref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
creating /<<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/cdhit_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/assembly_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/pubmlst_getter_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
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copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
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copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
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copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
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copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.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/00.params.json -> /<<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/01.filter.check_metadata.tsv -> /<<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.clusters.pickle -> /<<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
copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
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copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
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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
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/reads_2.fq -> /<<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
copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.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_ok_gene_start_mismatch/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
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copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
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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
copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.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_test_full_run_partial_asmbly/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
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copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
creating /<<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
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/reads_2.fq -> /<<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/genes.fa -> /<<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
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/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.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/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/references.fa -> /<<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/reads_2.fq -> /<<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/references.fa -> /<<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/reads_2.fq -> /<<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/references.fa -> /<<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/reads_2.fq -> /<<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/references.fa -> /<<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/reads_2.fq -> /<<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/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/references.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/reads_2.fq -> /<<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/genes.fa -> /<<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
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/references.fa -> /<<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/reads_2.fq -> /<<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/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
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ "python3.12" != "python3.12" ]; then \
PYBUILD_TEST_ARGS=-k "not test_load_fasta_files_and_write_clusters_file" dh_auto_test; \
else \
dh_auto_test; \
fi
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-4.4.0
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 .F [ 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%]
=================================== FAILURES ===================================
_____ TestPubmlstRefPreparer.test_load_fasta_files_and_write_clusters_file _____
self = <ariba.tests.pubmlst_ref_preparer_test.TestPubmlstRefPreparer testMethod=test_load_fasta_files_and_write_clusters_file>
def test_load_fasta_files_and_write_clusters_file(self):
'''test _load_fasta_files_and_write_clusters_file'''
indir = os.path.join(data_dir, 'pubmlst_ref_prepare.test_load_fa_and_clusters.in')
outdir = 'tmp.test.pubmlst_ref_prepare.test_load_fa_and_clusters'
os.mkdir(outdir)
> r_prep = pubmlst_ref_preparer.PubmlstRefPreparer('species', outdir)
ariba/tests/pubmlst_ref_preparer_test.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ariba/pubmlst_ref_preparer.py:19: in __init__
self.extern_progs, version_report_lines = versions.get_all_versions()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
raise_error = True, using_spades = True
def get_all_versions(raise_error=True, using_spades=True):
extern_progs = external_progs.ExternalProgs(fail_on_error=False, using_spades=using_spades)
report_lines = [
'ARIBA version: ' + ariba_version,
'\nExternal dependencies:',
'\n'.join(extern_progs.version_report),
'\nExternal dependencies OK: ' + str(extern_progs.all_deps_ok),
'\nPython version:',
str(sys.version),
'\nPython packages:',
]
python_packages_ok = True
for package in ['ariba', 'bs4', 'dendropy', 'pyfastaq', 'pymummer', 'pysam']:
try:
exec('import ' + package)
version = eval(package + '.__version__')
path = eval(package + '.__file__')
except:
version = 'NOT_FOUND'
path = 'NOT_FOUND'
python_packages_ok = False
if version != 'NOT_FOUND':
if package in package_min_versions and LooseVersion(version) < LooseVersion(package_min_versions[package]):
version += '... THIS IS TOO LOW. Needs>=' + package_min_versions[package]
python_packages_ok = False
elif package in package_max_versions and LooseVersion(version) > package_max_versions[package]:
version += '...THIS IS TOO HIGH. Needs <=' + package_max_versions[package]
python_packages_ok = False
report_lines.append(package + '\t' + version + '\t' + path)
all_ok = extern_progs.all_deps_ok and python_packages_ok
report_lines.extend([
'\nPython packages OK: ' + str(python_packages_ok),
'\nEverything looks OK: ' + str(all_ok),
])
if raise_error and not all_ok:
print(*report_lines, sep='\n', file=sys.stderr)
print('Some dependencies not satisfied. Cannot continue.', file=sys.stderr)
> sys.exit(1)
E SystemExit: 1
ariba/versions.py:65: SystemExit
----------------------------- Captured stderr call -----------------------------
WARNING: spades not found in path. Looked for spades.py
ARIBA version: local
External dependencies:
bowtie2 2.5.4 /usr/bin/bowtie2
cdhit 4.8.1 /usr/bin/cd-hit-est
nucmer 3.1 /usr/bin/nucmer
spades NA NOT_FOUND
External dependencies OK: True
Python version:
3.13.0 (main, Oct 7 2024, 21:58:50) [GCC 14.2.0]
Python packages:
ariba NOT_FOUND NOT_FOUND
bs4 NOT_FOUND NOT_FOUND
dendropy NOT_FOUND NOT_FOUND
pyfastaq NOT_FOUND NOT_FOUND
pymummer NOT_FOUND NOT_FOUND
pysam NOT_FOUND NOT_FOUND
Python packages OK: False
Everything looks OK: False
Some dependencies not satisfied. Cannot continue.
=============================== 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 {'locate_file', 'read_text'}
__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\.]+)'))
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_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
=========================== short test summary info ============================
FAILED ariba/tests/pubmlst_ref_preparer_test.py::TestPubmlstRefPreparer::test_load_fasta_files_and_write_clusters_file
======= 1 failed, 353 passed, 2 skipped, 9 warnings in 79.63s (0:01:19) ========
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: 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-4.4.0
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 77.29s (0:01:17) =============
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13
make[1]: *** [debian/rules:24: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-04T14:55:14Z
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: 79284
Build-Time: 175
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 158
Job: /tmp/debusine-fetch-exec-upload-7_nannyp/ariba_2.14.7+ds-3.dsc
Machine Architecture: arm64
Package: ariba
Package-Time: 381
Source-Version: 2.14.7+ds-3
Space: 79284
Status: attempted
Version: 2.14.7+ds-3+bd1
--------------------------------------------------------------------------------
Finished at 2024-11-04T14:55:14Z
Build needed 00:06:21, 79284k disk space