1s autopkgtest [10:35:02]: starting date and time: 2024-11-13 10:35:02+0000 2s autopkgtest [10:35:03]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 2s autopkgtest [10:35:03]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8w7soe52/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-37.secgroup --name adt-plucky-arm64-python-biopython-20241113-101405-juju-7f2275-prod-proposed-migration-environment-20-80e0b545-7c9a-4aa2-a1e0-686981182ff1 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 120s autopkgtest [10:37:01]: testbed dpkg architecture: arm64 120s autopkgtest [10:37:01]: testbed apt version: 2.9.8 120s autopkgtest [10:37:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 121s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 122s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 122s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 122s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 122s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 122s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 122s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 122s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 122s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 122s Fetched 1794 kB in 1s (1836 kB/s) 122s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade... 129s The following NEW packages will be installed: 129s python3.13-gdbm 129s The following packages will be upgraded: 129s libpython3-stdlib python3 python3-gdbm python3-minimal 130s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 101 kB of archives. 130s After this operation, 141 kB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 130s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 130s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 130s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 130s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 130s Fetched 101 kB in 0s (279 kB/s) 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 131s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 131s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 131s Setting up python3-minimal (3.12.7-1) ... 131s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 131s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 131s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 131s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 131s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 132s Selecting previously unselected package python3.13-gdbm. 132s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 132s Unpacking python3.13-gdbm (3.13.0-2) ... 132s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 132s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 132s Setting up python3.13-gdbm (3.13.0-2) ... 132s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 132s Setting up python3 (3.12.7-1) ... 132s Setting up python3-gdbm:arm64 (3.12.7-1) ... 132s Processing triggers for man-db (2.12.1-3) ... 133s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 135s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 135s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 135s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 137s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s autopkgtest [10:37:30]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 149s autopkgtest [10:37:30]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 155s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (dsc) [3543 B] 155s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (tar) [14.6 MB] 155s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (diff) [42.8 kB] 156s gpgv: Signature made Wed Oct 30 21:23:04 2024 UTC 156s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 156s gpgv: issuer "emollier@debian.org" 156s gpgv: Can't check signature: No public key 156s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4.dsc: no acceptable signature found 157s autopkgtest [10:37:38]: testing package python-biopython version 1.84+dfsg-4 158s autopkgtest [10:37:39]: build not needed 163s autopkgtest [10:37:44]: test dependencies: preparing testbed 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 166s Starting 2 pkgProblemResolver with broken count: 0 166s Done 166s The following additional packages will be installed: 166s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 166s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 166s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 166s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 166s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 166s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 166s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 166s python3-all python3-biopython python3-biopython-sql python3-cairo 166s python3-freetype python3-numpy python3-pil python3-reportlab 166s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 166s x11-common xfonts-encodings xfonts-utils xml-core 166s Suggested packages: 166s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 166s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 166s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 166s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 166s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 166s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 166s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 166s debhelper 166s Recommended packages: 166s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 166s The following NEW packages will be installed: 166s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 166s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 166s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 166s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 166s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 166s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 166s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 166s python-biopython-doc python3-all python3-biopython python3-biopython-sql 166s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 166s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 166s x11-common xfonts-encodings xfonts-utils xml-core 167s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 50.8 MB/50.8 MB of archives. 167s After this operation, 144 MB of additional disk space will be used. 167s Get:1 /tmp/autopkgtest.qKkx58/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 167s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 167s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 167s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 167s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 167s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 167s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 167s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 167s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 167s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 168s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 168s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 168s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 168s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 168s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 168s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 168s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 168s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 168s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 168s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 168s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 168s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 168s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 168s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 168s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 168s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 168s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 168s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 168s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 168s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 168s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 168s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 168s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 168s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 168s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 168s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 168s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 168s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 168s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 168s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 168s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 169s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 169s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 169s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 169s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 169s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 169s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 169s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 169s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 169s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 169s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 169s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 169s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 169s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 170s Fetched 50.8 MB in 3s (18.5 MB/s) 170s Selecting previously unselected package libpython3.13-minimal:arm64. 170s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79931 files and directories currently installed.) 170s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 170s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 170s Selecting previously unselected package python3.13-minimal. 170s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 170s Unpacking python3.13-minimal (3.13.0-2) ... 170s Selecting previously unselected package sgml-base. 170s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 170s Unpacking sgml-base (1.31) ... 170s Selecting previously unselected package fonts-dejavu-mono. 170s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 170s Unpacking fonts-dejavu-mono (2.37-8) ... 170s Selecting previously unselected package fonts-dejavu-core. 170s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 170s Unpacking fonts-dejavu-core (2.37-8) ... 171s Selecting previously unselected package libfontenc1:arm64. 171s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 171s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 171s Selecting previously unselected package x11-common. 171s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 171s Unpacking x11-common (1:7.7+23ubuntu3) ... 171s Selecting previously unselected package xfonts-encodings. 171s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 171s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 171s Selecting previously unselected package xfonts-utils. 171s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_arm64.deb ... 171s Unpacking xfonts-utils (1:7.7+7) ... 171s Selecting previously unselected package fonts-urw-base35. 171s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 171s Unpacking fonts-urw-base35 (20200910-8) ... 171s Selecting previously unselected package fontconfig-config. 171s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 172s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 172s Selecting previously unselected package libblas3:arm64. 172s Preparing to unpack .../11-libblas3_3.12.0-3build2_arm64.deb ... 172s Unpacking libblas3:arm64 (3.12.0-3build2) ... 172s Selecting previously unselected package libfontconfig1:arm64. 172s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 172s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 172s Selecting previously unselected package libpixman-1-0:arm64. 172s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_arm64.deb ... 172s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 172s Selecting previously unselected package libxcb-render0:arm64. 172s Preparing to unpack .../14-libxcb-render0_1.17.0-2_arm64.deb ... 172s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 172s Selecting previously unselected package libxcb-shm0:arm64. 172s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_arm64.deb ... 172s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 172s Selecting previously unselected package libxrender1:arm64. 172s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 172s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 172s Selecting previously unselected package libcairo2:arm64. 172s Preparing to unpack .../17-libcairo2_1.18.2-2_arm64.deb ... 172s Unpacking libcairo2:arm64 (1.18.2-2) ... 172s Selecting previously unselected package libdeflate0:arm64. 172s Preparing to unpack .../18-libdeflate0_1.22-1_arm64.deb ... 172s Unpacking libdeflate0:arm64 (1.22-1) ... 172s Selecting previously unselected package libgfortran5:arm64. 172s Preparing to unpack .../19-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 172s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 172s Selecting previously unselected package libgomp1:arm64. 172s Preparing to unpack .../20-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 172s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 172s Selecting previously unselected package libgraphite2-3:arm64. 172s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 172s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 172s Selecting previously unselected package libharfbuzz0b:arm64. 172s Preparing to unpack .../22-libharfbuzz0b_10.0.1-1_arm64.deb ... 172s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 172s Selecting previously unselected package libimagequant0:arm64. 172s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_arm64.deb ... 172s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 172s Selecting previously unselected package libjpeg-turbo8:arm64. 172s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 172s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 173s Selecting previously unselected package libjpeg8:arm64. 173s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ... 173s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 173s Selecting previously unselected package libjs-jquery. 173s Preparing to unpack .../26-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 173s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 173s Selecting previously unselected package libjs-underscore. 173s Preparing to unpack .../27-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 173s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 173s Selecting previously unselected package libjs-sphinxdoc. 173s Preparing to unpack .../28-libjs-sphinxdoc_7.4.7-4_all.deb ... 173s Unpacking libjs-sphinxdoc (7.4.7-4) 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180s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 180s Setting up python3-all (3.12.7-1) ... 180s Setting up xfonts-utils (1:7.7+7) ... 180s Setting up libraqm0:arm64 (0.10.1-1build1) ... 180s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 186s Setting up libjs-sphinxdoc (7.4.7-4) ... 186s Setting up python-biopython-doc (1.84+dfsg-4) ... 186s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 186s Setting up xml-core (0.19) ... 186s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 186s Setting up fonts-urw-base35 (20200910-8) ... 186s Setting up libcairo2:arm64 (1.18.2-2) ... 186s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 187s Setting up python3-cairo (1.26.1-2) ... 188s Setting up python3-rlpycairo (0.3.0-3) ... 188s Setting up python3-reportlab (4.2.5-1) ... 191s Processing triggers for libc-bin (2.40-1ubuntu3) ... 191s Processing triggers for systemd (256.5-2ubuntu4) ... 191s Processing triggers for man-db (2.12.1-3) ... 192s Processing triggers for sgml-base (1.31) ... 192s Setting up w3c-sgml-lib (1.3-3) ... 234s Setting up python3-biopython (1.84+dfsg-4) ... 238s Setting up python3-biopython-sql (1.84+dfsg-4) ... 238s Setting up autopkgtest-satdep (0) ... 246s (Reading database ... 86070 files and directories currently installed.) 246s Removing autopkgtest-satdep (0) ... 247s autopkgtest [10:39:08]: test dependencies: sh debian/tests/run-unit-test 247s autopkgtest [10:39:08]: test dependencies: [----------------------- 247s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 247s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 247s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 247s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 250s mkdir: created directory 'Bio' 250s mkdir: created directory 'Bio/Align' 250s mkdir: created directory 'Bio/Align/substitution_matrices' 250s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 250s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 251s Remove test test_Tutorial.py which is bound to fail 251s test_Ace ... ok 251s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 251s 252s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 252s 252s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 252s 252s test_Align_a2m ... loading tests failed: 252s Failed to import test module: test_Align_a2m 252s Traceback (most recent call last): 252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 252s from . import multiarray 252s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 252s from . import overrides 252s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 252s from numpy.core._multiarray_umath import ( 252s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 252s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 252s 252s During handling of the above exception, another exception occurred: 252s 252s Traceback (most recent call last): 252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 252s from numpy.__config__ import show as show_config 252s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 252s from numpy.core._multiarray_umath import ( 252s ...<3 lines>... 252s ) 252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 252s raise ImportError(msg) 252s ImportError: 252s 252s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 252s 252s Importing the numpy C-extensions failed. This error can happen for 252s many reasons, often due to issues with your setup or how NumPy was 252s installed. 252s 252s We have compiled some common reasons and troubleshooting tips at: 252s 252s https://numpy.org/devdocs/user/troubleshooting-importerror.html 252s 252s Please note and check the following: 252s 252s * The Python version is: Python3.13 from "/usr/bin/python3.13" 252s * The NumPy version is: "1.26.4" 252s 252s and make sure that they are the versions you expect. 252s Please carefully study the documentation linked above for further help. 252s 252s Original error was: No module named 'numpy.core._multiarray_umath' 252s 252s 252s The above exception was the direct cause of the following exception: 252s 252s Traceback (most recent call last): 252s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 252s module = __import__(module_name) 252s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 252s import numpy as np 252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 252s raise ImportError(msg) from e 252s ImportError: Error importing numpy: you should not try to import numpy from 252s its source directory; please exit the numpy source tree, and relaunch 252s your python interpreter from there. 252s 252s test_Align_bed ... loading tests failed: 252s Failed to import test module: test_Align_bed 252s Traceback (most recent call last): 252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 252s from . import multiarray 252s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 252s from . import overrides 252s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 252s from numpy.core._multiarray_umath import ( 252s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 252s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 252s 252s During handling of the above exception, another exception occurred: 252s 252s Traceback (most recent call last): 252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 252s from numpy.__config__ import show as show_config 252s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 252s from numpy.core._multiarray_umath import ( 252s ...<3 lines>... 252s ) 252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 252s raise ImportError(msg) 252s ImportError: 252s 252s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 252s 252s Importing the numpy C-extensions failed. This error can happen for 252s many reasons, often due to issues with your setup or how NumPy was 252s installed. 252s 252s We have compiled some common reasons and troubleshooting tips at: 252s 252s https://numpy.org/devdocs/user/troubleshooting-importerror.html 252s 252s Please note and check the following: 252s 252s * The Python version is: Python3.13 from "/usr/bin/python3.13" 252s * The NumPy version is: "1.26.4" 252s 252s and make sure that they are the versions you expect. 252s Please carefully study the documentation linked above for further help. 252s 252s Original error was: No module named 'numpy.core._multiarray_umath' 252s 252s 252s The above exception was the direct cause of the following exception: 252s 252s Traceback (most recent call last): 252s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 252s module = __import__(module_name) 252s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 252s import numpy as np 252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 252s raise ImportError(msg) from e 252s ImportError: Error importing numpy: you should not try to import numpy from 252s its source directory; please exit the numpy source tree, and relaunch 252s your python interpreter from there. 252s 252s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 252s test_Align_bigmaf ... loading tests failed: 252s Failed to import test module: test_Align_bigmaf 252s Traceback (most recent call last): 252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 252s from . import multiarray 252s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 252s from . import overrides 252s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 252s from numpy.core._multiarray_umath import ( 252s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 252s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 252s 252s During handling of the above exception, another exception occurred: 252s 252s Traceback (most recent call last): 252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 252s from numpy.__config__ import show as show_config 252s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 252s from numpy.core._multiarray_umath import ( 252s ...<3 lines>... 252s ) 252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 252s raise ImportError(msg) 252s ImportError: 252s 252s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 252s 252s Importing the numpy C-extensions failed. This error can happen for 252s many reasons, often due to issues with your setup or how NumPy was 252s installed. 252s 252s We have compiled some common reasons and troubleshooting tips at: 252s 252s https://numpy.org/devdocs/user/troubleshooting-importerror.html 252s 252s Please note and check the following: 252s 252s * The Python version is: Python3.13 from "/usr/bin/python3.13" 252s * The NumPy version is: "1.26.4" 252s 252s and make sure that they are the versions you expect. 252s Please carefully study the documentation linked above for further help. 252s 252s Original error was: No module named 'numpy.core._multiarray_umath' 252s 252s 252s The above exception was the direct cause of the following exception: 252s 252s Traceback (most recent call last): 252s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 252s module = __import__(module_name) 252s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 252s import numpy as np 252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 252s raise ImportError(msg) from e 252s ImportError: Error importing numpy: you should not try to import numpy from 252s its source directory; please exit the numpy source tree, and relaunch 252s your python interpreter from there. 252s 252s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 252s 253s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 253s test_Align_clustal ... loading tests failed: 253s Failed to import test module: test_Align_clustal 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 253s from . import multiarray 253s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 253s from . import overrides 253s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 253s from numpy.core._multiarray_umath import ( 253s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 253s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 253s 253s During handling of the above exception, another exception occurred: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 253s from numpy.__config__ import show as show_config 253s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 253s from numpy.core._multiarray_umath import ( 253s ...<3 lines>... 253s ) 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 253s raise ImportError(msg) 253s ImportError: 253s 253s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 253s 253s Importing the numpy C-extensions failed. This error can happen for 253s many reasons, often due to issues with your setup or how NumPy was 253s installed. 253s 253s We have compiled some common reasons and troubleshooting tips at: 253s 253s https://numpy.org/devdocs/user/troubleshooting-importerror.html 253s 253s Please note and check the following: 253s 253s * The Python version is: Python3.13 from "/usr/bin/python3.13" 253s * The NumPy version is: "1.26.4" 253s 253s and make sure that they are the versions you expect. 253s Please carefully study the documentation linked above for further help. 253s 253s Original error was: No module named 'numpy.core._multiarray_umath' 253s 253s 253s The above exception was the direct cause of the following exception: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 253s module = __import__(module_name) 253s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 253s import numpy as np 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 253s raise ImportError(msg) from e 253s ImportError: Error importing numpy: you should not try to import numpy from 253s its source directory; please exit the numpy source tree, and relaunch 253s your python interpreter from there. 253s 253s test_Align_codonalign ... loading tests failed: 253s Failed to import test module: test_Align_codonalign 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 253s from . import multiarray 253s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 253s from . import overrides 253s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 253s from numpy.core._multiarray_umath import ( 253s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 253s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 253s 253s During handling of the above exception, another exception occurred: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 253s from numpy.__config__ import show as show_config 253s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 253s from numpy.core._multiarray_umath import ( 253s ...<3 lines>... 253s ) 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 253s raise ImportError(msg) 253s ImportError: 253s 253s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 253s 253s Importing the numpy C-extensions failed. This error can happen for 253s many reasons, often due to issues with your setup or how NumPy was 253s installed. 253s 253s We have compiled some common reasons and troubleshooting tips at: 253s 253s https://numpy.org/devdocs/user/troubleshooting-importerror.html 253s 253s Please note and check the following: 253s 253s * The Python version is: Python3.13 from "/usr/bin/python3.13" 253s * The NumPy version is: "1.26.4" 253s 253s and make sure that they are the versions you expect. 253s Please carefully study the documentation linked above for further help. 253s 253s Original error was: No module named 'numpy.core._multiarray_umath' 253s 253s 253s The above exception was the direct cause of the following exception: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 253s module = __import__(module_name) 253s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 253s import numpy as np 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 253s raise ImportError(msg) from e 253s ImportError: Error importing numpy: you should not try to import numpy from 253s its source directory; please exit the numpy source tree, and relaunch 253s your python interpreter from there. 253s 253s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 253s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 253s test_Align_fasta ... loading tests failed: 253s Failed to import test module: test_Align_fasta 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 253s from . import multiarray 253s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 253s from . import overrides 253s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 253s from numpy.core._multiarray_umath import ( 253s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 253s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 253s 253s During handling of the above exception, another exception occurred: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 253s from numpy.__config__ import show as show_config 253s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 253s from numpy.core._multiarray_umath import ( 253s ...<3 lines>... 253s ) 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 253s raise ImportError(msg) 253s ImportError: 253s 253s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 253s 253s Importing the numpy C-extensions failed. This error can happen for 253s many reasons, often due to issues with your setup or how NumPy was 253s installed. 253s 253s We have compiled some common reasons and troubleshooting tips at: 253s 253s https://numpy.org/devdocs/user/troubleshooting-importerror.html 253s 253s Please note and check the following: 253s 253s * The Python version is: Python3.13 from "/usr/bin/python3.13" 253s * The NumPy version is: "1.26.4" 253s 253s and make sure that they are the versions you expect. 253s Please carefully study the documentation linked above for further help. 253s 253s Original error was: No module named 'numpy.core._multiarray_umath' 253s 253s 253s The above exception was the direct cause of the following exception: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 253s module = __import__(module_name) 253s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 253s import numpy as np 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 253s raise ImportError(msg) from e 253s ImportError: Error importing numpy: you should not try to import numpy from 253s its source directory; please exit the numpy source tree, and relaunch 253s your python interpreter from there. 253s 253s test_Align_hhr ... loading tests failed: 253s Failed to import test module: test_Align_hhr 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 253s from . import multiarray 253s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 253s from . import overrides 253s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 253s from numpy.core._multiarray_umath import ( 253s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 253s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 253s 253s During handling of the above exception, another exception occurred: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 253s from numpy.__config__ import show as show_config 253s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 253s from numpy.core._multiarray_umath import ( 253s ...<3 lines>... 253s ) 253s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 253s raise ImportError(msg) 253s ImportError: 253s 253s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 253s 253s Importing the numpy C-extensions failed. This error can happen for 253s many reasons, often due to issues with your setup or how NumPy was 253s installed. 253s 253s We have compiled some common reasons and troubleshooting tips at: 253s 253s https://numpy.org/devdocs/user/troubleshooting-importerror.html 253s 253s Please note and check the following: 253s 253s * The Python version is: Python3.13 from "/usr/bin/python3.13" 253s * The NumPy version is: "1.26.4" 253s 253s and make sure that they are the versions you expect. 253s Please carefully study the documentation linked above for further help. 253s 253s Original error was: No module named 'numpy.core._multiarray_umath' 253s 253s 253s The above exception was the direct cause of the following exception: 253s 253s Traceback (most recent call last): 253s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 253s module = __import__(module_name) 253s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 253s import numpy as np 253s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 253s raise ImportError(msg) from e 253s ImportError: Error importing numpy: you should not try to import numpy from 253s its source directory; please exit the numpy source tree, and relaunch 253s your python interpreter from there. 253s 253s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 253s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 253s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 253s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 253s 254s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 254s 254s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 254s 254s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 254s 254s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 254s 254s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 254s 254s test_Application ... ok 254s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 254s 255s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_Blast_Record ... loading tests failed: 255s Failed to import test module: test_Blast_Record 255s Traceback (most recent call last): 255s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 255s from . import multiarray 255s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 255s from . import overrides 255s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 255s from numpy.core._multiarray_umath import ( 255s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 255s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 255s 255s During handling of the above exception, another exception occurred: 255s 255s Traceback (most recent call last): 255s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 255s from numpy.__config__ import show as show_config 255s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 255s from numpy.core._multiarray_umath import ( 255s ...<3 lines>... 255s ) 255s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 255s raise ImportError(msg) 255s ImportError: 255s 255s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 255s 255s Importing the numpy C-extensions failed. This error can happen for 255s many reasons, often due to issues with your setup or how NumPy was 255s installed. 255s 255s We have compiled some common reasons and troubleshooting tips at: 255s 255s https://numpy.org/devdocs/user/troubleshooting-importerror.html 255s 255s Please note and check the following: 255s 255s * The Python version is: Python3.13 from "/usr/bin/python3.13" 255s * The NumPy version is: "1.26.4" 255s 255s and make sure that they are the versions you expect. 255s Please carefully study the documentation linked above for further help. 255s 255s Original error was: No module named 'numpy.core._multiarray_umath' 255s 255s 255s The above exception was the direct cause of the following exception: 255s 255s Traceback (most recent call last): 255s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 255s module = __import__(module_name) 255s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 255s from Bio.Blast.NCBIXML import HSP 255s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 255s import numpy as np 255s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 255s raise ImportError(msg) from e 255s ImportError: Error importing numpy: you should not try to import numpy from 255s its source directory; please exit the numpy source tree, and relaunch 255s your python interpreter from there. 255s 255s test_Blast_parser ... loading tests failed: 255s Failed to import test module: test_Blast_parser 255s Traceback (most recent call last): 255s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 255s from . import multiarray 255s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 255s from . import overrides 255s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 255s from numpy.core._multiarray_umath import ( 255s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 255s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 255s 255s During handling of the above exception, another exception occurred: 255s 255s Traceback (most recent call last): 255s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 255s from numpy.__config__ import show as show_config 255s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 255s from numpy.core._multiarray_umath import ( 255s ...<3 lines>... 255s ) 255s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 255s raise ImportError(msg) 255s ImportError: 255s 255s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 255s 255s Importing the numpy C-extensions failed. This error can happen for 255s many reasons, often due to issues with your setup or how NumPy was 255s installed. 255s 255s We have compiled some common reasons and troubleshooting tips at: 255s 255s https://numpy.org/devdocs/user/troubleshooting-importerror.html 255s 255s Please note and check the following: 255s 255s * The Python version is: Python3.13 from "/usr/bin/python3.13" 255s * The NumPy version is: "1.26.4" 255s 255s and make sure that they are the versions you expect. 255s Please carefully study the documentation linked above for further help. 255s 255s Original error was: No module named 'numpy.core._multiarray_umath' 255s 255s 255s The above exception was the direct cause of the following exception: 255s 255s Traceback (most recent call last): 255s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 255s module = __import__(module_name) 255s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 255s import numpy as np 255s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 255s raise ImportError(msg) from e 255s ImportError: Error importing numpy: you should not try to import numpy from 255s its source directory; please exit the numpy source tree, and relaunch 255s your python interpreter from there. 255s 255s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_Chi2 ... /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131: BiopythonWarning: Import of C module failed (cannot import name 'cnexus' from 'Bio.Nexus' (/usr/lib/python3/dist-packages/Bio/Nexus/__init__.py)). Falling back to slow Python implementation 255s warnings.warn( 255s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 255s 255s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 255s 255s test_CodonTable ... ok 255s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 255s 256s test_Compass ... ok 256s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 256s 256s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 256s 256s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 256s 256s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 256s 256s test_EmbossPrimer ... ok 260s test_Entrez ... ok 260s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 260s 261s test_Entrez_parser ... ok 261s test_Enzyme ... ok 261s test_ExPASy ... skipping. internet not available 261s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 261s 261s test_File ... ok 261s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 261s 261s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 261s 261s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 261s 261s test_GraphicsDistribution ... loading tests failed: 261s Failed to import test module: test_GraphicsDistribution 261s Traceback (most recent call last): 261s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 261s module = __import__(module_name) 261s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 261s from Bio.Graphics.Distribution import BarChartDistribution 261s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 261s from reportlab.graphics.charts.barcharts import BarChartProperties 261s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 261s from reportlab.lib import colors 261s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 261s from reportlab.lib.rl_accel import fp_str 261s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 261s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 261s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 261s from PIL import Image 261s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 261s from . import _imaging as core 261s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 261s 261s test_GraphicsGeneral ... loading tests failed: 261s Failed to import test module: test_GraphicsGeneral 261s Traceback (most recent call last): 261s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 261s module = __import__(module_name) 261s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 261s from Bio.Graphics.Comparative import ComparativeScatterPlot 261s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 261s from reportlab.graphics.charts.lineplots import LinePlot 261s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 261s from reportlab.lib import colors 261s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 261s from reportlab.lib.rl_accel import fp_str 261s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 261s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 261s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 261s from PIL import Image 261s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 261s from . import _imaging as core 261s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 261s 262s test_HMMCasino ... ok 262s test_HMMGeneral ... ok 262s test_KEGG ... ok 262s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 262s 262s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 262s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 263s test_KGML_nographics ... ok 263s test_KeyWList ... ok 263s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 263s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 263s 263s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 263s 263s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 263s 263s test_Medline ... ok 263s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 263s 263s test_NCBIXML ... loading tests failed: 263s Failed to import test module: test_NCBIXML 263s Traceback (most recent call last): 263s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 263s from . import multiarray 263s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 263s from . import overrides 263s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 263s from numpy.core._multiarray_umath import ( 263s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 263s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 263s 263s During handling of the above exception, another exception occurred: 263s 263s Traceback (most recent call last): 263s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 263s from numpy.__config__ import show as show_config 263s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 263s from numpy.core._multiarray_umath import ( 263s ...<3 lines>... 263s ) 263s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 263s raise ImportError(msg) 263s ImportError: 263s 263s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 263s 263s Importing the numpy C-extensions failed. This error can happen for 263s many reasons, often due to issues with your setup or how NumPy was 263s installed. 263s 263s We have compiled some common reasons and troubleshooting tips at: 263s 263s https://numpy.org/devdocs/user/troubleshooting-importerror.html 263s 263s Please note and check the following: 263s 263s * The Python version is: Python3.13 from "/usr/bin/python3.13" 263s * The NumPy version is: "1.26.4" 263s 263s and make sure that they are the versions you expect. 263s Please carefully study the documentation linked above for further help. 263s 263s Original error was: No module named 'numpy.core._multiarray_umath' 263s 263s 263s The above exception was the direct cause of the following exception: 263s 263s Traceback (most recent call last): 263s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 263s module = __import__(module_name) 263s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 263s from Bio.Blast import NCBIXML 263s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 263s import numpy as np 263s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 263s raise ImportError(msg) from e 263s ImportError: Error importing numpy: you should not try to import numpy from 263s its source directory; please exit the numpy source tree, and relaunch 263s your python interpreter from there. 263s 264s test_NCBI_BLAST_tools ... loading tests failed: 264s Failed to import test module: test_NCBI_BLAST_tools 264s Traceback (most recent call last): 264s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 264s from . import multiarray 264s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 264s from . import overrides 264s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 264s from numpy.core._multiarray_umath import ( 264s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 264s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 264s 264s During handling of the above exception, another exception occurred: 264s 264s Traceback (most recent call last): 264s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 264s from numpy.__config__ import show as show_config 264s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 264s from numpy.core._multiarray_umath import ( 264s ...<3 lines>... 264s ) 264s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 264s raise ImportError(msg) 264s ImportError: 264s 264s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 264s 264s Importing the numpy C-extensions failed. This error can happen for 264s many reasons, often due to issues with your setup or how NumPy was 264s installed. 264s 264s We have compiled some common reasons and troubleshooting tips at: 264s 264s https://numpy.org/devdocs/user/troubleshooting-importerror.html 264s 264s Please note and check the following: 264s 264s * The Python version is: Python3.13 from "/usr/bin/python3.13" 264s * The NumPy version is: "1.26.4" 264s 264s and make sure that they are the versions you expect. 264s Please carefully study the documentation linked above for further help. 264s 264s Original error was: No module named 'numpy.core._multiarray_umath' 264s 264s 264s The above exception was the direct cause of the following exception: 264s 264s Traceback (most recent call last): 264s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 264s module = __import__(module_name) 264s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 264s from Bio.Blast import Applications 264s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 264s import numpy as np 264s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 264s raise ImportError(msg) from e 264s ImportError: Error importing numpy: you should not try to import numpy from 264s its source directory; please exit the numpy source tree, and relaunch 264s your python interpreter from there. 264s 264s test_NCBI_qblast ... loading tests failed: 264s Failed to import test module: test_NCBI_qblast 264s Traceback (most recent call last): 264s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 264s from . import multiarray 264s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 264s from . import overrides 264s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 264s from numpy.core._multiarray_umath import ( 264s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 264s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 264s 264s During handling of the above exception, another exception occurred: 264s 264s Traceback (most recent call last): 264s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 264s from numpy.__config__ import show as show_config 264s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 264s from numpy.core._multiarray_umath import ( 264s ...<3 lines>... 264s ) 264s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 264s raise ImportError(msg) 264s ImportError: 264s 264s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 264s 264s Importing the numpy C-extensions failed. This error can happen for 264s many reasons, often due to issues with your setup or how NumPy was 264s installed. 264s 264s We have compiled some common reasons and troubleshooting tips at: 264s 264s https://numpy.org/devdocs/user/troubleshooting-importerror.html 264s 264s Please note and check the following: 264s 264s * The Python version is: Python3.13 from "/usr/bin/python3.13" 264s * The NumPy version is: "1.26.4" 264s 264s and make sure that they are the versions you expect. 264s Please carefully study the documentation linked above for further help. 264s 264s Original error was: No module named 'numpy.core._multiarray_umath' 264s 264s 264s The above exception was the direct cause of the following exception: 264s 264s Traceback (most recent call last): 264s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 264s module = __import__(module_name) 264s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 264s from Bio.Blast import NCBIWWW 264s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 264s import numpy as np 264s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 264s raise ImportError(msg) from e 264s ImportError: Error importing numpy: you should not try to import numpy from 264s its source directory; please exit the numpy source tree, and relaunch 264s your python interpreter from there. 264s 264s test_NMR ... ok 264s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 264s 264s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 264s 264s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 264s 264s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 264s 264s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 264s 264s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 264s 264s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 264s 264s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 264s 264s test_PDB_Disordered ... loading tests failed: 264s Failed to import test module: test_PDB_Disordered 264s Traceback (most recent call last): 264s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 264s from . import multiarray 264s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 264s from . import overrides 264s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 264s from numpy.core._multiarray_umath import ( 264s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 264s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 264s 264s During handling of the above exception, another exception occurred: 264s 264s Traceback (most recent call last): 264s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 264s from numpy.__config__ import show as show_config 264s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 264s from numpy.core._multiarray_umath import ( 264s ...<3 lines>... 264s ) 264s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 264s raise ImportError(msg) 264s ImportError: 264s 264s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 264s 264s Importing the numpy C-extensions failed. This error can happen for 264s many reasons, often due to issues with your setup or how NumPy was 264s installed. 264s 264s We have compiled some common reasons and troubleshooting tips at: 264s 264s https://numpy.org/devdocs/user/troubleshooting-importerror.html 264s 264s Please note and check the following: 264s 264s * The Python version is: Python3.13 from "/usr/bin/python3.13" 264s * The NumPy version is: "1.26.4" 264s 264s and make sure that they are the versions you expect. 264s Please carefully study the documentation linked above for further help. 264s 264s Original error was: No module named 'numpy.core._multiarray_umath' 264s 264s 264s The above exception was the direct cause of the following exception: 264s 264s Traceback (most recent call last): 264s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 264s module = __import__(module_name) 264s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 264s import numpy as np 264s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 264s raise ImportError(msg) from e 264s ImportError: Error importing numpy: you should not try to import numpy from 264s its source directory; please exit the numpy source tree, and relaunch 264s your python interpreter from there. 264s 264s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 264s 264s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 264s 265s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 265s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 265s 265s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 265s 265s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 265s 265s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 265s 265s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 265s 265s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 265s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 265s 265s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 265s 266s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 266s 266s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 266s 266s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 266s 266s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 266s 266s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 266s 266s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 266s 266s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 266s 266s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 266s 266s test_Pathway ... ok 266s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 266s 266s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 266s 266s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 266s 266s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 266s 266s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 266s 267s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 267s 267s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 267s 267s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 267s 267s test_PopGen_GenePop_nodepend ... ok 267s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 267s 267s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 267s 267s test_ProtParam ... ok 267s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 267s 267s test_Restriction ... ok 267s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 267s 267s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 267s 268s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 268s 268s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 268s 268s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 268s 268s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 268s 268s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 268s 268s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 268s 268s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 268s 268s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 268s 268s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 268s 268s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 268s 268s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 268s 268s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 268s 269s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 269s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 269s 270s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 270s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 270s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 270s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 270s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 270s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 270s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 270s 270s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 270s 271s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 271s 271s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 271s 271s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 271s 271s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 271s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 271s 272s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 272s 272s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 272s 272s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 272s 272s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 272s 272s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 272s 273s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 273s 273s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 273s 273s test_UniGene ... ok 273s test_UniProt ... skipping. internet not available 273s test_UniProt_GOA ... ok 273s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 273s 273s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 273s 273s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 276s test_bgzf ... ok 276s test_cellosaurus ... ok 276s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 276s 276s test_geo ... ok 276s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 276s 276s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 276s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 276s 276s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 276s 277s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 277s 277s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 277s 277s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 277s 277s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 277s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 277s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 277s 277s test_prodoc ... ok 277s test_prosite ... ok 277s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 277s 278s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 278s test_seq ... ok 278s test_translate ... ok 278s ---------------------------------------------------------------------- 278s Ran 217 tests in 26.492 seconds 278s 278s FAILED (failures = 15) 278s Skipping any tests requiring internet access 278s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 278s Operating system: posix linux 279s test_Ace ... ok 279s test_Affy ... ok 282s test_AlignIO ... ok 282s test_AlignIO_ClustalIO ... ok 282s test_AlignIO_EmbossIO ... ok 282s test_AlignIO_FastaIO ... ok 282s test_AlignIO_MauveIO ... ok 282s test_AlignIO_PhylipIO ... ok 282s test_AlignIO_convert ... ok 282s test_AlignInfo ... ok 282s test_Align_Alignment ... ok 282s test_Align_a2m ... ok 282s test_Align_bed ... ok 283s test_Align_bigbed ... ok 283s test_Align_bigmaf ... ok 284s test_Align_bigpsl ... ok 284s test_Align_chain ... ok 284s test_Align_clustal ... ok 287s test_Align_codonalign ... ok 288s test_Align_emboss ... ok 288s test_Align_exonerate ... ok 288s test_Align_fasta ... ok 288s test_Align_hhr ... ok 289s test_Align_maf ... ok 289s test_Align_mauve ... ok 289s test_Align_msf ... ok 289s test_Align_nexus ... ok 289s test_Align_phylip ... ok 290s test_Align_psl ... ok 290s test_Align_sam ... ok 292s test_Align_stockholm ... ok 293s test_Align_tabular ... ok 293s test_Application ... ok 293s test_BioSQL_MySQLdb_online ... skipping. internet not available 293s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 293s test_BioSQL_mysql_connector_online ... skipping. internet not available 293s test_BioSQL_psycopg2_online ... skipping. internet not available 299s test_BioSQL_sqlite3 ... ok 299s test_BioSQL_sqlite3_online ... skipping. internet not available 299s test_Blast_Record ... ok 300s test_Blast_parser ... ok 300s test_CAPS ... ok 300s test_Chi2 ... ok 300s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 301s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 301s test_Cluster ... ok 301s test_CodonTable ... ok 301s test_ColorSpiral ... ok 301s test_Compass ... ok 302s test_Consensus ... ok 303s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 303s test_EMBL_unittest ... ok 303s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 303s test_EmbossPrimer ... ok 307s test_Entrez ... ok 307s test_Entrez_online ... skipping. internet not available 308s test_Entrez_parser ... ok 308s test_Enzyme ... ok 308s test_ExPASy ... skipping. internet not available 308s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 308s test_File ... ok 309s test_GenBank ... ok 311s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 313s ok 314s test_GraphicsChromosome ... ok 314s test_GraphicsDistribution ... ok 315s test_GraphicsGeneral ... ok 316s test_HMMCasino ... ok 316s test_HMMGeneral ... ok 316s test_KEGG ... ok 316s test_KEGG_online ... skipping. internet not available 323s test_KGML_graphics ... ok 323s test_KGML_graphics_online ... skipping. internet not available 325s test_KGML_nographics ... ok 325s test_KeyWList ... ok 325s test_LogisticRegression ... ok 326s test_MafIO_index ... ok 326s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 326s test_MarkovModel ... ok 326s test_Medline ... ok 326s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 328s test_NCBIXML ... ok 328s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 328s test_NCBI_qblast ... ok 328s test_NMR ... ok 328s test_NaiveBayes ... ok 328s test_Nexus ... ok 328s test_PAML_baseml ... ok 329s test_PAML_codeml ... ok 329s test_PAML_yn00 ... ok 333s test_PDB_CEAligner ... ok 333s test_PDB_DSSP ... ok 333s test_PDB_Dice ... ok 333s test_PDB_Disordered ... ok 334s test_PDB_Exposure ... ok 334s test_PDB_FragmentMapper ... ok 336s test_PDB_KDTree ... ok 336s test_PDB_MMCIF2Dict ... ok 336s test_PDB_MMCIFIO ... ok 338s test_PDB_MMCIFParser ... ok 338s test_PDB_NACCESS ... ok 338s test_PDB_PDBIO ... ok 339s test_PDB_PDBList ... skipping. internet not available 347s test_PDB_PDBMLParser ... ok 348s test_PDB_PDBParser ... ok 348s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 348s test_PDB_Polypeptide ... ok 348s test_PDB_QCPSuperimposer ... ok 352s test_PDB_SASA ... ok 353s test_PDB_SMCRA ... ok 353s test_PDB_Selection ... ok 353s test_PDB_StructureAlignment ... ok 353s test_PDB_Superimposer ... ok 353s test_PDB_alphafold_db ... skipping. internet not available 353s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 353s 353s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 353s 353s test_PDB_parse_pdb_header ... ok 354s test_PDB_vectors ... ok 354s test_PQR ... ok 354s test_Pathway ... ok 354s test_Phd ... ok 354s test_Phylo ... ok 355s test_PhyloXML ... ok 355s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 355s test_Phylo_NeXML ... ok 355s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 355s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 355s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 355s test_PopGen_GenePop_nodepend ... ok 355s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 355s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 355s test_ProtParam ... ok 356s test_RCSBFormats ... ok 356s test_Restriction ... ok 356s test_SCOP_Astral ... ok 356s test_SCOP_Cla ... ok 356s test_SCOP_Des ... ok 356s test_SCOP_Dom ... ok 356s test_SCOP_Hie ... ok 356s test_SCOP_Raf ... ok 357s test_SCOP_Residues ... ok 357s test_SCOP_Scop ... ok 357s test_SVDSuperimposer ... ok 357s test_SearchIO_blast_tab ... ok 357s test_SearchIO_blast_tab_index ... ok 357s test_SearchIO_blast_xml ... ok 358s test_SearchIO_blast_xml_index ... ok 358s test_SearchIO_blat_psl ... ok 359s test_SearchIO_blat_psl_index ... ok 359s test_SearchIO_exonerate ... ok 359s test_SearchIO_exonerate_text_index ... ok 359s test_SearchIO_exonerate_vulgar_index ... ok 359s test_SearchIO_fasta_m10 ... ok 359s test_SearchIO_fasta_m10_index ... ok 359s test_SearchIO_hhsuite2_text ... ok 360s test_SearchIO_hmmer2_text ... ok 360s test_SearchIO_hmmer2_text_index ... ok 360s test_SearchIO_hmmer3_domtab ... ok 360s test_SearchIO_hmmer3_domtab_index ... ok 360s test_SearchIO_hmmer3_tab ... ok 360s test_SearchIO_hmmer3_tab_index ... ok 360s test_SearchIO_hmmer3_text ... ok 360s test_SearchIO_hmmer3_text_index ... ok 360s test_SearchIO_interproscan_xml ... ok 361s test_SearchIO_model ... ok 361s test_SearchIO_write ... ok 361s test_SeqFeature ... ok 379s test_SeqIO ... ok 379s test_SeqIO_AbiIO ... ok 379s test_SeqIO_FastaIO ... ok 379s test_SeqIO_Gck ... ok 379s test_SeqIO_Gfa ... ok 379s test_SeqIO_Insdc ... ok 379s test_SeqIO_NibIO ... ok 382s test_SeqIO_PdbIO ... ok 382s test_SeqIO_QualityIO ... ok 382s test_SeqIO_SeqXML ... ok 382s test_SeqIO_SnapGene ... ok 383s test_SeqIO_TwoBitIO ... ok 383s test_SeqIO_Xdna ... ok 384s test_SeqIO_features ... ok 400s test_SeqIO_index ... ok 400s test_SeqIO_online ... skipping. internet not available 400s test_SeqIO_write ... ok 400s test_SeqRecord ... ok 400s test_SeqUtils ... ok 401s test_Seq_objs ... ok 401s test_SffIO ... ok 402s test_SwissProt ... ok 402s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 402s test_TogoWS ... skipping. internet not available 402s test_TreeConstruction ... ok 402s test_UniGene ... ok 402s test_UniProt ... skipping. internet not available 402s test_UniProt_GOA ... ok 403s test_UniProt_Parser ... ok 403s test_align ... ok 403s test_align_substitution_matrices ... ok 405s test_bgzf ... ok 405s test_cellosaurus ... ok 410s test_codonalign ... ok 410s test_geo ... ok 410s test_kNN ... ok 410s test_motifs ... ok 417s test_motifs_online ... skipping. internet not available 417s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 417s warnings.warn( 417s ok 417s test_pairwise2_no_C ... ok 418s test_pairwise_aligner ... ok 418s test_pairwise_alignment_map ... ok 418s test_phenotype ... ok 418s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 418s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 418s test_prodoc ... ok 419s test_prosite ... ok 419s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 419s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 419s test_seq ... ok 419s test_translate ... ok 419s ---------------------------------------------------------------------- 419s Ran 217 tests in 140.340 seconds 419s 419s Skipping any tests requiring internet access 419s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 419s Operating system: posix linux 420s autopkgtest [10:42:01]: test dependencies: -----------------------] 422s autopkgtest [10:42:02]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 422s dependencies PASS 422s autopkgtest [10:42:03]: test full_suite: preparing testbed 547s autopkgtest [10:44:08]: testbed dpkg architecture: arm64 547s autopkgtest [10:44:08]: testbed apt version: 2.9.8 547s autopkgtest [10:44:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 548s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 548s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 548s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 549s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 549s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 549s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 549s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 549s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 549s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 549s Fetched 1794 kB in 1s (2248 kB/s) 549s Reading package lists... 552s Reading package lists... 552s Building dependency tree... 552s Reading state information... 553s Calculating upgrade... 553s The following NEW packages will be installed: 553s python3.13-gdbm 553s The following packages will be upgraded: 553s libpython3-stdlib python3 python3-gdbm python3-minimal 554s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 554s Need to get 101 kB of archives. 554s After this operation, 141 kB of additional disk space will be used. 554s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 554s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 554s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 554s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 554s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 554s Fetched 101 kB in 0s (287 kB/s) 555s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 555s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 555s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 555s Setting up python3-minimal (3.12.7-1) ... 555s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 555s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 555s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 555s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 555s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 555s Selecting previously unselected package python3.13-gdbm. 555s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 555s Unpacking python3.13-gdbm (3.13.0-2) ... 555s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 555s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 555s Setting up python3.13-gdbm (3.13.0-2) ... 555s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 555s Setting up python3 (3.12.7-1) ... 556s Setting up python3-gdbm:arm64 (3.12.7-1) ... 556s Processing triggers for man-db (2.12.1-3) ... 557s Reading package lists... 557s Building dependency tree... 557s Reading state information... 558s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 559s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 559s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 559s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 559s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 560s Reading package lists... 560s Reading package lists... 560s Building dependency tree... 560s Reading state information... 561s Calculating upgrade... 562s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 562s Reading package lists... 562s Building dependency tree... 562s Reading state information... 563s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 570s Reading package lists... 571s Building dependency tree... 571s Reading state information... 571s Starting pkgProblemResolver with broken count: 0 571s Starting 2 pkgProblemResolver with broken count: 0 571s Done 572s The following additional packages will be installed: 572s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 572s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 572s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 572s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 572s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 572s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 572s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 572s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 572s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 572s intltool-debian libaom3 libapache-pom-java libarchive-zip-perl 572s libargtable2-0 libasan8 libavahi-client3 libavahi-common-data 572s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 572s libcommons-logging-java libcommons-parent-java libcups2t64 libde265-0 572s libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 572s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 572s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 572s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 572s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 572s libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 572s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 572s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 572s liblerc4 liblqr-1-0 liblsan0 libltdl7 libmagickcore-6.q16-7t64 572s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 572s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 572s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libpq5 libptexenc1 572s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.13 572s libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 572s libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 572s libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 572s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 572s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 572s libxt6t64 libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm 572s phylip po-debconf poppler-data prank preview-latex-style probcons 572s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 572s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 572s python3-brotli python3-cairo python3-contourpy python3-cycler 572s python3-dateutil python3-decorator python3-defusedxml python3-dev 572s python3-docutils python3-fonttools python3-freetype python3-fs 572s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 572s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 572s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 572s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 572s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 572s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 572s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 572s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 572s python3.13-dev python3.13-minimal python3.13-tk sgml-base sphinx-common 572s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 572s texlive-binaries texlive-fonts-recommended texlive-latex-base 572s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 572s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 572s xfonts-encodings xfonts-utils xml-core zlib1g-dev 572s Suggested packages: 572s autoconf-archive gnu-standards autoconf-doc blt-demo samtools cpp-doc 572s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 572s python3-wheel emboss-doc emboss-test embassy clustalw bison flex-doc 572s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-14-doc 572s gcc-multilib manpages-dev gdb gcc-doc gdb-aarch64-linux-gnu gettext-doc 572s libasprintf-dev libgettextpo-dev hevea-doc imagemagick-6-doc autotrace 572s cups-bsd | lpr | lprng enscript ffmpeg gimp gnuplot grads graphviz hp2xx 572s html2ps libwmf-bin mplayer povray radiance sane-utils transfig libraw-bin 572s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 572s cups-common libfftw3-bin libfftw3-dev libgd-tools libheif-plugin-x265 572s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 572s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 572s libheif-plugin-rav1e libheif-plugin-svtenc libjs-jquery-ui-docs 572s liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc libstdc++-14-doc 572s tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 572s phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho 572s | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic 572s fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra muscle3 572s phyml python3-psycopg2 raxml python-cycler-doc docutils-doc 572s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 572s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 572s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 572s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 572s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 572s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 572s gfortran python-numpy-doc python3-pytest python-pil-doc python-rdflib-doc 572s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 572s rl-renderpm python-scipy-doc python3-stemmer dvisvgm fonts-freefont-otf 572s latexmk libjs-mathjax sphinx-doc tex-gyre texlive-fonts-extra 572s texlive-plain-generic python-sympy-doc tix python3-tk-dbg python3.13-venv 572s python3.13-doc binfmt-support sgml-base-doc boxshade seaview 572s t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 572s hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex 572s icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science 572s texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex 572s texlive-pictures-doc vprerex wise-doc 572s Recommended packages: 572s primer3 libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 572s fonts-droid-fallback libheif-plugin-aomenc javascript-common libjson-xs-perl 572s libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 572s python3-cssselect python3-html5lib python3-olefile python3-sparqlwrapper 572s fonts-dejavu-extra isympy-common amap-align clustalw dialign-tx fsa kalign 572s libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align 572s lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 572s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 572s libx11-protocol-perl x11-utils x11-xserver-utils 573s The following NEW packages will be installed: 573s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 573s build-essential bwa clustalo cpp cpp-14 cpp-14-aarch64-linux-gnu 573s cpp-aarch64-linux-gnu debhelper debugedit dh-autoreconf dh-python 573s dh-strip-nondeterminism dialign docutils-common dssp dwz emboss emboss-data 573s emboss-lib fasttree flex fontconfig-config fonts-dejavu-core 573s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 573s fonts-urw-base35 g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu 573s gcc gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext 573s ghostscript hevea hicolor-icon-theme imagemagick imagemagick-6-common 573s imagemagick-6.q16 intltool-debian libaom3 libapache-pom-java 573s libarchive-zip-perl libargtable2-0 libasan8 libavahi-client3 573s libavahi-common-data libavahi-common3 libblas3 libcairo2 libcc1-0 573s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 573s libcups2t64 libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev 573s libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java 573s libfontconfig1 libfontenc1 libgcc-14-dev libgd3 libgfortran5 libgomp1 573s libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b 573s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libhpdf-2.3.0 573s libhwasan0 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 573s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 573s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 573s liblbfgsb0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 573s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 573s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmysqlclient21 573s libnetpbm11t64 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java 573s libpixman-1-0 libpotrace0 libpq5 libptexenc1 libpython3-all-dev 573s libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev 573s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 573s libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 573s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 573s libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 573s libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 573s libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip 573s po-debconf poppler-data prank preview-latex-style probcons 573s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 573s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 573s python3-brotli python3-cairo python3-contourpy python3-cycler 573s python3-dateutil python3-decorator python3-defusedxml python3-dev 573s python3-docutils python3-fonttools python3-freetype python3-fs 573s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 573s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 573s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 573s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 573s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 573s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 573s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 573s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 573s python3.13-dev python3.13-minimal python3.13-tk sgml-base sphinx-common 573s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 573s texlive-binaries texlive-fonts-recommended texlive-latex-base 573s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 573s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 573s xfonts-encodings xfonts-utils xml-core zlib1g-dev 573s 0 upgraded, 260 newly installed, 0 to remove and 0 not upgraded. 573s Need to get 403 MB/403 MB of archives. 573s After this operation, 1818 MB of additional disk space will be used. 573s Get:1 /tmp/autopkgtest.qKkx58/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [1000 B] 573s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 573s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 flex arm64 2.6.4-8.2build1 [291 kB] 573s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 573s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 573s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu4 [392 kB] 573s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 573s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 573s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 573s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 573s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 573s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 573s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 574s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 574s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 574s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 574s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libaom3 arm64 3.11.0~rc1-1 [1837 kB] 574s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-aomdec arm64 1.18.1-2 [10.9 kB] 574s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libde265-0 arm64 1.0.15-1build4 [146 kB] 574s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-libde265 arm64 1.18.1-2 [8612 B] 574s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif1 arm64 1.18.1-2 [274 kB] 574s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 574s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 574s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 574s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 574s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblqr-1-0 arm64 0.4.2-2.1build2 [27.1 kB] 574s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB] 574s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 574s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libraw23t64 arm64 0.21.3-1 [377 kB] 574s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 574s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 574s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 574s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 574s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 574s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 574s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 574s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmagickcore-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1build1 [1760 kB] 574s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmagickwand-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1build1 [276 kB] 574s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 poppler-data all 0.4.12-1 [2060 kB] 574s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 574s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 574s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 574s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 574s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 574s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 574s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 574s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 574s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 574s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 574s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 574s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 574s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 574s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 574s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 574s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 574s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 575s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 575s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 575s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 575s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 575s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 575s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 575s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 575s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 575s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 575s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 575s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 575s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 575s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 575s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 575s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 575s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 575s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 576s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 576s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 576s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 576s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 576s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 bwa arm64 0.7.18-1 [201 kB] 576s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 libargtable2-0 arm64 13-2 [14.7 kB] 576s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 clustalo arm64 1.2.4-8build1 [190 kB] 576s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 576s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 576s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 576s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 576s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 576s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 576s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 576s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 576s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 576s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 576s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 576s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 576s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 576s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 dialign arm64 2.2.1-13 [152 kB] 576s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 576s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 576s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcifpp-data all 7.0.7-3 [480 kB] 576s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcifpp7 arm64 7.0.7-3 [994 kB] 576s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 dssp arm64 4.4.10-1 [753 kB] 576s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 576s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 576s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 576s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 576s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB] 576s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB] 576s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build3 [434 kB] 577s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 mysql-common all 5.8+1.1.1 [6800 B] 577s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libmysqlclient21 arm64 8.0.40-1 [1241 kB] 578s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libpq5 arm64 17.0-1 [248 kB] 578s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss-lib arm64 6.6.0+dfsg-12ubuntu2 [2853 kB] 578s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 579s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss arm64 6.6.0+dfsg-12ubuntu2 [934 kB] 579s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 579s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lmodern all 2.005-1 [4799 kB] 579s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 579s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 579s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 579s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-13ubuntu6 [29.6 kB] 579s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-13ubuntu6 [23.3 kB] 579s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-13ubuntu6 [27.2 kB] 579s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.10-1ubuntu2 [271 kB] 579s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libidn12 arm64 1.42-2 [56.9 kB] 579s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libijs-0.35 arm64 0.35-15.1build1 [15.3 kB] 579s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] 579s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB] 579s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 579s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 579s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 579s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs10 arm64 10.03.1~dfsg1-0ubuntu2 [3579 kB] 579s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 ghostscript arm64 10.03.1~dfsg1-0ubuntu2 [43.6 kB] 579s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetpbm11t64 arm64 2:11.08.01-1 [114 kB] 579s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 netpbm arm64 2:11.08.01-1 [2125 kB] 579s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 tex-common all 6.18 [32.8 kB] 579s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B] 579s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5 [64.1 kB] 579s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5 [41.6 kB] 579s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5 [60.1 kB] 579s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5 [122 kB] 579s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] 579s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 579s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 579s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 579s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 579s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmpfi0 arm64 1.5.4+ds-4 [35.3 kB] 579s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB] 579s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] 579s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 579s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libxaw7 arm64 2:1.0.16-1 [184 kB] 579s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 579s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2build1 [29.2 kB] 579s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-5 [8326 kB] 580s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 580s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-base all 2024.20241102-1 [22.5 MB] 580s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-1 [13.5 kB] 580s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick-6.q16 arm64 8:6.9.13.12+dfsg1-1build1 [254 kB] 580s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick arm64 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 580s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 hevea arm64 2.36-2 [2333 kB] 580s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 33-2 [5874 B] 580s Get:159 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 580s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 580s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 580s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.2-2 [128 kB] 580s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 580s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 580s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 580s Get:166 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 580s Get:167 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 580s Get:168 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 580s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 580s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 580s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedcrypto7t64 arm64 2.28.8-1 [209 kB] 580s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedx509-1t64 arm64 2.28.8-1 [47.2 kB] 580s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedtls14t64 arm64 2.28.8-1 [82.2 kB] 580s Get:174 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 580s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB] 581s Get:176 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-dev arm64 3.12.7-1 [10.3 kB] 581s Get:177 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 581s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13 arm64 3.13.0-2 [2262 kB] 581s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.0-2 [5386 kB] 581s Get:180 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-all-dev arm64 3.12.7-1 [916 B] 581s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 581s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 581s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 mafft arm64 7.505-1 [756 kB] 581s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 581s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6 [14.7 MB] 582s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 582s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 prank arm64 0.0.170427+dfsg-3 [325 kB] 582s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 preview-latex-style all 13.2-1 [347 kB] 582s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 probcons arm64 1.12-14 [129 kB] 582s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 583s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 583s Get:192 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 583s Get:193 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 583s Get:194 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] 583s Get:195 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-dev arm64 3.12.7-1 [26.7 kB] 583s Get:196 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.0-2 [507 kB] 583s Get:197 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all-dev arm64 3.12.7-1 [914 B] 583s Get:198 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 583s Get:199 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 583s Get:200 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 583s Get:201 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 583s Get:202 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 583s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 583s Get:204 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 583s Get:205 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 583s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 583s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 583s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 583s Get:209 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 583s Get:210 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 584s Get:211 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 584s Get:212 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 584s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 584s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 584s Get:215 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 584s Get:216 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 584s Get:217 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 584s Get:218 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB] 584s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 4.2-1 [10.0 kB] 584s Get:220 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 584s Get:221 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 585s Get:222 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 585s Get:223 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 585s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 585s Get:225 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 585s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 585s Get:227 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 585s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 585s Get:229 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 585s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 585s Get:231 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 585s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-isodate all 0.6.1-3 [24.3 kB] 585s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 585s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 585s Get:235 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 585s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build2 [77.9 kB] 585s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 585s Get:238 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-mysqldb arm64 1.4.6-2build3 [47.5 kB] 585s Get:239 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 585s Get:240 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 7.4.7-4 [775 kB] 585s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 585s Get:242 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 585s Get:243 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 7.4.7-4 [593 kB] 585s Get:244 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 585s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numpydoc all 1.6.0-2 [50.5 kB] 585s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rdflib all 7.0.0-1 [405 kB] 585s Get:247 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 585s Get:248 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 585s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 585s Get:250 http://ftpmaster.internal/ubuntu plucky/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [879 kB] 585s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 585s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-base all 2024.20241102-1 [1260 kB] 585s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 585s Get:254 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 585s Get:255 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-recommended all 2024.20241102-1 [8739 kB] 586s Get:256 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-pictures all 2024.20241102-1 [17.0 MB] 586s Get:257 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-extra all 2024.20241102-1 [24.2 MB] 587s Get:258 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise-data all 2.4.1-25 [83.0 kB] 587s Get:259 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise arm64 2.4.1-25 [802 kB] 587s Get:260 http://ftpmaster.internal/ubuntu plucky/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 587s Preconfiguring packages ... 587s Fetched 403 MB in 14s (28.6 MB/s) 587s Selecting previously unselected package m4. 587s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79931 files and directories currently installed.) 587s Preparing to unpack .../000-m4_1.4.19-4build1_arm64.deb ... 587s Unpacking m4 (1.4.19-4build1) ... 588s Selecting previously unselected package flex. 588s Preparing to unpack .../001-flex_2.6.4-8.2build1_arm64.deb ... 588s Unpacking flex (2.6.4-8.2build1) ... 588s Selecting previously unselected package fonts-lato. 588s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 588s Unpacking fonts-lato (2.015-1) ... 588s Selecting previously unselected package libgomp1:arm64. 588s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 588s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 588s Selecting previously unselected package libfftw3-double3:arm64. 588s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_arm64.deb ... 588s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu4) ... 588s Selecting previously unselected package fonts-dejavu-mono. 588s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 588s Unpacking fonts-dejavu-mono (2.37-8) ... 588s Selecting previously unselected package fonts-dejavu-core. 588s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 588s Unpacking fonts-dejavu-core (2.37-8) ... 588s Selecting previously unselected package libfontenc1:arm64. 588s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 588s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 588s Selecting previously unselected package x11-common. 588s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu3_all.deb ... 588s Unpacking x11-common (1:7.7+23ubuntu3) ... 588s Selecting previously unselected package xfonts-encodings. 588s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 588s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 588s Selecting previously unselected package xfonts-utils. 588s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_arm64.deb ... 588s Unpacking xfonts-utils (1:7.7+7) ... 588s Selecting previously unselected package fonts-urw-base35. 588s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 588s Unpacking fonts-urw-base35 (20200910-8) ... 588s Selecting previously unselected package fontconfig-config. 588s Preparing to unpack .../012-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 589s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 589s Selecting previously unselected package libfontconfig1:arm64. 589s Preparing to unpack .../013-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 589s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 589s Selecting previously unselected package libsharpyuv0:arm64. 589s Preparing to unpack .../014-libsharpyuv0_1.4.0-0.1_arm64.deb ... 589s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 589s Selecting previously unselected package libaom3:arm64. 589s Preparing to unpack .../015-libaom3_3.11.0~rc1-1_arm64.deb ... 589s Unpacking libaom3:arm64 (3.11.0~rc1-1) ... 589s Selecting previously unselected package libheif-plugin-aomdec:arm64. 589s Preparing to unpack .../016-libheif-plugin-aomdec_1.18.1-2_arm64.deb ... 589s Unpacking libheif-plugin-aomdec:arm64 (1.18.1-2) ... 589s Selecting previously unselected package libde265-0:arm64. 589s Preparing to unpack .../017-libde265-0_1.0.15-1build4_arm64.deb ... 589s Unpacking libde265-0:arm64 (1.0.15-1build4) ... 589s Selecting previously unselected package libheif-plugin-libde265:arm64. 589s Preparing to unpack .../018-libheif-plugin-libde265_1.18.1-2_arm64.deb ... 589s Unpacking libheif-plugin-libde265:arm64 (1.18.1-2) ... 589s Selecting previously unselected package libheif1:arm64. 589s Preparing to unpack .../019-libheif1_1.18.1-2_arm64.deb ... 589s Unpacking libheif1:arm64 (1.18.1-2) ... 589s Selecting previously unselected package libjbig0:arm64. 589s Preparing to unpack .../020-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 589s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 589s Selecting previously unselected package libjpeg-turbo8:arm64. 589s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 589s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 589s Selecting previously unselected package libjpeg8:arm64. 589s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_arm64.deb ... 589s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 589s Selecting previously unselected package liblcms2-2:arm64. 589s Preparing to unpack .../023-liblcms2-2_2.16-2_arm64.deb ... 589s Unpacking liblcms2-2:arm64 (2.16-2) ... 589s Selecting previously unselected package liblqr-1-0:arm64. 589s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_arm64.deb ... 589s Unpacking liblqr-1-0:arm64 (0.4.2-2.1build2) ... 589s Selecting previously unselected package libltdl7:arm64. 589s Preparing to unpack .../025-libltdl7_2.4.7-7build1_arm64.deb ... 589s Unpacking libltdl7:arm64 (2.4.7-7build1) ... 589s Selecting previously unselected package libopenjp2-7:arm64. 589s Preparing to unpack .../026-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 589s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 589s Selecting previously unselected package libraw23t64:arm64. 589s Preparing to unpack .../027-libraw23t64_0.21.3-1_arm64.deb ... 589s Unpacking libraw23t64:arm64 (0.21.3-1) ... 589s Selecting previously unselected package libdeflate0:arm64. 589s Preparing to unpack .../028-libdeflate0_1.22-1_arm64.deb ... 589s Unpacking libdeflate0:arm64 (1.22-1) ... 589s Selecting previously unselected package liblerc4:arm64. 589s Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 589s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 589s Selecting previously unselected package libwebp7:arm64. 589s Preparing to unpack .../030-libwebp7_1.4.0-0.1_arm64.deb ... 589s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 589s Selecting previously unselected package libtiff6:arm64. 590s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 590s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 590s Selecting previously unselected package libwebpdemux2:arm64. 590s Preparing to unpack .../032-libwebpdemux2_1.4.0-0.1_arm64.deb ... 590s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 590s Selecting previously unselected package libwebpmux3:arm64. 590s Preparing to unpack .../033-libwebpmux3_1.4.0-0.1_arm64.deb ... 590s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 590s Selecting previously unselected package imagemagick-6-common. 590s Preparing to unpack .../034-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 590s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 590s Selecting previously unselected package libmagickcore-6.q16-7t64:arm64. 590s Preparing to unpack .../035-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 590s Unpacking libmagickcore-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1build1) ... 590s Selecting previously unselected package libmagickwand-6.q16-7t64:arm64. 590s Preparing to unpack .../036-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 590s Unpacking libmagickwand-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1build1) ... 590s Selecting previously unselected package poppler-data. 590s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 590s Unpacking poppler-data (0.4.12-1) ... 590s Selecting previously unselected package libpython3.13-minimal:arm64. 590s Preparing to unpack .../038-libpython3.13-minimal_3.13.0-2_arm64.deb ... 590s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 590s Selecting previously unselected package python3.13-minimal. 590s Preparing to unpack .../039-python3.13-minimal_3.13.0-2_arm64.deb ... 590s Unpacking python3.13-minimal (3.13.0-2) ... 590s Selecting previously unselected package sgml-base. 590s Preparing to unpack .../040-sgml-base_1.31_all.deb ... 590s Unpacking sgml-base (1.31) ... 590s Selecting previously unselected package autoconf. 590s Preparing to unpack .../041-autoconf_2.72-3_all.deb ... 590s Unpacking autoconf (2.72-3) ... 590s Selecting previously unselected package autotools-dev. 590s Preparing to unpack .../042-autotools-dev_20220109.1_all.deb ... 590s Unpacking autotools-dev (20220109.1) ... 590s Selecting previously unselected package automake. 590s Preparing to unpack .../043-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 590s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 590s Selecting previously unselected package autopoint. 590s Preparing to unpack .../044-autopoint_0.22.5-2_all.deb ... 590s Unpacking autopoint (0.22.5-2) ... 590s Selecting previously unselected package libtcl8.6:arm64. 590s Preparing to unpack .../045-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 590s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 590s Selecting previously unselected package libxrender1:arm64. 590s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 590s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 591s Selecting previously unselected package libxft2:arm64. 591s Preparing to unpack .../047-libxft2_2.3.6-1build1_arm64.deb ... 591s Unpacking libxft2:arm64 (2.3.6-1build1) ... 591s Selecting previously unselected package libxss1:arm64. 591s Preparing to unpack .../048-libxss1_1%3a1.2.3-1build3_arm64.deb ... 591s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 591s Selecting previously unselected package libtk8.6:arm64. 591s Preparing to unpack .../049-libtk8.6_8.6.15-1_arm64.deb ... 591s Unpacking libtk8.6:arm64 (8.6.15-1) ... 591s Selecting previously unselected package tk8.6-blt2.5. 591s Preparing to unpack .../050-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 591s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 591s Selecting previously unselected package blt. 591s Preparing to unpack .../051-blt_2.5.3+dfsg-7build1_arm64.deb ... 591s Unpacking blt (2.5.3+dfsg-7build1) ... 591s Selecting previously unselected package libisl23:arm64. 591s Preparing to unpack .../052-libisl23_0.27-1_arm64.deb ... 591s Unpacking libisl23:arm64 (0.27-1) ... 591s Selecting previously unselected package libmpc3:arm64. 591s Preparing to unpack .../053-libmpc3_1.3.1-1build2_arm64.deb ... 591s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 591s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 591s Preparing to unpack .../054-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 591s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 591s Selecting previously unselected package cpp-14. 591s Preparing to unpack .../055-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 591s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 591s Selecting previously unselected package cpp-aarch64-linux-gnu. 591s Preparing to unpack .../056-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 591s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 591s Selecting previously unselected package cpp. 591s Preparing to unpack .../057-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 591s Unpacking cpp (4:14.1.0-2ubuntu1) ... 591s Selecting previously unselected package libcc1-0:arm64. 591s Preparing to unpack .../058-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 591s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 591s Selecting previously unselected package libitm1:arm64. 591s Preparing to unpack .../059-libitm1_14.2.0-8ubuntu1_arm64.deb ... 591s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 591s Selecting previously unselected package libasan8:arm64. 591s Preparing to unpack .../060-libasan8_14.2.0-8ubuntu1_arm64.deb ... 591s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 591s Selecting previously unselected package liblsan0:arm64. 591s Preparing to unpack .../061-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 591s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package libtsan2:arm64. 592s Preparing to unpack .../062-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package libubsan1:arm64. 592s Preparing to unpack .../063-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package libhwasan0:arm64. 592s Preparing to unpack .../064-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package libgcc-14-dev:arm64. 592s Preparing to unpack .../065-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 592s Preparing to unpack .../066-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package gcc-14. 592s Preparing to unpack .../067-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 592s Selecting previously unselected package gcc-aarch64-linux-gnu. 592s Preparing to unpack .../068-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 592s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 592s Selecting previously unselected package gcc. 592s Preparing to unpack .../069-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 592s Unpacking gcc (4:14.1.0-2ubuntu1) ... 592s Selecting previously unselected package libstdc++-14-dev:arm64. 592s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 592s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 593s Selecting previously unselected package g++-14-aarch64-linux-gnu. 593s Preparing to unpack .../071-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 593s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 593s Selecting previously unselected package g++-14. 593s Preparing to unpack .../072-g++-14_14.2.0-8ubuntu1_arm64.deb ... 593s Unpacking g++-14 (14.2.0-8ubuntu1) ... 593s Selecting previously unselected package g++-aarch64-linux-gnu. 593s Preparing to unpack .../073-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 593s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 593s Selecting previously unselected package g++. 593s Preparing to unpack .../074-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 593s Unpacking g++ (4:14.1.0-2ubuntu1) ... 593s Selecting previously unselected package build-essential. 593s Preparing to unpack .../075-build-essential_12.10ubuntu1_arm64.deb ... 593s Unpacking build-essential (12.10ubuntu1) ... 593s Selecting previously unselected package bwa. 593s Preparing to unpack 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Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 593s Unpacking libarchive-zip-perl (1.68-1) ... 593s Selecting previously unselected package libfile-stripnondeterminism-perl. 593s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 593s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 593s Selecting previously unselected package dh-strip-nondeterminism. 594s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.0-1_all.deb ... 594s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 594s Selecting previously unselected package debugedit. 594s Preparing to unpack .../085-debugedit_1%3a5.1-1_arm64.deb ... 594s Unpacking debugedit (1:5.1-1) ... 594s Selecting previously unselected package dwz. 594s Preparing to unpack .../086-dwz_0.15-1build6_arm64.deb ... 594s Unpacking dwz (0.15-1build6) ... 594s Selecting previously unselected package gettext. 594s Preparing to unpack .../087-gettext_0.22.5-2_arm64.deb ... 594s Unpacking gettext (0.22.5-2) ... 594s Selecting previously unselected package intltool-debian. 594s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 594s Unpacking intltool-debian (0.35.0+20060710.6) ... 594s Selecting previously unselected package po-debconf. 594s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 594s Unpacking po-debconf (1.0.21+nmu1) ... 594s Selecting previously unselected package debhelper. 594s Preparing to unpack .../090-debhelper_13.20ubuntu1_all.deb ... 594s Unpacking debhelper (13.20ubuntu1) ... 594s Selecting previously unselected package dh-python. 594s Preparing to unpack .../091-dh-python_6.20241024_all.deb ... 594s Unpacking dh-python (6.20241024) ... 594s Selecting previously unselected package dialign. 594s Preparing to unpack .../092-dialign_2.2.1-13_arm64.deb ... 594s Unpacking dialign (2.2.1-13) ... 594s Selecting previously unselected package xml-core. 594s Preparing to unpack .../093-xml-core_0.19_all.deb ... 594s Unpacking xml-core (0.19) ... 594s Selecting previously unselected package docutils-common. 594s Preparing to unpack .../094-docutils-common_0.21.2+dfsg-2_all.deb ... 594s Unpacking docutils-common (0.21.2+dfsg-2) ... 594s Selecting previously unselected package libcifpp-data. 594s Preparing to unpack .../095-libcifpp-data_7.0.7-3_all.deb ... 594s Unpacking libcifpp-data (7.0.7-3) ... 594s Selecting previously unselected package libcifpp7:arm64. 594s Preparing to unpack .../096-libcifpp7_7.0.7-3_arm64.deb ... 594s Unpacking libcifpp7:arm64 (7.0.7-3) ... 594s Selecting previously unselected package dssp. 594s Preparing to unpack .../097-dssp_4.4.10-1_arm64.deb ... 594s Unpacking dssp (4.4.10-1) ... 594s Selecting previously unselected package libimagequant0:arm64. 594s Preparing to unpack .../098-libimagequant0_2.18.0-1build1_arm64.deb ... 594s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 594s Selecting previously unselected package libgraphite2-3:arm64. 594s Preparing to unpack .../099-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 594s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 594s Selecting previously unselected package libharfbuzz0b:arm64. 594s Preparing to unpack .../100-libharfbuzz0b_10.0.1-1_arm64.deb ... 594s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 594s Selecting previously unselected package libraqm0:arm64. 594s Preparing to unpack .../101-libraqm0_0.10.1-1build1_arm64.deb ... 594s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 594s Selecting previously unselected package libxpm4:arm64. 594s Preparing to unpack .../102-libxpm4_1%3a3.5.17-1build2_arm64.deb ... 594s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ... 594s Selecting previously unselected package libgd3:arm64. 594s Preparing to unpack .../103-libgd3_2.3.3-12ubuntu3_arm64.deb ... 594s Unpacking libgd3:arm64 (2.3.3-12ubuntu3) ... 595s Selecting previously unselected package libhpdf-2.3.0:arm64. 595s Preparing to unpack .../104-libhpdf-2.3.0_2.3.0+dfsg-1build3_arm64.deb ... 595s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 595s Selecting previously unselected package mysql-common. 595s Preparing to unpack .../105-mysql-common_5.8+1.1.1_all.deb ... 595s Unpacking mysql-common (5.8+1.1.1) ... 595s Selecting previously unselected package libmysqlclient21:arm64. 595s Preparing to unpack .../106-libmysqlclient21_8.0.40-1_arm64.deb ... 595s Unpacking libmysqlclient21:arm64 (8.0.40-1) ... 595s Selecting previously unselected package libpq5:arm64. 595s Preparing to unpack .../107-libpq5_17.0-1_arm64.deb ... 595s Unpacking libpq5:arm64 (17.0-1) ... 595s Selecting previously unselected package emboss-lib. 595s Preparing to unpack .../108-emboss-lib_6.6.0+dfsg-12ubuntu2_arm64.deb ... 595s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 595s Selecting previously unselected package emboss-data. 595s Preparing to unpack .../109-emboss-data_6.6.0+dfsg-12ubuntu2_all.deb ... 595s Unpacking emboss-data (6.6.0+dfsg-12ubuntu2) ... 598s Selecting previously unselected package emboss. 598s Preparing to unpack .../110-emboss_6.6.0+dfsg-12ubuntu2_arm64.deb ... 598s Unpacking emboss (6.6.0+dfsg-12ubuntu2) ... 598s Selecting previously unselected package fonts-font-awesome. 598s Preparing to unpack .../111-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 598s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 599s Selecting previously unselected package fonts-lmodern. 599s Preparing to unpack .../112-fonts-lmodern_2.005-1_all.deb ... 599s Unpacking fonts-lmodern (2.005-1) ... 599s Selecting previously unselected package fonts-lyx. 599s Preparing to unpack .../113-fonts-lyx_2.4.2.1-1_all.deb ... 599s Unpacking fonts-lyx (2.4.2.1-1) ... 599s Selecting previously unselected package libgs-common. 599s Preparing to unpack .../114-libgs-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 599s Unpacking libgs-common (10.03.1~dfsg1-0ubuntu2) ... 599s Selecting previously unselected package libgs10-common. 599s Preparing to unpack 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(2:1.2.4-1) ... 599s Selecting previously unselected package libxt6t64:arm64. 599s Preparing to unpack .../126-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 599s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 599s Selecting previously unselected package libgs10:arm64. 599s Preparing to unpack .../127-libgs10_10.03.1~dfsg1-0ubuntu2_arm64.deb ... 599s Unpacking libgs10:arm64 (10.03.1~dfsg1-0ubuntu2) ... 599s Selecting previously unselected package ghostscript. 599s Preparing to unpack .../128-ghostscript_10.03.1~dfsg1-0ubuntu2_arm64.deb ... 599s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu2) ... 599s Selecting previously unselected package libnetpbm11t64:arm64. 599s Preparing to unpack .../129-libnetpbm11t64_2%3a11.08.01-1_arm64.deb ... 599s Unpacking libnetpbm11t64:arm64 (2:11.08.01-1) ... 599s Selecting previously unselected package netpbm. 599s Preparing to unpack .../130-netpbm_2%3a11.08.01-1_arm64.deb ... 599s Unpacking netpbm (2:11.08.01-1) ... 600s Selecting previously unselected package tex-common. 600s Preparing to unpack .../131-tex-common_6.18_all.deb ... 600s Unpacking tex-common (6.18) ... 600s Selecting previously unselected package libpaper-utils. 600s Preparing to unpack .../132-libpaper-utils_1.1.29build1_arm64.deb ... 600s Unpacking libpaper-utils (1.1.29build1) ... 600s Selecting previously unselected package libkpathsea6:arm64. 600s Preparing to unpack .../133-libkpathsea6_2024.20240313.70630+ds-5_arm64.deb ... 600s Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-5) ... 600s Selecting previously unselected package libptexenc1:arm64. 600s Preparing to unpack .../134-libptexenc1_2024.20240313.70630+ds-5_arm64.deb ... 600s Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-5) ... 600s Selecting previously unselected package libsynctex2:arm64. 600s Preparing to unpack .../135-libsynctex2_2024.20240313.70630+ds-5_arm64.deb ... 600s Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-5) ... 600s Selecting previously unselected package libtexlua53-5:arm64. 600s Preparing to unpack .../136-libtexlua53-5_2024.20240313.70630+ds-5_arm64.deb ... 600s Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-5) ... 600s Selecting previously unselected package t1utils. 600s Preparing to unpack .../137-t1utils_1.41-4build3_arm64.deb ... 600s Unpacking t1utils (1.41-4build3) ... 600s Selecting previously unselected package libpixman-1-0:arm64. 600s Preparing to unpack .../138-libpixman-1-0_0.44.0-3_arm64.deb ... 600s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 600s Selecting previously unselected package libxcb-render0:arm64. 600s Preparing to unpack .../139-libxcb-render0_1.17.0-2_arm64.deb ... 600s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 600s Selecting previously unselected package libxcb-shm0:arm64. 600s Preparing to unpack .../140-libxcb-shm0_1.17.0-2_arm64.deb ... 600s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 600s Selecting previously unselected package libcairo2:arm64. 600s Preparing to unpack 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package hicolor-icon-theme. 602s Preparing to unpack .../152-hicolor-icon-theme_0.18-1_all.deb ... 602s Unpacking hicolor-icon-theme (0.18-1) ... 602s Selecting previously unselected package imagemagick-6.q16. 602s Preparing to unpack .../153-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 602s Unpacking imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 602s Selecting previously unselected package imagemagick. 602s Preparing to unpack .../154-imagemagick_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 602s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 602s Selecting previously unselected package hevea. 602s Preparing to unpack .../155-hevea_2.36-2_arm64.deb ... 602s Unpacking hevea (2.36-2) ... 602s Selecting previously unselected package libapache-pom-java. 602s Preparing to unpack .../156-libapache-pom-java_33-2_all.deb ... 602s Unpacking libapache-pom-java (33-2) ... 602s Selecting previously unselected package libblas3:arm64. 602s Preparing to unpack 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Unpacking liblapack3:arm64 (3.12.0-3build2) ... 603s Selecting previously unselected package liblbfgsb0:arm64. 603s Preparing to unpack .../168-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 603s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 603s Selecting previously unselected package libmbedcrypto7t64:arm64. 603s Preparing to unpack .../169-libmbedcrypto7t64_2.28.8-1_arm64.deb ... 603s Unpacking libmbedcrypto7t64:arm64 (2.28.8-1) ... 603s Selecting previously unselected package libmbedx509-1t64:arm64. 603s Preparing to unpack .../170-libmbedx509-1t64_2.28.8-1_arm64.deb ... 603s Unpacking libmbedx509-1t64:arm64 (2.28.8-1) ... 603s Selecting previously unselected package libmbedtls14t64:arm64. 603s Preparing to unpack .../171-libmbedtls14t64_2.28.8-1_arm64.deb ... 603s Unpacking libmbedtls14t64:arm64 (2.28.8-1) ... 603s Selecting previously unselected package zlib1g-dev:arm64. 603s Preparing to unpack .../172-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 603s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 603s Selecting previously unselected package libpython3.12-dev:arm64. 603s Preparing to unpack .../173-libpython3.12-dev_3.12.7-3_arm64.deb ... 603s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ... 603s Selecting previously unselected package libpython3-dev:arm64. 603s Preparing to unpack .../174-libpython3-dev_3.12.7-1_arm64.deb ... 603s Unpacking libpython3-dev:arm64 (3.12.7-1) ... 603s Selecting previously unselected package libpython3.13-stdlib:arm64. 603s Preparing to unpack .../175-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 603s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 603s Selecting previously unselected package libpython3.13:arm64. 603s Preparing to unpack .../176-libpython3.13_3.13.0-2_arm64.deb ... 603s Unpacking libpython3.13:arm64 (3.13.0-2) ... 603s Selecting previously unselected package libpython3.13-dev:arm64. 603s Preparing to unpack .../177-libpython3.13-dev_3.13.0-2_arm64.deb ... 603s Unpacking libpython3.13-dev:arm64 (3.13.0-2) ... 604s Selecting previously unselected package libpython3-all-dev:arm64. 604s Preparing to unpack .../178-libpython3-all-dev_3.12.7-1_arm64.deb ... 604s Unpacking libpython3-all-dev:arm64 (3.12.7-1) ... 604s Selecting previously unselected package libqhull-r8.0:arm64. 604s Preparing to unpack .../179-libqhull-r8.0_2020.2-6build1_arm64.deb ... 604s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 604s Selecting previously unselected package libxslt1.1:arm64. 604s Preparing to unpack .../180-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 604s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 604s Selecting previously unselected package mafft. 604s Preparing to unpack .../181-mafft_7.505-1_arm64.deb ... 604s Unpacking mafft (7.505-1) ... 604s Selecting previously unselected package ncbi-data. 604s Preparing to unpack .../182-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 604s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 604s Selecting previously unselected package ncbi-blast+. 604s Preparing to unpack .../183-ncbi-blast+_2.16.0+ds-6_arm64.deb ... 604s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 604s Selecting previously unselected package phylip. 604s Preparing to unpack .../184-phylip_1%3a3.697+dfsg-4build1_arm64.deb ... 604s Unpacking phylip (1:3.697+dfsg-4build1) ... 604s Selecting previously unselected package prank. 604s Preparing to unpack .../185-prank_0.0.170427+dfsg-3_arm64.deb ... 604s Unpacking prank (0.0.170427+dfsg-3) ... 604s Selecting previously unselected package preview-latex-style. 604s Preparing to unpack .../186-preview-latex-style_13.2-1_all.deb ... 604s Unpacking preview-latex-style (13.2-1) ... 605s Selecting previously unselected package probcons. 605s Preparing to unpack .../187-probcons_1.12-14_arm64.deb ... 605s Unpacking probcons (1.12-14) ... 605s Selecting previously unselected package python-biopython-doc. 605s Preparing to unpack .../188-python-biopython-doc_1.84+dfsg-4_all.deb ... 605s Unpacking python-biopython-doc (1.84+dfsg-4) ... 605s Selecting previously unselected package python-matplotlib-data. 605s Preparing to unpack .../189-python-matplotlib-data_3.8.3-3_all.deb ... 605s Unpacking python-matplotlib-data (3.8.3-3) ... 605s Selecting previously unselected package python3.13. 605s Preparing to unpack .../190-python3.13_3.13.0-2_arm64.deb ... 605s Unpacking python3.13 (3.13.0-2) ... 605s Selecting previously unselected package python3-all. 605s Preparing to unpack .../191-python3-all_3.12.7-1_arm64.deb ... 605s Unpacking python3-all (3.12.7-1) ... 605s Selecting previously unselected package python3.12-dev. 605s Preparing to unpack .../192-python3.12-dev_3.12.7-3_arm64.deb ... 605s Unpacking python3.12-dev (3.12.7-3) ... 605s Selecting previously unselected package python3-dev. 605s Preparing to unpack .../193-python3-dev_3.12.7-1_arm64.deb ... 605s Unpacking python3-dev (3.12.7-1) ... 605s Selecting previously unselected package python3.13-dev. 605s Preparing to unpack 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Selecting previously unselected package python3-tk:arm64. 606s Preparing to unpack .../200-python3-tk_3.12.7-1_arm64.deb ... 606s Unpacking python3-tk:arm64 (3.12.7-1) ... 606s Selecting previously unselected package python3-pil.imagetk:arm64. 606s Preparing to unpack .../201-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 606s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 606s Selecting previously unselected package python3-pil:arm64. 606s Preparing to unpack .../202-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 606s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 606s Selecting previously unselected package python3-cairo. 606s Preparing to unpack .../203-python3-cairo_1.26.1-2_arm64.deb ... 606s Unpacking python3-cairo (1.26.1-2) ... 606s Selecting previously unselected package python3-freetype. 606s Preparing to unpack .../204-python3-freetype_2.5.1-1_all.deb ... 606s Unpacking python3-freetype (2.5.1-1) ... 606s Selecting previously unselected package python3-rlpycairo. 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616s Setting up x11-common (1:7.7+23ubuntu3) ... 616s Setting up libpq5:arm64 (17.0-1) ... 616s Setting up libdeflate0:arm64 (1.22-1) ... 616s Setting up python3-tabulate (0.9.0-1) ... 616s Setting up m4 (1.4.19-4build1) ... 616s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 616s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 616s Setting up libpaper-utils (1.1.29build1) ... 616s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 616s Setting up python3-freetype (2.5.1-1) ... 616s Setting up emboss-data (6.6.0+dfsg-12ubuntu2) ... 616s Setting up python3-networkx (3.2.1-4ubuntu1) ... 619s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 619s Setting up libnetpbm11t64:arm64 (2:11.08.01-1) ... 619s Setting up python3-tz (2024.1-2) ... 619s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 619s Setting up poppler-data (0.4.12-1) ... 620s Setting up unicode-data (15.1.0-1) ... 620s Setting up python3-mysqldb (1.4.6-2build3) ... 620s Setting up python3-six (1.16.0-7) ... 620s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 620s Setting up tex-common (6.18) ... 620s update-language: texlive-base not installed and configured, doing nothing! 620s Setting up python3-isodate (0.6.1-3) ... 620s Setting up python3-roman (4.2-1) ... 621s Setting up python3-decorator (5.1.1-5) ... 621s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 621s Setting up autotools-dev (20220109.1) ... 621s Setting up libblas3:arm64 (3.12.0-3build2) ... 621s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 621s Setting up python3-packaging (24.1-1) ... 621s Setting up libexpat1-dev:arm64 (2.6.2-2) ... 621s Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.2build1) ... 621s Setting up libjbig2dec0:arm64 (0.20-1build3) ... 621s Setting up python3-snowballstemmer (2.2.0-4build1) ... 622s Setting up libteckit0:arm64 (2.5.12+ds1-1) ... 622s Setting up 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python3-dateutil (2.9.0-2) ... 625s Setting up fasttree (2.1.11-2) ... 625s Setting up sgml-base (1.31) ... 625s Setting up python3-msgpack (1.0.3-3build2) ... 625s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 625s Setting up libtsan2:arm64 (14.2.0-8ubuntu1) ... 625s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 625s Setting up python3-mpmath (1.3.0-1) ... 626s Setting up libisl23:arm64 (0.27-1) ... 626s Setting up libde265-0:arm64 (1.0.15-1build4) ... 626s Setting up python-matplotlib-data (3.8.3-3) ... 626s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 626s Setting up python3-appdirs (1.4.4-4) ... 626s Setting up dialign (2.2.1-13) ... 626s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 626s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 626s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 626s Setting up xdg-utils (1.2.1-0ubuntu1) ... 626s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 626s Setting up 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auto mode 663s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 663s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 663s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 663s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 663s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 663s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 663s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 663s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 663s Setting up python3-matplotlib (3.8.3-3) ... 666s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 666s Setting up hevea (2.36-2) ... 666s Setting up 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updmap-sys. This may take some time... done. 702s Running mktexlsr /var/lib/texmf ... done. 702s Building format(s) --all. 768s This may take some time... done. 785s (Reading database ... 127865 files and directories currently installed.) 785s Removing autopkgtest-satdep (0) ... 799s autopkgtest [10:48:20]: test full_suite: sh debian/tests/run-unit-test 799s autopkgtest [10:48:20]: test full_suite: [----------------------- 799s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 799s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 801s mkdir: created directory 'Bio' 801s mkdir: created directory 'Bio/Align' 801s mkdir: created directory 'Bio/Align/substitution_matrices' 801s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 801s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 801s Remove test test_Tutorial.py which is bound to fail 802s test_Ace ... ok 802s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 802s 802s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 802s 802s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 802s 802s test_Align_a2m ... loading tests failed: 802s Failed to import test module: test_Align_a2m 802s Traceback (most recent call last): 802s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 802s from . import multiarray 802s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 802s from . import overrides 802s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 802s from numpy.core._multiarray_umath import ( 802s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 802s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 802s 802s During handling of the above exception, another exception occurred: 802s 802s Traceback (most recent call last): 802s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 802s from numpy.__config__ import show as show_config 802s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 802s from numpy.core._multiarray_umath import ( 802s ...<3 lines>... 802s ) 802s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 802s raise ImportError(msg) 802s ImportError: 802s 802s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 802s 802s Importing the numpy C-extensions failed. This error can happen for 802s many reasons, often due to issues with your setup or how NumPy was 802s installed. 802s 802s We have compiled some common reasons and troubleshooting tips at: 802s 802s https://numpy.org/devdocs/user/troubleshooting-importerror.html 802s 802s Please note and check the following: 802s 802s * The Python version is: Python3.13 from "/usr/bin/python3.13" 802s * The NumPy version is: "1.26.4" 802s 802s and make sure that they are the versions you expect. 802s Please carefully study the documentation linked above for further help. 802s 802s Original error was: No module named 'numpy.core._multiarray_umath' 802s 802s 802s The above exception was the direct cause of the following exception: 802s 802s Traceback (most recent call last): 802s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 802s module = __import__(module_name) 802s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 802s import numpy as np 802s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 802s raise ImportError(msg) from e 802s ImportError: Error importing numpy: you should not try to import numpy from 802s its source directory; please exit the numpy source tree, and relaunch 802s your python interpreter from there. 802s 802s test_Align_bed ... loading tests failed: 802s Failed to import test module: test_Align_bed 802s Traceback (most recent call last): 802s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 802s from . import multiarray 802s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 802s from . import overrides 802s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 802s from numpy.core._multiarray_umath import ( 802s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 802s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 802s 802s During handling of the above exception, another exception occurred: 802s 802s Traceback (most recent call last): 802s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 802s from numpy.__config__ import show as show_config 802s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 802s from numpy.core._multiarray_umath import ( 802s ...<3 lines>... 802s ) 802s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 802s raise ImportError(msg) 802s ImportError: 802s 802s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 802s 802s Importing the numpy C-extensions failed. This error can happen for 802s many reasons, often due to issues with your setup or how NumPy was 802s installed. 802s 802s We have compiled some common reasons and troubleshooting tips at: 802s 802s https://numpy.org/devdocs/user/troubleshooting-importerror.html 802s 802s Please note and check the following: 802s 802s * The Python version is: Python3.13 from "/usr/bin/python3.13" 802s * The NumPy version is: "1.26.4" 802s 802s and make sure that they are the versions you expect. 802s Please carefully study the documentation linked above for further help. 802s 802s Original error was: No module named 'numpy.core._multiarray_umath' 802s 802s 802s The above exception was the direct cause of the following exception: 802s 802s Traceback (most recent call last): 802s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 802s module = __import__(module_name) 802s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 802s import numpy as np 802s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 802s raise ImportError(msg) from e 802s ImportError: Error importing numpy: you should not try to import numpy from 802s its source directory; please exit the numpy source tree, and relaunch 802s your python interpreter from there. 802s 802s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 802s 802s test_Align_bigmaf ... loading tests failed: 802s Failed to import test module: test_Align_bigmaf 802s Traceback (most recent call last): 802s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 802s from . import multiarray 802s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 802s from . import overrides 802s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 802s from numpy.core._multiarray_umath import ( 802s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 802s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 802s 802s During handling of the above exception, another exception occurred: 802s 802s Traceback (most recent call last): 802s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 802s from numpy.__config__ import show as show_config 802s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 802s from numpy.core._multiarray_umath import ( 802s ...<3 lines>... 802s ) 802s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 802s raise ImportError(msg) 802s ImportError: 802s 802s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 802s 802s Importing the numpy C-extensions failed. This error can happen for 802s many reasons, often due to issues with your setup or how NumPy was 802s installed. 802s 802s We have compiled some common reasons and troubleshooting tips at: 802s 802s https://numpy.org/devdocs/user/troubleshooting-importerror.html 802s 802s Please note and check the following: 802s 802s * The Python version is: Python3.13 from "/usr/bin/python3.13" 802s * The NumPy version is: "1.26.4" 802s 802s and make sure that they are the versions you expect. 802s Please carefully study the documentation linked above for further help. 802s 802s Original error was: No module named 'numpy.core._multiarray_umath' 802s 802s 802s The above exception was the direct cause of the following exception: 802s 802s Traceback (most recent call last): 802s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 802s module = __import__(module_name) 802s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 802s import numpy as np 802s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 802s raise ImportError(msg) from e 802s ImportError: Error importing numpy: you should not try to import numpy from 802s its source directory; please exit the numpy source tree, and relaunch 802s your python interpreter from there. 802s 803s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_clustal ... loading tests failed: 803s Failed to import test module: test_Align_clustal 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 803s from . import multiarray 803s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 803s from . import overrides 803s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 803s from numpy.core._multiarray_umath import ( 803s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 803s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 803s 803s During handling of the above exception, another exception occurred: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 803s from numpy.__config__ import show as show_config 803s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 803s from numpy.core._multiarray_umath import ( 803s ...<3 lines>... 803s ) 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 803s raise ImportError(msg) 803s ImportError: 803s 803s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 803s 803s Importing the numpy C-extensions failed. This error can happen for 803s many reasons, often due to issues with your setup or how NumPy was 803s installed. 803s 803s We have compiled some common reasons and troubleshooting tips at: 803s 803s https://numpy.org/devdocs/user/troubleshooting-importerror.html 803s 803s Please note and check the following: 803s 803s * The Python version is: Python3.13 from "/usr/bin/python3.13" 803s * The NumPy version is: "1.26.4" 803s 803s and make sure that they are the versions you expect. 803s Please carefully study the documentation linked above for further help. 803s 803s Original error was: No module named 'numpy.core._multiarray_umath' 803s 803s 803s The above exception was the direct cause of the following exception: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 803s module = __import__(module_name) 803s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 803s import numpy as np 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 803s raise ImportError(msg) from e 803s ImportError: Error importing numpy: you should not try to import numpy from 803s its source directory; please exit the numpy source tree, and relaunch 803s your python interpreter from there. 803s 803s test_Align_codonalign ... loading tests failed: 803s Failed to import test module: test_Align_codonalign 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 803s from . import multiarray 803s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 803s from . import overrides 803s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 803s from numpy.core._multiarray_umath import ( 803s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 803s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 803s 803s During handling of the above exception, another exception occurred: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 803s from numpy.__config__ import show as show_config 803s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 803s from numpy.core._multiarray_umath import ( 803s ...<3 lines>... 803s ) 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 803s raise ImportError(msg) 803s ImportError: 803s 803s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 803s 803s Importing the numpy C-extensions failed. This error can happen for 803s many reasons, often due to issues with your setup or how NumPy was 803s installed. 803s 803s We have compiled some common reasons and troubleshooting tips at: 803s 803s https://numpy.org/devdocs/user/troubleshooting-importerror.html 803s 803s Please note and check the following: 803s 803s * The Python version is: Python3.13 from "/usr/bin/python3.13" 803s * The NumPy version is: "1.26.4" 803s 803s and make sure that they are the versions you expect. 803s Please carefully study the documentation linked above for further help. 803s 803s Original error was: No module named 'numpy.core._multiarray_umath' 803s 803s 803s The above exception was the direct cause of the following exception: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 803s module = __import__(module_name) 803s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 803s import numpy as np 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 803s raise ImportError(msg) from e 803s ImportError: Error importing numpy: you should not try to import numpy from 803s its source directory; please exit the numpy source tree, and relaunch 803s your python interpreter from there. 803s 803s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_fasta ... loading tests failed: 803s Failed to import test module: test_Align_fasta 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 803s from . import multiarray 803s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 803s from . import overrides 803s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 803s from numpy.core._multiarray_umath import ( 803s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 803s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 803s 803s During handling of the above exception, another exception occurred: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 803s from numpy.__config__ import show as show_config 803s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 803s from numpy.core._multiarray_umath import ( 803s ...<3 lines>... 803s ) 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 803s raise ImportError(msg) 803s ImportError: 803s 803s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 803s 803s Importing the numpy C-extensions failed. This error can happen for 803s many reasons, often due to issues with your setup or how NumPy was 803s installed. 803s 803s We have compiled some common reasons and troubleshooting tips at: 803s 803s https://numpy.org/devdocs/user/troubleshooting-importerror.html 803s 803s Please note and check the following: 803s 803s * The Python version is: Python3.13 from "/usr/bin/python3.13" 803s * The NumPy version is: "1.26.4" 803s 803s and make sure that they are the versions you expect. 803s Please carefully study the documentation linked above for further help. 803s 803s Original error was: No module named 'numpy.core._multiarray_umath' 803s 803s 803s The above exception was the direct cause of the following exception: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 803s module = __import__(module_name) 803s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 803s import numpy as np 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 803s raise ImportError(msg) from e 803s ImportError: Error importing numpy: you should not try to import numpy from 803s its source directory; please exit the numpy source tree, and relaunch 803s your python interpreter from there. 803s 803s test_Align_hhr ... loading tests failed: 803s Failed to import test module: test_Align_hhr 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 803s from . import multiarray 803s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 803s from . import overrides 803s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 803s from numpy.core._multiarray_umath import ( 803s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 803s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 803s 803s During handling of the above exception, another exception occurred: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 803s from numpy.__config__ import show as show_config 803s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 803s from numpy.core._multiarray_umath import ( 803s ...<3 lines>... 803s ) 803s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 803s raise ImportError(msg) 803s ImportError: 803s 803s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 803s 803s Importing the numpy C-extensions failed. This error can happen for 803s many reasons, often due to issues with your setup or how NumPy was 803s installed. 803s 803s We have compiled some common reasons and troubleshooting tips at: 803s 803s https://numpy.org/devdocs/user/troubleshooting-importerror.html 803s 803s Please note and check the following: 803s 803s * The Python version is: Python3.13 from "/usr/bin/python3.13" 803s * The NumPy version is: "1.26.4" 803s 803s and make sure that they are the versions you expect. 803s Please carefully study the documentation linked above for further help. 803s 803s Original error was: No module named 'numpy.core._multiarray_umath' 803s 803s 803s The above exception was the direct cause of the following exception: 803s 803s Traceback (most recent call last): 803s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 803s module = __import__(module_name) 803s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 803s import numpy as np 803s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 803s raise ImportError(msg) from e 803s ImportError: Error importing numpy: you should not try to import numpy from 803s its source directory; please exit the numpy source tree, and relaunch 803s your python interpreter from there. 803s 803s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 803s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 803s 804s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_Application ... ok 804s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_Blast_Record ... loading tests failed: 804s Failed to import test module: test_Blast_Record 804s Traceback (most recent call last): 804s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 804s from . import multiarray 804s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 804s from . import overrides 804s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 804s from numpy.core._multiarray_umath import ( 804s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 804s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 804s 804s During handling of the above exception, another exception occurred: 804s 804s Traceback (most recent call last): 804s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 804s from numpy.__config__ import show as show_config 804s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 804s from numpy.core._multiarray_umath import ( 804s ...<3 lines>... 804s ) 804s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 804s raise ImportError(msg) 804s ImportError: 804s 804s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 804s 804s Importing the numpy C-extensions failed. This error can happen for 804s many reasons, often due to issues with your setup or how NumPy was 804s installed. 804s 804s We have compiled some common reasons and troubleshooting tips at: 804s 804s https://numpy.org/devdocs/user/troubleshooting-importerror.html 804s 804s Please note and check the following: 804s 804s * The Python version is: Python3.13 from "/usr/bin/python3.13" 804s * The NumPy version is: "1.26.4" 804s 804s and make sure that they are the versions you expect. 804s Please carefully study the documentation linked above for further help. 804s 804s Original error was: No module named 'numpy.core._multiarray_umath' 804s 804s 804s The above exception was the direct cause of the following exception: 804s 804s Traceback (most recent call last): 804s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 804s module = __import__(module_name) 804s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 804s from Bio.Blast.NCBIXML import HSP 804s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 804s import numpy as np 804s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 804s raise ImportError(msg) from e 804s ImportError: Error importing numpy: you should not try to import numpy from 804s its source directory; please exit the numpy source tree, and relaunch 804s your python interpreter from there. 804s 804s test_Blast_parser ... loading tests failed: 804s Failed to import test module: test_Blast_parser 804s Traceback (most recent call last): 804s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 804s from . import multiarray 804s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 804s from . import overrides 804s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 804s from numpy.core._multiarray_umath import ( 804s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 804s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 804s 804s During handling of the above exception, another exception occurred: 804s 804s Traceback (most recent call last): 804s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 804s from numpy.__config__ import show as show_config 804s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 804s from numpy.core._multiarray_umath import ( 804s ...<3 lines>... 804s ) 804s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 804s raise ImportError(msg) 804s ImportError: 804s 804s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 804s 804s Importing the numpy C-extensions failed. This error can happen for 804s many reasons, often due to issues with your setup or how NumPy was 804s installed. 804s 804s We have compiled some common reasons and troubleshooting tips at: 804s 804s https://numpy.org/devdocs/user/troubleshooting-importerror.html 804s 804s Please note and check the following: 804s 804s * The Python version is: Python3.13 from "/usr/bin/python3.13" 804s * The NumPy version is: "1.26.4" 804s 804s and make sure that they are the versions you expect. 804s Please carefully study the documentation linked above for further help. 804s 804s Original error was: No module named 'numpy.core._multiarray_umath' 804s 804s 804s The above exception was the direct cause of the following exception: 804s 804s Traceback (most recent call last): 804s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 804s module = __import__(module_name) 804s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 804s import numpy as np 804s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 804s raise ImportError(msg) from e 804s ImportError: Error importing numpy: you should not try to import numpy from 804s its source directory; please exit the numpy source tree, and relaunch 804s your python interpreter from there. 804s 804s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_Chi2 ... /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131: BiopythonWarning: Import of C module failed (cannot import name 'cnexus' from 'Bio.Nexus' (/usr/lib/python3/dist-packages/Bio/Nexus/__init__.py)). Falling back to slow Python implementation 804s warnings.warn( 804s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 804s 804s test_CodonTable ... ok 804s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 804s 804s test_Compass ... ok 804s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 804s 804s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 804s 805s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 805s 805s test_EmbossPrimer ... ok 809s test_Entrez ... ok 809s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 809s 809s test_Entrez_parser ... ok 809s test_Enzyme ... ok 809s test_ExPASy ... skipping. internet not available 809s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 809s 809s test_File ... ok 809s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 809s 810s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 810s 810s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 810s 810s test_GraphicsDistribution ... loading tests failed: 810s Failed to import test module: test_GraphicsDistribution 810s Traceback (most recent call last): 810s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 810s module = __import__(module_name) 810s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 810s from Bio.Graphics.Distribution import BarChartDistribution 810s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 810s from reportlab.graphics.charts.barcharts import BarChartProperties 810s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 810s from reportlab.lib import colors 810s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 810s from reportlab.lib.rl_accel import fp_str 810s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 810s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 810s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 810s from PIL import Image 810s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 810s from . import _imaging as core 810s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 810s 810s test_GraphicsGeneral ... loading tests failed: 810s Failed to import test module: test_GraphicsGeneral 810s Traceback (most recent call last): 810s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 810s module = __import__(module_name) 810s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 810s from Bio.Graphics.Comparative import ComparativeScatterPlot 810s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 810s from reportlab.graphics.charts.lineplots import LinePlot 810s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 810s from reportlab.lib import colors 810s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 810s from reportlab.lib.rl_accel import fp_str 810s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 810s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 810s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 810s from PIL import Image 810s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 810s from . import _imaging as core 810s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 810s 810s test_HMMCasino ... ok 810s test_HMMGeneral ... ok 810s test_KEGG ... ok 810s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 810s 810s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 810s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 811s test_KGML_nographics ... ok 811s test_KeyWList ... ok 811s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 811s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 811s 811s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 811s 811s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 811s 811s test_Medline ... ok 811s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 811s 811s test_NCBIXML ... loading tests failed: 811s Failed to import test module: test_NCBIXML 811s Traceback (most recent call last): 811s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 811s from . import multiarray 811s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 811s from . import overrides 811s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 811s from numpy.core._multiarray_umath import ( 811s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 811s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 811s 811s During handling of the above exception, another exception occurred: 811s 811s Traceback (most recent call last): 811s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 811s from numpy.__config__ import show as show_config 811s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 811s from numpy.core._multiarray_umath import ( 811s ...<3 lines>... 811s ) 811s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 811s raise ImportError(msg) 811s ImportError: 811s 811s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 811s 811s Importing the numpy C-extensions failed. This error can happen for 811s many reasons, often due to issues with your setup or how NumPy was 811s installed. 811s 811s We have compiled some common reasons and troubleshooting tips at: 811s 811s https://numpy.org/devdocs/user/troubleshooting-importerror.html 811s 811s Please note and check the following: 811s 811s * The Python version is: Python3.13 from "/usr/bin/python3.13" 811s * The NumPy version is: "1.26.4" 811s 811s and make sure that they are the versions you expect. 811s Please carefully study the documentation linked above for further help. 811s 811s Original error was: No module named 'numpy.core._multiarray_umath' 811s 811s 811s The above exception was the direct cause of the following exception: 811s 811s Traceback (most recent call last): 811s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 811s module = __import__(module_name) 811s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 811s from Bio.Blast import NCBIXML 811s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 811s import numpy as np 811s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 811s raise ImportError(msg) from e 811s ImportError: Error importing numpy: you should not try to import numpy from 811s its source directory; please exit the numpy source tree, and relaunch 811s your python interpreter from there. 811s 812s test_NCBI_BLAST_tools ... loading tests failed: 812s Failed to import test module: test_NCBI_BLAST_tools 812s Traceback (most recent call last): 812s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 812s from . import multiarray 812s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 812s from . import overrides 812s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 812s from numpy.core._multiarray_umath import ( 812s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 812s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 812s 812s During handling of the above exception, another exception occurred: 812s 812s Traceback (most recent call last): 812s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 812s from numpy.__config__ import show as show_config 812s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 812s from numpy.core._multiarray_umath import ( 812s ...<3 lines>... 812s ) 812s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 812s raise ImportError(msg) 812s ImportError: 812s 812s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 812s 812s Importing the numpy C-extensions failed. This error can happen for 812s many reasons, often due to issues with your setup or how NumPy was 812s installed. 812s 812s We have compiled some common reasons and troubleshooting tips at: 812s 812s https://numpy.org/devdocs/user/troubleshooting-importerror.html 812s 812s Please note and check the following: 812s 812s * The Python version is: Python3.13 from "/usr/bin/python3.13" 812s * The NumPy version is: "1.26.4" 812s 812s and make sure that they are the versions you expect. 812s Please carefully study the documentation linked above for further help. 812s 812s Original error was: No module named 'numpy.core._multiarray_umath' 812s 812s 812s The above exception was the direct cause of the following exception: 812s 812s Traceback (most recent call last): 812s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 812s module = __import__(module_name) 812s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 812s from Bio.Blast import Applications 812s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 812s import numpy as np 812s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 812s raise ImportError(msg) from e 812s ImportError: Error importing numpy: you should not try to import numpy from 812s its source directory; please exit the numpy source tree, and relaunch 812s your python interpreter from there. 812s 812s test_NCBI_qblast ... loading tests failed: 812s Failed to import test module: test_NCBI_qblast 812s Traceback (most recent call last): 812s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 812s from . import multiarray 812s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 812s from . import overrides 812s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 812s from numpy.core._multiarray_umath import ( 812s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 812s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 812s 812s During handling of the above exception, another exception occurred: 812s 812s Traceback (most recent call last): 812s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 812s from numpy.__config__ import show as show_config 812s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 812s from numpy.core._multiarray_umath import ( 812s ...<3 lines>... 812s ) 812s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 812s raise ImportError(msg) 812s ImportError: 812s 812s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 812s 812s Importing the numpy C-extensions failed. This error can happen for 812s many reasons, often due to issues with your setup or how NumPy was 812s installed. 812s 812s We have compiled some common reasons and troubleshooting tips at: 812s 812s https://numpy.org/devdocs/user/troubleshooting-importerror.html 812s 812s Please note and check the following: 812s 812s * The Python version is: Python3.13 from "/usr/bin/python3.13" 812s * The NumPy version is: "1.26.4" 812s 812s and make sure that they are the versions you expect. 812s Please carefully study the documentation linked above for further help. 812s 812s Original error was: No module named 'numpy.core._multiarray_umath' 812s 812s 812s The above exception was the direct cause of the following exception: 812s 812s Traceback (most recent call last): 812s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 812s module = __import__(module_name) 812s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 812s from Bio.Blast import NCBIWWW 812s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 812s import numpy as np 812s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 812s raise ImportError(msg) from e 812s ImportError: Error importing numpy: you should not try to import numpy from 812s its source directory; please exit the numpy source tree, and relaunch 812s your python interpreter from there. 812s 812s test_NMR ... ok 812s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 812s 812s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 812s 812s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 812s 812s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 812s 812s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 812s 812s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_Disordered ... loading tests failed: 812s Failed to import test module: test_PDB_Disordered 812s Traceback (most recent call last): 812s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 812s from . import multiarray 812s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 812s from . import overrides 812s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 812s from numpy.core._multiarray_umath import ( 812s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 812s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 812s 812s During handling of the above exception, another exception occurred: 812s 812s Traceback (most recent call last): 812s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 812s from numpy.__config__ import show as show_config 812s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 812s from numpy.core._multiarray_umath import ( 812s ...<3 lines>... 812s ) 812s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 812s raise ImportError(msg) 812s ImportError: 812s 812s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 812s 812s Importing the numpy C-extensions failed. This error can happen for 812s many reasons, often due to issues with your setup or how NumPy was 812s installed. 812s 812s We have compiled some common reasons and troubleshooting tips at: 812s 812s https://numpy.org/devdocs/user/troubleshooting-importerror.html 812s 812s Please note and check the following: 812s 812s * The Python version is: Python3.13 from "/usr/bin/python3.13" 812s * The NumPy version is: "1.26.4" 812s 812s and make sure that they are the versions you expect. 812s Please carefully study the documentation linked above for further help. 812s 812s Original error was: No module named 'numpy.core._multiarray_umath' 812s 812s 812s The above exception was the direct cause of the following exception: 812s 812s Traceback (most recent call last): 812s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 812s module = __import__(module_name) 812s File "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 812s import numpy as np 812s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 812s raise ImportError(msg) from e 812s ImportError: Error importing numpy: you should not try to import numpy from 812s its source directory; please exit the numpy source tree, and relaunch 812s your python interpreter from there. 812s 812s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 812s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 812s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 812s 812s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 812s 812s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 812s 813s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 813s 813s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 813s 813s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 813s 813s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 813s 813s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 813s 813s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 813s 813s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 813s 813s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 813s 813s test_Pathway ... ok 813s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 813s 813s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_PopGen_GenePop_nodepend ... ok 813s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 813s 813s test_ProtParam ... ok 813s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 813s 814s test_Restriction ... ok 814s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 814s 814s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 814s 814s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 814s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 814s 815s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 815s 815s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 815s 815s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 815s 815s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 815s 815s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 815s 816s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 816s 816s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 816s 816s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 816s 816s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 816s 816s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 816s 816s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 816s 816s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 816s 816s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 816s 817s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 817s 817s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 817s 817s test_UniGene ... ok 817s test_UniProt ... skipping. internet not available 817s test_UniProt_GOA ... ok 817s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 817s 817s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 817s 817s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 819s test_bgzf ... ok 819s test_cellosaurus ... ok 819s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 819s 819s test_geo ... ok 819s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 819s 819s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 820s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 820s 820s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 820s 820s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 820s 820s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 820s 820s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 820s 820s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 820s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 820s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 820s 820s test_prodoc ... ok 820s test_prosite ... ok 820s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 820s 820s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 820s test_seq ... ok 820s test_translate ... ok 820s Skipping any tests requiring internet access 820s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 820s Operating system: posix linux 820s ---------------------------------------------------------------------- 820s Ran 217 tests in 18.439 seconds 820s 820s FAILED (failures = 15) 821s test_Ace ... ok 821s test_Affy ... ok 824s test_AlignIO ... ok 824s test_AlignIO_ClustalIO ... ok 824s test_AlignIO_EmbossIO ... ok 824s test_AlignIO_FastaIO ... ok 824s test_AlignIO_MauveIO ... ok 824s test_AlignIO_PhylipIO ... ok 824s test_AlignIO_convert ... ok 824s test_AlignInfo ... ok 824s test_Align_Alignment ... ok 824s test_Align_a2m ... ok 824s test_Align_bed ... ok 825s test_Align_bigbed ... ok 825s test_Align_bigmaf ... ok 826s test_Align_bigpsl ... ok 826s test_Align_chain ... ok 826s test_Align_clustal ... ok 831s test_Align_codonalign ... ok 831s test_Align_emboss ... ok 831s test_Align_exonerate ... ok 831s test_Align_fasta ... ok 831s test_Align_hhr ... ok 832s test_Align_maf ... ok 832s test_Align_mauve ... ok 832s test_Align_msf ... ok 832s test_Align_nexus ... ok 832s test_Align_phylip ... ok 833s test_Align_psl ... ok 833s test_Align_sam ... ok 835s test_Align_stockholm ... ok 835s test_Align_tabular ... ok 835s test_Application ... ok 835s test_BioSQL_MySQLdb_online ... skipping. internet not available 835s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 835s test_BioSQL_mysql_connector_online ... skipping. internet not available 836s test_BioSQL_psycopg2_online ... skipping. internet not available 840s test_BioSQL_sqlite3 ... ok 840s test_BioSQL_sqlite3_online ... skipping. internet not available 840s test_Blast_Record ... ok 841s test_Blast_parser ... ok 841s test_CAPS ... ok 841s test_Chi2 ... ok 841s test_ClustalOmega_tool ... ok 842s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 842s test_Cluster ... ok 842s test_CodonTable ... ok 842s test_ColorSpiral ... ok 842s test_Compass ... ok 843s test_Consensus ... ok 845s test_Dialign_tool ... ok 845s test_EMBL_unittest ... ok 852s test_Emboss ... ok 852s test_EmbossPrimer ... ok 856s test_Entrez ... ok 856s test_Entrez_online ... skipping. internet not available 857s test_Entrez_parser ... ok 857s test_Enzyme ... ok 857s test_ExPASy ... skipping. internet not available 857s test_Fasttree_tool ... ok 857s test_File ... ok 857s test_GenBank ... ok 859s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 861s ok 862s test_GraphicsChromosome ... ok 862s test_GraphicsDistribution ... ok 863s test_GraphicsGeneral ... ok 863s test_HMMCasino ... ok 863s test_HMMGeneral ... ok 863s test_KEGG ... ok 863s test_KEGG_online ... skipping. internet not available 868s test_KGML_graphics ... ok 869s test_KGML_graphics_online ... skipping. internet not available 870s test_KGML_nographics ... ok 870s test_KeyWList ... ok 870s test_LogisticRegression ... ok 871s test_MafIO_index ... ok 872s test_Mafft_tool ... ok 873s test_MarkovModel ... ok 873s test_Medline ... ok 873s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 873s test_NCBIXML ... ok 876s test_NCBI_BLAST_tools ... ok 876s test_NCBI_qblast ... ok 876s test_NMR ... ok 876s test_NaiveBayes ... ok 876s test_Nexus ... ok 876s test_PAML_baseml ... ok 877s test_PAML_codeml ... ok 877s test_PAML_yn00 ... ok 880s test_PDB_CEAligner ... ok 881s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 881s Configuration error: 881s 881s The attempt to retrieve compound information for "SO4" failed. 881s 881s This information is searched for in a CCD file called components.cif or 881s components.cif.gz which should be located in one of the following directories: 881s 881s "/usr/share/libcifpp" 881s "/var/cache/libcifpp" 881s "/tmp/autopkgtest.qKkx58/autopkgtest_tmp/libcifpp-data" 881s "/usr/share/libcifpp" 881s "/usr/share/libcifpp" 881s 881s (Note that you can add a directory to the search paths by setting the 881s LIBCIFPP_DATA_DIR environmental variable) 881s 881s On Linux an optional cron script might have been installed that automatically updates 881s components.cif and mmCIF dictionary files. This script only works when the file 881s libcifpp.conf contains an uncommented line with the text: 881s 881s update=true 881s 881s If you do not have a working cron script, you can manually update the files 881s in /var/cache/libcifpp using the following commands: 881s 881s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 881s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 881s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 881s 881s The current order of compound factory objects is: 881s 881s CCD components.cif resource 881s CCD components.cif resource 881s Unknown compound: SO4 881s Missing compound information for SO4 881s 881s warnings.warn(err) 882s ok 882s test_PDB_Dice ... ok 882s test_PDB_Disordered ... ok 882s test_PDB_Exposure ... ok 882s test_PDB_FragmentMapper ... ok 884s test_PDB_KDTree ... ok 884s test_PDB_MMCIF2Dict ... ok 884s test_PDB_MMCIFIO ... ok 886s test_PDB_MMCIFParser ... ok 886s test_PDB_NACCESS ... ok 886s test_PDB_PDBIO ... ok 886s test_PDB_PDBList ... skipping. internet not available 894s test_PDB_PDBMLParser ... ok 894s test_PDB_PDBParser ... ok 894s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 894s test_PDB_Polypeptide ... ok 894s test_PDB_QCPSuperimposer ... ok 898s test_PDB_SASA ... ok 898s test_PDB_SMCRA ... ok 898s test_PDB_Selection ... ok 899s test_PDB_StructureAlignment ... ok 899s test_PDB_Superimposer ... ok 899s test_PDB_alphafold_db ... skipping. internet not available 902s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 902s warnings.warn( 902s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 902s warnings.warn( 902s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 902s warnings.warn( 902s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 902s warnings.warn( 902s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 902s warnings.warn( 903s ok 912s test_PDB_internal_coords ... ok 912s test_PDB_parse_pdb_header ... ok 912s test_PDB_vectors ... ok 913s test_PQR ... ok 913s test_Pathway ... ok 913s test_Phd ... ok 914s test_Phylo ... ok 914s test_PhyloXML ... ok 915s test_Phylo_CDAO ... ok 915s test_Phylo_NeXML ... ok 915s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 919s test_Phylo_matplotlib ... ok 920s test_Phylo_networkx ... ok 920s test_PopGen_GenePop_nodepend ... ok 922s test_Prank_tool ... ok 923s test_Probcons_tool ... ok 924s test_ProtParam ... ok 925s test_RCSBFormats ... ok 925s test_Restriction ... ok 926s test_SCOP_Astral ... ok 927s test_SCOP_Cla ... ok 927s test_SCOP_Des ... ok 928s test_SCOP_Dom ... ok 929s test_SCOP_Hie ... ok 929s test_SCOP_Raf ... ok 930s test_SCOP_Residues ... ok 931s test_SCOP_Scop ... ok 931s test_SVDSuperimposer ... ok 932s test_SearchIO_blast_tab ... ok 933s test_SearchIO_blast_tab_index ... ok 933s test_SearchIO_blast_xml ... ok 935s test_SearchIO_blast_xml_index ... ok 936s test_SearchIO_blat_psl ... ok 937s test_SearchIO_blat_psl_index ... ok 937s test_SearchIO_exonerate ... ok 938s test_SearchIO_exonerate_text_index ... ok 939s test_SearchIO_exonerate_vulgar_index ... ok 939s test_SearchIO_fasta_m10 ... ok 940s test_SearchIO_fasta_m10_index ... ok 941s test_SearchIO_hhsuite2_text ... ok 941s test_SearchIO_hmmer2_text ... ok 942s test_SearchIO_hmmer2_text_index ... ok 943s test_SearchIO_hmmer3_domtab ... ok 943s test_SearchIO_hmmer3_domtab_index ... ok 944s test_SearchIO_hmmer3_tab ... ok 945s test_SearchIO_hmmer3_tab_index ... ok 945s test_SearchIO_hmmer3_text ... ok 946s test_SearchIO_hmmer3_text_index ... ok 947s test_SearchIO_interproscan_xml ... ok 947s test_SearchIO_model ... ok 948s test_SearchIO_write ... ok 949s test_SeqFeature ... ok 966s test_SeqIO ... ok 967s test_SeqIO_AbiIO ... ok 968s test_SeqIO_FastaIO ... ok 968s test_SeqIO_Gck ... ok 969s test_SeqIO_Gfa ... ok 969s test_SeqIO_Insdc ... ok 970s test_SeqIO_NibIO ... ok 973s test_SeqIO_PdbIO ... ok 974s test_SeqIO_QualityIO ... ok 974s test_SeqIO_SeqXML ... ok 975s test_SeqIO_SnapGene ... ok 976s test_SeqIO_TwoBitIO ... ok 977s test_SeqIO_Xdna ... ok 978s test_SeqIO_features ... ok 994s test_SeqIO_index ... ok 995s test_SeqIO_online ... skipping. internet not available 996s test_SeqIO_write ... ok 996s test_SeqRecord ... ok 997s test_SeqUtils ... ok 999s test_Seq_objs ... ok 999s test_SffIO ... ok 1000s test_SwissProt ... ok 1003s test_TCoffee_tool ... ok 1003s test_TogoWS ... skipping. internet not available 1004s test_TreeConstruction ... ok 1005s test_UniGene ... ok 1005s test_UniProt ... skipping. internet not available 1006s test_UniProt_GOA ... ok 1007s test_UniProt_Parser ... ok 1007s test_align ... ok 1008s test_align_substitution_matrices ... ok 1011s test_bgzf ... ok 1012s test_cellosaurus ... ok 1018s test_codonalign ... ok 1018s test_geo ... ok 1019s test_kNN ... ok 1020s test_motifs ... ok 1021s test_motifs_online ... skipping. internet not available 1021s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 1021s warnings.warn( 1021s ok 1022s test_pairwise2_no_C ... ok 1023s test_pairwise_aligner ... ok 1023s test_pairwise_alignment_map ... ok 1031s test_phenotype ... ok 1031s test_phenotype_fit ... ok 1032s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 1033s test_prodoc ... ok 1033s test_prosite ... ok 1034s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1034s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1035s test_seq ... ok 1036s test_translate ... ok 1036s ---------------------------------------------------------------------- 1036s Ran 217 tests in 215.494 seconds 1036s 1036s Skipping any tests requiring internet access 1036s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 1036s Operating system: posix linux 1039s autopkgtest [10:52:20]: test full_suite: -----------------------] 1040s full_suite PASS 1040s autopkgtest [10:52:21]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1040s autopkgtest [10:52:21]: @@@@@@@@@@@@@@@@@@@@ summary 1040s dependencies PASS 1040s full_suite PASS 1055s nova [W] Skipping flock in bos03-arm64 1055s Creating nova instance adt-plucky-arm64-python-biopython-20241113-101405-juju-7f2275-prod-proposed-migration-environment-20-80e0b545-7c9a-4aa2-a1e0-686981182ff1 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 1055s nova [W] Skipping flock in bos03-arm64 1055s Creating nova instance adt-plucky-arm64-python-biopython-20241113-101405-juju-7f2275-prod-proposed-migration-environment-20-80e0b545-7c9a-4aa2-a1e0-686981182ff1 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...