cmd: autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-ch_adllf/multiqc_1.21+dfsg-2_all.deb /tmp/debusine-fetch-exec-upload-ch_adllf/python3-rich_13.9.4-0.1_all.deb /tmp/debusine-fetch-exec-upload-ch_adllf/multiqc_1.21+dfsg-2.dsc -- unshare --arch amd64 --release sid --tarball /var/lib/debusine/worker/system-images/1099747/system.tar.xz
output (contains stdout and stderr):
autopkgtest [14:01:51]: starting date and time: 2024-12-18 14:01:51+0000
autopkgtest [14:01:51]: version 5.38~bpo12+1
autopkgtest [14:01:51]: host debusine-worker-amd64-hades-01; command line: /usr/bin/autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-ch_adllf/multiqc_1.21+dfsg-2_all.deb /tmp/debusine-fetch-exec-upload-ch_adllf/python3-rich_13.9.4-0.1_all.deb /tmp/debusine-fetch-exec-upload-ch_adllf/multiqc_1.21+dfsg-2.dsc -- unshare --arch amd64 --release sid --tarball /var/lib/debusine/worker/system-images/1099747/system.tar.xz
autopkgtest [14:01:56]: testbed dpkg architecture: amd64
autopkgtest [14:01:56]: testbed apt version: 2.9.17
autopkgtest [14:01:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Get:1 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7350 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 Components [4974 kB]
Fetched 22.6 MB in 2s (9727 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
gcc-14-base gettext gettext-base libatomic1 libgcc-s1 libgomp1 libstdc++6
7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2779 kB of archives.
After this operation, 1024 B of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-11 [9284 B]
Get:2 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-11 [48.0 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-11 [713 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-11 [137 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-11 [72.7 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 gettext-base amd64 0.22.5-3 [200 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 gettext amd64 0.22.5-3 [1600 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2779 kB in 0s (36.4 MB/s)
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../libatomic1_14.2.0-11_amd64.deb ...
Unpacking libatomic1:amd64 (14.2.0-11) over (14.2.0-8) ...
Preparing to unpack .../gcc-14-base_14.2.0-11_amd64.deb ...
Unpacking gcc-14-base:amd64 (14.2.0-11) over (14.2.0-8) ...
Setting up gcc-14-base:amd64 (14.2.0-11) ...
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../libstdc++6_14.2.0-11_amd64.deb ...
Unpacking libstdc++6:amd64 (14.2.0-11) over (14.2.0-8) ...
Setting up libstdc++6:amd64 (14.2.0-11) ...
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../libgomp1_14.2.0-11_amd64.deb ...
Unpacking libgomp1:amd64 (14.2.0-11) over (14.2.0-8) ...
Preparing to unpack .../libgcc-s1_14.2.0-11_amd64.deb ...
Unpacking libgcc-s1:amd64 (14.2.0-11) over (14.2.0-8) ...
Setting up libgcc-s1:amd64 (14.2.0-11) ...
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../gettext-base_0.22.5-3_amd64.deb ...
Unpacking gettext-base (0.22.5-3) over (0.22.5-2) ...
Preparing to unpack .../gettext_0.22.5-3_amd64.deb ...
Unpacking gettext (0.22.5-3) over (0.22.5-2) ...
Setting up gettext-base (0.22.5-3) ...
Setting up libgomp1:amd64 (14.2.0-11) ...
Setting up libatomic1:amd64 (14.2.0-11) ...
Setting up gettext (0.22.5-3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
autopkgtest [14:02:03]: testbed running kernel: Linux 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22)
autopkgtest [14:02:03]: @@@@@@@@@@@@@@@@@@@@ source /tmp/debusine-fetch-exec-upload-ch_adllf/multiqc_1.21+dfsg-2.dsc
gpgv: Signature made Sat Aug 31 11:27:49 2024 UTC
gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A
gpgv: issuer "tchet@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for /tmp/autopkgtest.lltcqc/multiqc_1.21+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting multiqc in src
dpkg-source: info: unpacking multiqc_1.21+dfsg.orig.tar.xz
dpkg-source: info: unpacking multiqc_1.21+dfsg.orig-debian-tests-data.tar.xz
dpkg-source: info: unpacking multiqc_1.21+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying removeHighcharts.patch
autopkgtest [14:02:05]: testing package multiqc version 1.21+dfsg-2
autopkgtest [14:02:05]: build not needed
autopkgtest [14:02:05]: test run-unit-test: preparing testbed
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
apt-utils
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 328 kB of archives.
After this operation, 1097 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 apt-utils amd64 2.9.17 [328 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 328 kB in 0s (7130 kB/s)
Selecting previously unselected package apt-utils.
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../apt-utils_2.9.17_amd64.deb ...
Unpacking apt-utils (2.9.17) ...
Setting up apt-utils (2.9.17) ...
Processing triggers for man-db (2.13.0-1) ...
Ign:1 file:/tmp/autopkgtest.lltcqc/binaries InRelease
Get:2 file:/tmp/autopkgtest.lltcqc/binaries Release [816 B]
Get:2 file:/tmp/autopkgtest.lltcqc/binaries Release [816 B]
Ign:3 file:/tmp/autopkgtest.lltcqc/binaries Release.gpg
Get:4 file:/tmp/autopkgtest.lltcqc/binaries Packages [5213 B]
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Starting pkgProblemResolver with broken count: 0
Starting 2 pkgProblemResolver with broken count: 0
Done
The following NEW packages will be installed:
blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono
fonts-glyphicons-halflings fonts-lyx libblas3 libdeflate0 libexpat1
libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libgraphite2-3
libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libjs-bootstrap
libjs-jquery libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-ui
liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libnsl2 libopenjp2-7
libpng16-16t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib
libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtirpc-common
libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6
libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1
libxslt1.1 libxss1 media-types multiqc python-matplotlib-data python3
python3-attr python3-autocommand python3-brotli python3-certifi
python3-chardet python3-charset-normalizer python3-click python3-colorama
python3-coloredlogs python3-colormath python3-contourpy python3-cycler
python3-dateutil python3-decorator python3-fastjsonschema python3-fonttools
python3-fs python3-humanfriendly python3-humanize python3-idna
python3-importlib-metadata python3-inflect python3-jaraco.context
python3-jaraco.functools python3-jinja2 python3-jsonschema
python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver
python3-lxml python3-lz4 python3-lzstring python3-markdown
python3-markdown-it python3-markupsafe python3-matplotlib python3-mdurl
python3-minimal python3-more-itertools python3-mpmath python3-nbformat
python3-networkx python3-numpy python3-packaging python3-pil
python3-pil.imagetk python3-pkg-resources python3-platformdirs
python3-plotly python3-pyaml-env python3-pygments python3-pyparsing
python3-referencing python3-requests python3-rich python3-rich-click
python3-rpds-py python3-scipy python3-spectra python3-sympy python3-tenacity
python3-tk python3-traitlets python3-typeguard python3-typing-extensions
python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-yaml
python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk
tk8.6-blt2.5 unicode-data x11-common
0 upgraded, 136 newly installed, 0 to remove and 0 not upgraded.
Need to get 92.0 MB/92.9 MB of archives.
After this operation, 500 MB of additional disk space will be used.
Get:1 file:/tmp/autopkgtest.lltcqc/binaries python3-rich 13.9.4-0.1 [203 kB]
Get:2 file:/tmp/autopkgtest.lltcqc/binaries multiqc 1.21+dfsg-2 [781 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.8-3 [677 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B]
Get:14 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB]
Get:32 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB]
Get:33 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B]
Get:35 http://deb.debian.org/debian sid/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB]
Get:36 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB]
Get:37 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB]
Get:39 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB]
Get:41 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get:42 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB]
Get:43 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get:44 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get:45 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get:46 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB]
Get:47 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:48 http://deb.debian.org/debian sid/main amd64 libjs-jquery-metadata all 12-4 [6532 B]
Get:49 http://deb.debian.org/debian sid/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:51 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB]
Get:52 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB]
Get:53 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get:54 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get:55 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB]
Get:56 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB]
Get:57 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get:58 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB]
Get:59 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB]
Get:60 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB]
Get:62 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB]
Get:63 http://deb.debian.org/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB]
Get:64 http://deb.debian.org/debian sid/main amd64 python3-colorama all 0.4.6-4 [36.2 kB]
Get:65 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:66 http://deb.debian.org/debian sid/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get:67 http://deb.debian.org/debian sid/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB]
Get:68 http://deb.debian.org/debian sid/main amd64 python3-click all 8.1.7-2 [94.3 kB]
Get:69 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB]
Get:70 http://deb.debian.org/debian sid/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB]
Get:71 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:72 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:73 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get:74 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:75 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:76 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:77 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get:78 http://deb.debian.org/debian sid/main amd64 python3-humanize all 4.11.0-1 [52.7 kB]
Get:79 http://deb.debian.org/debian sid/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB]
Get:80 http://deb.debian.org/debian sid/main amd64 python3-jinja2 all 3.1.3-1.1 [120 kB]
Get:81 http://deb.debian.org/debian sid/main amd64 python3-markdown all 3.7-2 [85.2 kB]
Get:82 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get:83 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:84 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB]
Get:85 http://deb.debian.org/debian sid/main amd64 python3.12-tk amd64 3.12.8-3 [113 kB]
Get:86 http://deb.debian.org/debian sid/main amd64 python3.13-tk amd64 3.13.1-2 [103 kB]
Get:87 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.13.1-1 [9464 B]
Get:88 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB]
Get:89 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:90 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB]
Get:91 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB]
Get:92 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B]
Get:93 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB]
Get:94 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.2-1 [31.0 kB]
Get:95 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get:96 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-5.1 [95.2 kB]
Get:97 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB]
Get:98 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB]
Get:99 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:100 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.14.1-3 [20.5 MB]
Get:101 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get:102 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-1 [4147 kB]
Get:103 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB]
Get:104 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get:105 http://deb.debian.org/debian sid/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB]
Get:106 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB]
Get:107 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.55.0-3 [1634 kB]
Get:108 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB]
Get:109 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get:110 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB]
Get:111 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get:112 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB]
Get:113 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.8-2 [41.6 kB]
Get:114 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 2.2.3-4 [112 kB]
Get:115 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:116 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get:117 http://deb.debian.org/debian sid/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB]
Get:118 http://deb.debian.org/debian sid/main amd64 python3-rpds-py amd64 0.21.0-2 [287 kB]
Get:119 http://deb.debian.org/debian sid/main amd64 python3-referencing all 0.35.1-2 [23.5 kB]
Get:120 http://deb.debian.org/debian sid/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get:121 http://deb.debian.org/debian sid/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB]
Get:122 http://deb.debian.org/debian sid/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB]
Get:123 http://deb.debian.org/debian sid/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB]
Get:124 http://deb.debian.org/debian sid/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB]
Get:125 http://deb.debian.org/debian sid/main amd64 python3-tenacity all 8.4.2+really8.4.1-1 [46.0 kB]
Get:126 http://deb.debian.org/debian sid/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB]
Get:127 http://deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB]
Get:128 http://deb.debian.org/debian sid/main amd64 python3-pyaml-env all 1.2.1-2 [9032 B]
Get:129 http://deb.debian.org/debian sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B]
Get:130 http://deb.debian.org/debian sid/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB]
Get:131 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get:132 http://deb.debian.org/debian sid/main amd64 python3-rich-click all 1.6.0-1 [20.8 kB]
Get:133 http://deb.debian.org/debian sid/main amd64 python3-networkx all 3.2.1-5 [13.0 MB]
Get:134 http://deb.debian.org/debian sid/main amd64 python3-colormath all 3.0.0-4 [34.7 kB]
Get:135 http://deb.debian.org/debian sid/main amd64 python3-spectra all 0.0.11-4 [16.5 kB]
Get:136 http://deb.debian.org/debian sid/main amd64 python3-lzstring all 1.0.4-3 [5544 B]
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/usr/lib/python3/dist-packages/pyaml_env/parse_config.py:58: SyntaxWarning: invalid escape sequence '\w'
type_tag_pattern = re.compile(f'({type_tag}\w+\s)')
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/usr/lib/python3/dist-packages/colormath/chromatic_adaptation.py:85: SyntaxWarning: invalid escape sequence '\*'
logger.debug(" \* Applying adaptation matrix: %s", adaptation)
/usr/lib/python3/dist-packages/colormath/color_appearance_models.py:684: SyntaxWarning: invalid escape sequence '\s'
"""
/usr/lib/python3/dist-packages/colormath/color_appearance_models.py:788: SyntaxWarning: invalid escape sequence '\s'
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/usr/lib/python3/dist-packages/colormath/color_conversions.py:40: SyntaxWarning: invalid escape sequence '\*'
logger.debug(" \* Applying RGB conversion matrix: %s->%s",
/usr/lib/python3/dist-packages/colormath/color_conversions.py:488: SyntaxWarning: invalid escape sequence '\-'
logger.debug(" \- Target RGB space: %s", target_rgb)
/usr/lib/python3/dist-packages/colormath/color_conversions.py:490: SyntaxWarning: invalid escape sequence '\-'
logger.debug(" \- Target native illuminant: %s", target_illum)
/usr/lib/python3/dist-packages/colormath/color_conversions.py:491: SyntaxWarning: invalid escape sequence '\-'
logger.debug(" \- XYZ color's illuminant: %s", cobj.illuminant)
/usr/lib/python3/dist-packages/colormath/color_conversions.py:497: SyntaxWarning: invalid escape sequence '\*'
logger.debug(" \* Applying transformation from %s to %s ",
/usr/lib/python3/dist-packages/colormath/color_conversions.py:503: SyntaxWarning: invalid escape sequence '\*'
logger.debug(" \* New values: %.3f, %.3f, %.3f",
/usr/lib/python3/dist-packages/colormath/color_objects.py:452: SyntaxWarning: invalid escape sequence '\-'
logger.debug(" \- Original illuminant: %s", self.illuminant)
/usr/lib/python3/dist-packages/colormath/color_objects.py:453: SyntaxWarning: invalid escape sequence '\-'
logger.debug(" \- Target illuminant: %s", target_illuminant)
/usr/lib/python3/dist-packages/colormath/color_objects.py:459: SyntaxWarning: invalid escape sequence '\*'
logger.debug(" \* Applying transformation from %s to %s ",
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autopkgtest [14:02:55]: test run-unit-test: [-----------------------
/// MultiQC 🎄 | v1.21
Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]
MultiQC aggregates results from bioinformatics analyses across many samples
into a single report.
It searches a given directory for analysis logs and compiles a HTML report.
It's a general use tool, perfect for summarising the output from numerous
bioinformatics tools.
To run, supply with one or more directory to scan for analysis results. For
example, to run in the current working directory, use 'multiqc .'
╭─ Main options ───────────────────────────────────────────────────────────────╮
│ --force -f Overwrite any existing reports │
│ --config -c Specific config file to load, after those in MultiQC │
│ dir / home dir / working dir. │
│ (PATH) │
│ --cl-config Specify MultiQC config YAML on the command line │
│ (TEXT) │
│ --filename -n Report filename. Use 'stdout' to print to standard │
│ out. │
│ (TEXT) │
│ --outdir -o Create report in the specified output directory. │
│ (TEXT) │
│ --ignore -x Ignore analysis files (GLOB EXPRESSION) │
│ --ignore-samples Ignore sample names (GLOB EXPRESSION) │
│ --ignore-symlinks Ignore symlinked directories and files │
│ --file-list -l Supply a file containing a list of file paths to be │
│ searched, one per row │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Choosing modules to run ────────────────────────────────────────────────────╮
│ --module -m Use only this module. Can specify multiple times. │
│ (MODULE NAME) │
│ --exclude -e Do not use this module. Can specify multiple times. │
│ (MODULE NAME) │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Sample handling ────────────────────────────────────────────────────────────╮
│ --dirs -d Prepend directory to sample names │
│ --dirs-depth -dd Prepend n directories to sample names. Negative number │
│ to take from start of path. │
│ (INTEGER) │
│ --fullnames -s Do not clean the sample names (leave as full file │
│ name) │
│ --fn_as_s_name Use the log filename as the sample name │
│ --replace-names TSV file to rename sample names during report │
│ generation │
│ (PATH) │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Report customisation ───────────────────────────────────────────────────────╮
│ --title -i Report title. Printed as page header, used for │
│ filename if not otherwise specified. │
│ (TEXT) │
│ --comment -b Custom comment, will be printed at the top of the │
│ report. │
│ (TEXT) │
│ --template -t Report template to use. │
│ (default|gathered|geo|highcharts|sections|simple) │
│ --sample-names TSV file containing alternative sample names for │
│ renaming buttons in the report │
│ (PATH) │
│ --sample-filters TSV file containing show/hide patterns for the report │
│ (PATH) │
│ --custom-css-file Custom CSS file to add to the final report (PATH) │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Output files ───────────────────────────────────────────────────────────────╮
│ --flat -fp Use only flat plots (static images) │
│ --interactive -ip Use only interactive plots (in-browser Javascript) │
│ --export -p Export plots as static images in addition to the report │
│ --data-dir Force the parsed data directory to be created. │
│ --no-data-dir Prevent the parsed data directory from being created. │
│ --data-format -k Output parsed data in a different format. │
│ (tsv|csv|json|yaml) │
│ --zip-data-dir -z Compress the data directory. │
│ --no-report Do not generate a report, only export data and plots │
│ --pdf Creates PDF report with the 'simple' template. Requires │
│ Pandoc to be installed. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ MultiQC behaviour ──────────────────────────────────────────────────────────╮
│ --verbose -v Increase output verbosity. (INTEGER RANGE) │
│ --quiet -q Only show log warnings │
│ --strict Don't catch exceptions, run additional code checks │
│ to help development. │
│ --development,--dev Development mode. Do not compress and minimise JS, │
│ export uncompressed plot data │
│ --require-logs Require all explicitly requested modules to have │
│ log files. If not, MultiQC will exit with an error. │
│ --profile-runtime Add analysis of how long MultiQC takes to run to │
│ the report │
│ --no-megaqc-upload Don't upload generated report to MegaQC, even if │
│ MegaQC options are found │
│ --no-ansi Disable coloured log output │
│ --version Show the version and exit. │
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
See http://multiqc.info for more details.
FIXME: The test data should be delivered in a separate binary package once freeze is over
/// MultiQC 🔍 | v1.21
| multiqc | Search path : /tmp/autopkgtest.lltcqc/autopkgtest_tmp/data
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 121/121
| feature_counts | Found 8 reports
| star | Found 8 reports
| cutadapt | Found 16 reports
| fastqc | Found 32 reports
| multiqc | Report : multiqc_report.html
| multiqc | Data : multiqc_data
| multiqc | Could not include file 'assets/js/packages/jszip.min.js': [Errno 2] No such file or directory: '/tmp/tmpkc50qqbx/assets/js/packages/jszip.min.js'
| multiqc | Could not include file 'assets/js/packages/plotly-2.27.0.min.js': [Errno 2] No such file or directory: '/tmp/tmpkc50qqbx/assets/js/packages/plotly-2.27.0.min.js'
| multiqc | MultiQC complete
-e
PASS
autopkgtest [14:02:57]: test run-unit-test: -----------------------]
autopkgtest [14:02:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test PASS
autopkgtest [14:02:57]: @@@@@@@@@@@@@@@@@@@@ summary
run-unit-test PASS
aborted: False
returncode: 0
Files in working directory:
artifact-dir
artifact-dir/binaries
artifact-dir/binaries/multiqc.deb
artifact-dir/binaries/python3-rich.deb
artifact-dir/log
artifact-dir/run-unit-test-packages
artifact-dir/run-unit-test-stderr
artifact-dir/run-unit-test-stdout
artifact-dir/summary
artifact-dir/testbed-packages
artifact-dir/testinfo.json
artifact-dir/testpkg-version
--------------------