0s autopkgtest [21:18:37]: starting date and time: 2024-11-13 21:18:37+0000 0s autopkgtest [21:18:37]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [21:18:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uqi18brx/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-40.secgroup --name adt-plucky-ppc64el-python-biopython-20241113-211837-juju-7f2275-prod-proposed-migration-environment-2-62acb108-b152-42e3-8330-d78f3f674de7 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -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/ 88s autopkgtest [21:20:05]: testbed dpkg architecture: ppc64el 88s autopkgtest [21:20:05]: testbed apt version: 2.9.8 88s autopkgtest [21:20:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 89s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [679 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 90s Fetched 1978 kB in 1s (1897 kB/s) 90s Reading package lists... 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade... 93s The following NEW packages will be installed: 93s python3.13-gdbm 93s The following packages will be upgraded: 93s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 93s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 93s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 94s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 4700 kB of archives. 94s After this operation, 215 kB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 94s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 94s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 94s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 94s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 94s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 94s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 94s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 94s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 94s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 94s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 94s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 94s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 95s Fetched 4700 kB in 1s (5460 kB/s) 95s (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 ... 73767 files and directories currently installed.) 95s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 95s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 95s Setting up python3-minimal (3.12.7-1) ... 95s (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 ... 73767 files and directories currently installed.) 95s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 95s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 95s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 95s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 96s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 96s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 96s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 96s (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 ... 73767 files and directories currently installed.) 96s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 96s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 96s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 96s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 96s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 96s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 96s Selecting previously unselected package python3.13-gdbm. 96s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 96s Unpacking python3.13-gdbm (3.13.0-2) ... 96s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 96s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 96s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 96s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 96s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 96s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 96s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 96s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 96s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 96s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 96s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 96s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 96s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 96s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 96s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 96s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 96s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 96s Setting up libutempter0:ppc64el (1.2.1-4) ... 96s Setting up whiptail (0.52.24-2ubuntu4) ... 96s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 96s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 96s Setting up python3.13-gdbm (3.13.0-2) ... 96s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 96s Setting up bpftrace (0.21.2-2ubuntu2) ... 96s Setting up python3 (3.12.7-1) ... 97s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 97s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 97s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 97s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 97s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 97s Processing triggers for man-db (2.12.1-3) ... 98s Processing triggers for libc-bin (2.40-1ubuntu3) ... 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 99s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 99s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 99s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 101s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s autopkgtest [21:20:21]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 105s autopkgtest [21:20:22]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 108s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (dsc) [3543 B] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (tar) [14.6 MB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (diff) [42.8 kB] 109s gpgv: Signature made Wed Oct 30 21:23:04 2024 UTC 109s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 109s gpgv: issuer "emollier@debian.org" 109s gpgv: Can't check signature: No public key 109s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4.dsc: no acceptable signature found 110s autopkgtest [21:20:27]: testing package python-biopython version 1.84+dfsg-4 110s autopkgtest [21:20:27]: build not needed 115s autopkgtest [21:20:32]: test dependencies: preparing testbed 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s The following additional packages will be installed: 117s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 117s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 117s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 117s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 117s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 117s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 117s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 117s python3-all python3-biopython python3-biopython-sql python3-cairo 117s python3-freetype python3-numpy python3-pil python3-reportlab 117s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 117s x11-common xfonts-encodings xfonts-utils xml-core 117s Suggested packages: 117s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 117s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 117s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 117s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 117s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 117s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 117s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 117s debhelper 117s Recommended packages: 117s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 117s The following NEW packages will be installed: 117s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 117s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 117s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 117s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 117s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 117s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 117s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 117s python-biopython-doc python3-all python3-biopython python3-biopython-sql 117s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 117s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 117s x11-common xfonts-encodings xfonts-utils xml-core 117s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 117s Need to get 53.8 MB/53.8 MB of archives. 117s After this operation, 157 MB of additional disk space will be used. 117s Get:1 /tmp/autopkgtest.KHTw7M/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [740 B] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 118s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 118s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 118s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 118s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 118s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 118s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 118s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 119s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 119s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 119s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 119s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 119s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 119s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 119s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 119s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 119s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 119s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 119s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 119s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 119s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 119s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 119s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 119s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 119s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 120s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 120s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 120s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 120s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB] 120s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 120s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 120s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 120s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 120s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 120s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 120s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 120s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 120s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 120s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 120s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 120s Get:42 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 121s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 121s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 121s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 121s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 121s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 121s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 121s Get:49 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 121s Get:50 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 121s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 121s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 121s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 121s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB] 121s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 121s Fetched 53.8 MB in 3s (15.5 MB/s) 121s Selecting previously unselected package libpython3.13-minimal:ppc64el. 121s (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 ... 73775 files and directories currently installed.) 121s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 121s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 122s Selecting previously unselected package python3.13-minimal. 122s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ... 122s Unpacking python3.13-minimal (3.13.0-2) ... 122s Selecting previously unselected package sgml-base. 122s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 122s Unpacking sgml-base (1.31) ... 122s Selecting previously unselected package fonts-dejavu-mono. 122s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 122s Unpacking fonts-dejavu-mono (2.37-8) ... 122s Selecting previously unselected package fonts-dejavu-core. 122s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 122s Unpacking fonts-dejavu-core (2.37-8) ... 122s Selecting previously unselected package libfontenc1:ppc64el. 122s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 122s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 122s Selecting previously unselected package x11-common. 122s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 122s Unpacking x11-common (1:7.7+23ubuntu3) ... 122s Selecting previously unselected package xfonts-encodings. 122s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 122s Unpacking xfonts-encodings 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previously unselected package libpixman-1-0:ppc64el. 123s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_ppc64el.deb ... 123s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 123s Selecting previously unselected package libxcb-render0:ppc64el. 123s Preparing to unpack .../14-libxcb-render0_1.17.0-2_ppc64el.deb ... 123s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 123s Selecting previously unselected package libxcb-shm0:ppc64el. 123s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_ppc64el.deb ... 123s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 123s Selecting previously unselected package libxrender1:ppc64el. 123s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 123s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 123s Selecting previously unselected package libcairo2:ppc64el. 123s Preparing to unpack .../17-libcairo2_1.18.2-2_ppc64el.deb ... 123s Unpacking libcairo2:ppc64el (1.18.2-2) ... 123s Selecting previously unselected package libdeflate0:ppc64el. 123s Preparing to unpack .../18-libdeflate0_1.22-1_ppc64el.deb ... 123s Unpacking libdeflate0:ppc64el (1.22-1) ... 123s Selecting previously unselected package libgfortran5:ppc64el. 123s Preparing to unpack .../19-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 123s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 123s Selecting previously unselected package libgomp1:ppc64el. 123s Preparing to unpack .../20-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 123s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 123s Selecting previously unselected package libgraphite2-3:ppc64el. 123s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 123s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 123s Selecting previously unselected package libharfbuzz0b:ppc64el. 123s Preparing to unpack .../22-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 123s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 123s Selecting previously unselected package libimagequant0:ppc64el. 123s 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unpack .../28-libjs-sphinxdoc_7.4.7-4_all.deb ... 123s Unpacking libjs-sphinxdoc (7.4.7-4) ... 123s Selecting previously unselected package liblapack3:ppc64el. 123s Preparing to unpack .../29-liblapack3_3.12.0-3build2_ppc64el.deb ... 123s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 123s Selecting previously unselected package liblcms2-2:ppc64el. 123s Preparing to unpack .../30-liblcms2-2_2.16-2_ppc64el.deb ... 123s Unpacking liblcms2-2:ppc64el (2.16-2) ... 123s Selecting previously unselected package liblerc4:ppc64el. 123s Preparing to unpack .../31-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 123s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 123s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 123s Preparing to unpack .../32-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ... 123s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ... 123s Selecting previously unselected package libraqm0:ppc64el. 123s Preparing to unpack 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previously unselected package libopenjp2-7:ppc64el. 124s Preparing to unpack .../44-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 124s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 124s Selecting previously unselected package python3-pil:ppc64el. 124s Preparing to unpack .../45-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 124s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 124s Selecting previously unselected package python3-cairo. 124s Preparing to unpack .../46-python3-cairo_1.26.1-2_ppc64el.deb ... 124s Unpacking python3-cairo (1.26.1-2) ... 124s Selecting previously unselected package python3-freetype. 124s Preparing to unpack .../47-python3-freetype_2.5.1-1_all.deb ... 124s Unpacking python3-freetype (2.5.1-1) ... 124s Selecting previously unselected package python3-rlpycairo. 124s Preparing to unpack .../48-python3-rlpycairo_0.3.0-3_all.deb ... 124s Unpacking python3-rlpycairo (0.3.0-3) ... 124s Selecting previously unselected package python3-reportlab. 124s Preparing to unpack .../49-python3-reportlab_4.2.5-1_all.deb ... 124s Unpacking python3-reportlab (4.2.5-1) ... 124s Selecting previously unselected package xml-core. 124s Preparing to unpack .../50-xml-core_0.19_all.deb ... 124s Unpacking xml-core (0.19) ... 124s Selecting previously unselected package w3c-sgml-lib. 124s Preparing to unpack .../51-w3c-sgml-lib_1.3-3_all.deb ... 124s Unpacking w3c-sgml-lib (1.3-3) ... 124s Selecting previously unselected package python3-biopython. 124s Preparing to unpack .../52-python3-biopython_1.84+dfsg-4_ppc64el.deb ... 124s Unpacking python3-biopython (1.84+dfsg-4) ... 125s Selecting previously unselected package python3-biopython-sql. 125s Preparing to unpack .../53-python3-biopython-sql_1.84+dfsg-4_all.deb ... 125s Unpacking python3-biopython-sql (1.84+dfsg-4) ... 125s Selecting previously unselected package autopkgtest-satdep. 125s Preparing to unpack .../54-1-autopkgtest-satdep.deb ... 125s Unpacking autopkgtest-satdep (0) ... 125s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 125s Setting up liblcms2-2:ppc64el (2.16-2) ... 125s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 125s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 125s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 125s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 125s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 125s Setting up x11-common (1:7.7+23ubuntu3) ... 125s Setting up libdeflate0:ppc64el (1.22-1) ... 125s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 125s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 125s Setting up python3-freetype (2.5.1-1) ... 126s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 126s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ... 126s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 126s Setting up libblas3:ppc64el (3.12.0-3build2) ... 126s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 126s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 126s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 126s Setting up fonts-dejavu-mono (2.37-8) ... 126s Setting up fonts-dejavu-core (2.37-8) ... 126s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 126s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 126s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 126s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 126s Setting up python3.13-minimal (3.13.0-2) ... 127s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 127s Setting up sgml-base (1.31) ... 127s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 127s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 127s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 127s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 127s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 127s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 127s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 127s Setting up python3.13 (3.13.0-2) ... 128s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 128s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 128s Setting up python3-all (3.12.7-1) ... 128s Setting up xfonts-utils (1:7.7+7) ... 128s Setting up libraqm0:ppc64el (0.10.1-1build1) ... 128s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 133s Setting up libjs-sphinxdoc (7.4.7-4) ... 133s Setting up python-biopython-doc (1.84+dfsg-4) ... 133s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 133s Setting up xml-core (0.19) ... 133s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 133s Setting up fonts-urw-base35 (20200910-8) ... 133s Setting up libcairo2:ppc64el (1.18.2-2) ... 133s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ... 134s Setting up python3-cairo (1.26.1-2) ... 134s Setting up python3-rlpycairo (0.3.0-3) ... 134s Setting up python3-reportlab (4.2.5-1) ... 136s Processing triggers for libc-bin (2.40-1ubuntu3) ... 136s Processing triggers for systemd (256.5-2ubuntu4) ... 136s Processing triggers for man-db (2.12.1-3) ... 137s Processing triggers for sgml-base (1.31) ... 137s Setting up w3c-sgml-lib (1.3-3) ... 171s Setting up python3-biopython (1.84+dfsg-4) ... 174s Setting up python3-biopython-sql (1.84+dfsg-4) ... 174s Setting up autopkgtest-satdep (0) ... 178s (Reading database ... 79914 files and directories currently installed.) 178s Removing autopkgtest-satdep (0) ... 179s autopkgtest [21:21:36]: test dependencies: sh debian/tests/run-unit-test 179s autopkgtest [21:21:36]: test dependencies: [----------------------- 179s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 179s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 179s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 179s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 181s mkdir: created directory 'Bio' 181s mkdir: created directory 'Bio/Align' 181s mkdir: created directory 'Bio/Align/substitution_matrices' 181s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 181s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 181s Remove test test_Tutorial.py which is bound to fail 182s test_Ace ... ok 182s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 182s 182s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 182s 182s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 182s 182s test_Align_a2m ... loading tests failed: 182s Failed to import test module: test_Align_a2m 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 182s test_Align_bed ... loading tests failed: 182s Failed to import test module: test_Align_bed 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 182s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_Align_bigmaf ... loading tests failed: 182s Failed to import test module: test_Align_bigmaf 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 182s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_Align_clustal ... loading tests failed: 182s Failed to import test module: test_Align_clustal 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 182s test_Align_codonalign ... loading tests failed: 182s Failed to import test module: test_Align_codonalign 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 182s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 182s 182s test_Align_fasta ... loading tests failed: 182s Failed to import test module: test_Align_fasta 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 182s test_Align_hhr ... loading tests failed: 182s Failed to import test module: test_Align_hhr 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 182s from . import multiarray 182s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 182s from . import overrides 182s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 182s from numpy.core._multiarray_umath import ( 182s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 182s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 182s 182s During handling of the above exception, another exception occurred: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 182s from numpy.__config__ import show as show_config 182s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 182s from numpy.core._multiarray_umath import ( 182s ...<3 lines>... 182s ) 182s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 182s raise ImportError(msg) 182s ImportError: 182s 182s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 182s 182s Importing the numpy C-extensions failed. This error can happen for 182s many reasons, often due to issues with your setup or how NumPy was 182s installed. 182s 182s We have compiled some common reasons and troubleshooting tips at: 182s 182s https://numpy.org/devdocs/user/troubleshooting-importerror.html 182s 182s Please note and check the following: 182s 182s * The Python version is: Python3.13 from "/usr/bin/python3.13" 182s * The NumPy version is: "1.26.4" 182s 182s and make sure that they are the versions you expect. 182s Please carefully study the documentation linked above for further help. 182s 182s Original error was: No module named 'numpy.core._multiarray_umath' 182s 182s 182s The above exception was the direct cause of the following exception: 182s 182s Traceback (most recent call last): 182s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 182s module = __import__(module_name) 182s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 182s import numpy as np 182s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 182s raise ImportError(msg) from e 182s ImportError: Error importing numpy: you should not try to import numpy from 182s its source directory; please exit the numpy source tree, and relaunch 182s your python interpreter from there. 182s 183s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Application ... ok 183s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Blast_Record ... loading tests failed: 183s Failed to import test module: test_Blast_Record 183s Traceback (most recent call last): 183s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 183s from . import multiarray 183s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 183s from . import overrides 183s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 183s from numpy.core._multiarray_umath import ( 183s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 183s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 183s 183s During handling of the above exception, another exception occurred: 183s 183s Traceback (most recent call last): 183s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 183s from numpy.__config__ import show as show_config 183s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 183s from numpy.core._multiarray_umath import ( 183s ...<3 lines>... 183s ) 183s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 183s raise ImportError(msg) 183s ImportError: 183s 183s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 183s 183s Importing the numpy C-extensions failed. This error can happen for 183s many reasons, often due to issues with your setup or how NumPy was 183s installed. 183s 183s We have compiled some common reasons and troubleshooting tips at: 183s 183s https://numpy.org/devdocs/user/troubleshooting-importerror.html 183s 183s Please note and check the following: 183s 183s * The Python version is: Python3.13 from "/usr/bin/python3.13" 183s * The NumPy version is: "1.26.4" 183s 183s and make sure that they are the versions you expect. 183s Please carefully study the documentation linked above for further help. 183s 183s Original error was: No module named 'numpy.core._multiarray_umath' 183s 183s 183s The above exception was the direct cause of the following exception: 183s 183s Traceback (most recent call last): 183s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 183s module = __import__(module_name) 183s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 183s from Bio.Blast.NCBIXML import HSP 183s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 183s import numpy as np 183s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 183s raise ImportError(msg) from e 183s ImportError: Error importing numpy: you should not try to import numpy from 183s its source directory; please exit the numpy source tree, and relaunch 183s your python interpreter from there. 183s 183s test_Blast_parser ... loading tests failed: 183s Failed to import test module: test_Blast_parser 183s Traceback (most recent call last): 183s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 183s from . import multiarray 183s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 183s from . import overrides 183s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 183s from numpy.core._multiarray_umath import ( 183s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 183s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 183s 183s During handling of the above exception, another exception occurred: 183s 183s Traceback (most recent call last): 183s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 183s from numpy.__config__ import show as show_config 183s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 183s from numpy.core._multiarray_umath import ( 183s ...<3 lines>... 183s ) 183s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 183s raise ImportError(msg) 183s ImportError: 183s 183s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 183s 183s Importing the numpy C-extensions failed. This error can happen for 183s many reasons, often due to issues with your setup or how NumPy was 183s installed. 183s 183s We have compiled some common reasons and troubleshooting tips at: 183s 183s https://numpy.org/devdocs/user/troubleshooting-importerror.html 183s 183s Please note and check the following: 183s 183s * The Python version is: Python3.13 from "/usr/bin/python3.13" 183s * The NumPy version is: "1.26.4" 183s 183s and make sure that they are the versions you expect. 183s Please carefully study the documentation linked above for further help. 183s 183s Original error was: No module named 'numpy.core._multiarray_umath' 183s 183s 183s The above exception was the direct cause of the following exception: 183s 183s Traceback (most recent call last): 183s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 183s module = __import__(module_name) 183s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 183s import numpy as np 183s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 183s raise ImportError(msg) from e 183s ImportError: Error importing numpy: you should not try to import numpy from 183s its source directory; please exit the numpy source tree, and relaunch 183s your python interpreter from there. 183s 183s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s 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 183s warnings.warn( 183s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 183s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 183s 184s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 184s 184s test_CodonTable ... ok 184s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 184s 184s test_Compass ... ok 184s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 184s 184s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 184s 184s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 184s 184s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 184s 184s test_EmbossPrimer ... ok 188s test_Entrez ... ok 188s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 188s 189s test_Entrez_parser ... ok 189s test_Enzyme ... ok 189s test_ExPASy ... skipping. internet not available 189s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 189s 189s test_File ... ok 189s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 189s 189s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 189s 189s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 189s 189s test_GraphicsDistribution ... loading tests failed: 189s Failed to import test module: test_GraphicsDistribution 189s Traceback (most recent call last): 189s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 189s module = __import__(module_name) 189s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 189s from Bio.Graphics.Distribution import BarChartDistribution 189s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 189s from reportlab.graphics.charts.barcharts import BarChartProperties 189s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 189s from reportlab.lib import colors 189s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 189s from reportlab.lib.rl_accel import fp_str 189s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 189s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 189s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 189s from PIL import Image 189s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 189s from . import _imaging as core 189s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 189s 189s test_GraphicsGeneral ... loading tests failed: 189s Failed to import test module: test_GraphicsGeneral 189s Traceback (most recent call last): 189s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 189s module = __import__(module_name) 189s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 189s from Bio.Graphics.Comparative import ComparativeScatterPlot 189s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 189s from reportlab.graphics.charts.lineplots import LinePlot 189s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 189s from reportlab.lib import colors 189s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 189s from reportlab.lib.rl_accel import fp_str 189s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 189s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 189s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 189s from PIL import Image 189s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 189s from . import _imaging as core 189s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 189s 189s test_HMMCasino ... ok 189s test_HMMGeneral ... ok 189s test_KEGG ... ok 189s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 189s 189s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 189s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 190s test_KGML_nographics ... ok 190s test_KeyWList ... ok 190s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 190s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 190s 190s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 190s 190s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 190s 190s test_Medline ... ok 190s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 190s 191s test_NCBIXML ... loading tests failed: 191s Failed to import test module: test_NCBIXML 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 191s from . import multiarray 191s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 191s from . import overrides 191s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 191s from numpy.core._multiarray_umath import ( 191s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 191s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 191s 191s During handling of the above exception, another exception occurred: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 191s from numpy.__config__ import show as show_config 191s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 191s from numpy.core._multiarray_umath import ( 191s ...<3 lines>... 191s ) 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 191s raise ImportError(msg) 191s ImportError: 191s 191s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 191s 191s Importing the numpy C-extensions failed. This error can happen for 191s many reasons, often due to issues with your setup or how NumPy was 191s installed. 191s 191s We have compiled some common reasons and troubleshooting tips at: 191s 191s https://numpy.org/devdocs/user/troubleshooting-importerror.html 191s 191s Please note and check the following: 191s 191s * The Python version is: Python3.13 from "/usr/bin/python3.13" 191s * The NumPy version is: "1.26.4" 191s 191s and make sure that they are the versions you expect. 191s Please carefully study the documentation linked above for further help. 191s 191s Original error was: No module named 'numpy.core._multiarray_umath' 191s 191s 191s The above exception was the direct cause of the following exception: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 191s module = __import__(module_name) 191s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 191s from Bio.Blast import NCBIXML 191s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 191s import numpy as np 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 191s raise ImportError(msg) from e 191s ImportError: Error importing numpy: you should not try to import numpy from 191s its source directory; please exit the numpy source tree, and relaunch 191s your python interpreter from there. 191s 191s test_NCBI_BLAST_tools ... loading tests failed: 191s Failed to import test module: test_NCBI_BLAST_tools 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 191s from . import multiarray 191s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 191s from . import overrides 191s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 191s from numpy.core._multiarray_umath import ( 191s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 191s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 191s 191s During handling of the above exception, another exception occurred: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 191s from numpy.__config__ import show as show_config 191s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 191s from numpy.core._multiarray_umath import ( 191s ...<3 lines>... 191s ) 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 191s raise ImportError(msg) 191s ImportError: 191s 191s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 191s 191s Importing the numpy C-extensions failed. This error can happen for 191s many reasons, often due to issues with your setup or how NumPy was 191s installed. 191s 191s We have compiled some common reasons and troubleshooting tips at: 191s 191s https://numpy.org/devdocs/user/troubleshooting-importerror.html 191s 191s Please note and check the following: 191s 191s * The Python version is: Python3.13 from "/usr/bin/python3.13" 191s * The NumPy version is: "1.26.4" 191s 191s and make sure that they are the versions you expect. 191s Please carefully study the documentation linked above for further help. 191s 191s Original error was: No module named 'numpy.core._multiarray_umath' 191s 191s 191s The above exception was the direct cause of the following exception: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 191s module = __import__(module_name) 191s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 191s from Bio.Blast import Applications 191s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 191s import numpy as np 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 191s raise ImportError(msg) from e 191s ImportError: Error importing numpy: you should not try to import numpy from 191s its source directory; please exit the numpy source tree, and relaunch 191s your python interpreter from there. 191s 191s test_NCBI_qblast ... loading tests failed: 191s Failed to import test module: test_NCBI_qblast 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 191s from . import multiarray 191s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 191s from . import overrides 191s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 191s from numpy.core._multiarray_umath import ( 191s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 191s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 191s 191s During handling of the above exception, another exception occurred: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 191s from numpy.__config__ import show as show_config 191s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 191s from numpy.core._multiarray_umath import ( 191s ...<3 lines>... 191s ) 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 191s raise ImportError(msg) 191s ImportError: 191s 191s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 191s 191s Importing the numpy C-extensions failed. This error can happen for 191s many reasons, often due to issues with your setup or how NumPy was 191s installed. 191s 191s We have compiled some common reasons and troubleshooting tips at: 191s 191s https://numpy.org/devdocs/user/troubleshooting-importerror.html 191s 191s Please note and check the following: 191s 191s * The Python version is: Python3.13 from "/usr/bin/python3.13" 191s * The NumPy version is: "1.26.4" 191s 191s and make sure that they are the versions you expect. 191s Please carefully study the documentation linked above for further help. 191s 191s Original error was: No module named 'numpy.core._multiarray_umath' 191s 191s 191s The above exception was the direct cause of the following exception: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 191s module = __import__(module_name) 191s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 191s from Bio.Blast import NCBIWWW 191s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 191s import numpy as np 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 191s raise ImportError(msg) from e 191s ImportError: Error importing numpy: you should not try to import numpy from 191s its source directory; please exit the numpy source tree, and relaunch 191s your python interpreter from there. 191s 191s test_NMR ... ok 191s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 191s 191s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 191s 191s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_Disordered ... loading tests failed: 191s Failed to import test module: test_PDB_Disordered 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 191s from . import multiarray 191s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 191s from . import overrides 191s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 191s from numpy.core._multiarray_umath import ( 191s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 191s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 191s 191s During handling of the above exception, another exception occurred: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 191s from numpy.__config__ import show as show_config 191s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 191s from numpy.core._multiarray_umath import ( 191s ...<3 lines>... 191s ) 191s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 191s raise ImportError(msg) 191s ImportError: 191s 191s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 191s 191s Importing the numpy C-extensions failed. This error can happen for 191s many reasons, often due to issues with your setup or how NumPy was 191s installed. 191s 191s We have compiled some common reasons and troubleshooting tips at: 191s 191s https://numpy.org/devdocs/user/troubleshooting-importerror.html 191s 191s Please note and check the following: 191s 191s * The Python version is: Python3.13 from "/usr/bin/python3.13" 191s * The NumPy version is: "1.26.4" 191s 191s and make sure that they are the versions you expect. 191s Please carefully study the documentation linked above for further help. 191s 191s Original error was: No module named 'numpy.core._multiarray_umath' 191s 191s 191s The above exception was the direct cause of the following exception: 191s 191s Traceback (most recent call last): 191s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 191s module = __import__(module_name) 191s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 191s import numpy as np 191s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 191s raise ImportError(msg) from e 191s ImportError: Error importing numpy: you should not try to import numpy from 191s its source directory; please exit the numpy source tree, and relaunch 191s your python interpreter from there. 191s 191s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 191s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 191s 191s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 191s 191s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 191s 191s test_Pathway ... ok 191s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 191s 191s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 191s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 191s 192s test_PopGen_GenePop_nodepend ... ok 192s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_ProtParam ... ok 192s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 192s 192s test_Restriction ... ok 192s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 192s 192s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 192s 192s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 192s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 192s 193s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 193s 193s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 193s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 193s 193s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 193s 194s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 194s 194s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 194s 194s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 194s 194s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 194s 194s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 194s 194s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 194s 194s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 194s 194s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 194s 194s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 194s 194s test_UniGene ... ok 194s test_UniProt ... skipping. internet not available 194s test_UniProt_GOA ... ok 194s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 194s 194s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 194s 194s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 197s test_bgzf ... ok 197s test_cellosaurus ... ok 197s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 197s 197s test_geo ... ok 197s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 197s 197s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 197s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 197s 197s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 197s 197s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 197s 197s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 197s 198s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 198s 198s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 198s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 198s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 198s 198s test_prodoc ... ok 198s test_prosite ... ok 198s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 198s 198s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 198s test_seq ... ok 198s test_translate ... ok 198s ---------------------------------------------------------------------- 198s Ran 217 tests in 16.371 seconds 198s 198s FAILED (failures = 15) 198s Skipping any tests requiring internet access 198s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 198s Operating system: posix linux 198s test_Ace ... ok 198s test_Affy ... ok 203s test_AlignIO ... ok 203s test_AlignIO_ClustalIO ... ok 203s test_AlignIO_EmbossIO ... ok 203s test_AlignIO_FastaIO ... ok 203s test_AlignIO_MauveIO ... ok 203s test_AlignIO_PhylipIO ... ok 203s test_AlignIO_convert ... ok 203s test_AlignInfo ... ok 203s test_Align_Alignment ... ok 203s test_Align_a2m ... ok 203s test_Align_bed ... ok 204s test_Align_bigbed ... ok 204s test_Align_bigmaf ... ok 205s test_Align_bigpsl ... ok 205s test_Align_chain ... ok 205s test_Align_clustal ... ok 209s test_Align_codonalign ... ok 209s test_Align_emboss ... ok 210s test_Align_exonerate ... ok 210s test_Align_fasta ... ok 210s test_Align_hhr ... ok 211s test_Align_maf ... ok 211s test_Align_mauve ... ok 211s test_Align_msf ... ok 211s test_Align_nexus ... ok 212s test_Align_phylip ... ok 212s test_Align_psl ... ok 213s test_Align_sam ... ok 215s test_Align_stockholm ... ok 215s test_Align_tabular ... ok 215s test_Application ... ok 216s test_BioSQL_MySQLdb_online ... skipping. internet not available 216s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 216s test_BioSQL_mysql_connector_online ... skipping. internet not available 216s test_BioSQL_psycopg2_online ... skipping. internet not available 222s test_BioSQL_sqlite3 ... ok 222s test_BioSQL_sqlite3_online ... skipping. internet not available 222s test_Blast_Record ... ok 223s test_Blast_parser ... ok 223s test_CAPS ... ok 223s test_Chi2 ... ok 223s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 223s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 223s test_Cluster ... ok 223s test_CodonTable ... ok 224s test_ColorSpiral ... ok 224s test_Compass ... ok 226s test_Consensus ... ok 226s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 226s test_EMBL_unittest ... ok 226s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 226s test_EmbossPrimer ... ok 230s test_Entrez ... ok 230s test_Entrez_online ... skipping. internet not available 231s test_Entrez_parser ... ok 231s test_Enzyme ... ok 231s test_ExPASy ... skipping. internet not available 231s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 231s test_File ... ok 231s test_GenBank ... ok 234s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 237s ok 238s test_GraphicsChromosome ... ok 238s test_GraphicsDistribution ... ok 239s test_GraphicsGeneral ... ok 240s test_HMMCasino ... ok 240s test_HMMGeneral ... ok 240s test_KEGG ... ok 240s test_KEGG_online ... skipping. internet not available 247s test_KGML_graphics ... ok 247s test_KGML_graphics_online ... skipping. internet not available 248s test_KGML_nographics ... ok 248s test_KeyWList ... ok 248s test_LogisticRegression ... ok 249s test_MafIO_index ... ok 249s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 250s test_MarkovModel ... ok 250s test_Medline ... ok 250s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 251s test_NCBIXML ... ok 251s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 251s test_NCBI_qblast ... ok 251s test_NMR ... ok 251s test_NaiveBayes ... ok 251s test_Nexus ... ok 251s test_PAML_baseml ... ok 252s test_PAML_codeml ... ok 252s test_PAML_yn00 ... ok 255s test_PDB_CEAligner ... ok 256s test_PDB_DSSP ... ok 256s test_PDB_Dice ... ok 256s test_PDB_Disordered ... ok 256s test_PDB_Exposure ... ok 256s test_PDB_FragmentMapper ... ok 259s test_PDB_KDTree ... ok 259s test_PDB_MMCIF2Dict ... ok 259s test_PDB_MMCIFIO ... ok 261s test_PDB_MMCIFParser ... ok 261s test_PDB_NACCESS ... ok 261s test_PDB_PDBIO ... ok 261s test_PDB_PDBList ... skipping. internet not available 270s test_PDB_PDBMLParser ... ok 270s test_PDB_PDBParser ... ok 271s 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 271s test_PDB_Polypeptide ... ok 271s test_PDB_QCPSuperimposer ... ok 275s test_PDB_SASA ... ok 276s test_PDB_SMCRA ... ok 276s test_PDB_Selection ... ok 276s test_PDB_StructureAlignment ... ok 276s test_PDB_Superimposer ... ok 276s test_PDB_alphafold_db ... skipping. internet not available 277s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 277s 277s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 277s 277s test_PDB_parse_pdb_header ... ok 277s test_PDB_vectors ... ok 277s test_PQR ... ok 277s test_Pathway ... ok 277s test_Phd ... ok 277s test_Phylo ... ok 278s test_PhyloXML ... ok 278s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 278s test_Phylo_NeXML ... ok 278s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 278s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 278s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 278s test_PopGen_GenePop_nodepend ... ok 278s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 278s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 278s test_ProtParam ... ok 279s test_RCSBFormats ... ok 279s test_Restriction ... ok 279s test_SCOP_Astral ... ok 279s test_SCOP_Cla ... ok 279s test_SCOP_Des ... ok 279s test_SCOP_Dom ... ok 279s test_SCOP_Hie ... ok 279s test_SCOP_Raf ... ok 279s test_SCOP_Residues ... ok 279s test_SCOP_Scop ... ok 279s test_SVDSuperimposer ... ok 280s test_SearchIO_blast_tab ... ok 280s test_SearchIO_blast_tab_index ... ok 280s test_SearchIO_blast_xml ... ok 281s test_SearchIO_blast_xml_index ... ok 281s test_SearchIO_blat_psl ... ok 282s test_SearchIO_blat_psl_index ... ok 282s test_SearchIO_exonerate ... ok 282s test_SearchIO_exonerate_text_index ... ok 282s test_SearchIO_exonerate_vulgar_index ... ok 282s test_SearchIO_fasta_m10 ... ok 282s test_SearchIO_fasta_m10_index ... ok 282s test_SearchIO_hhsuite2_text ... ok 283s test_SearchIO_hmmer2_text ... ok 283s test_SearchIO_hmmer2_text_index ... ok 283s test_SearchIO_hmmer3_domtab ... ok 283s test_SearchIO_hmmer3_domtab_index ... ok 283s test_SearchIO_hmmer3_tab ... ok 283s test_SearchIO_hmmer3_tab_index ... ok 283s test_SearchIO_hmmer3_text ... ok 283s test_SearchIO_hmmer3_text_index ... ok 283s test_SearchIO_interproscan_xml ... ok 283s test_SearchIO_model ... ok 284s test_SearchIO_write ... ok 284s test_SeqFeature ... ok 306s test_SeqIO ... ok 306s test_SeqIO_AbiIO ... ok 306s test_SeqIO_FastaIO ... ok 306s test_SeqIO_Gck ... ok 306s test_SeqIO_Gfa ... ok 306s test_SeqIO_Insdc ... ok 306s test_SeqIO_NibIO ... ok 309s test_SeqIO_PdbIO ... ok 309s test_SeqIO_QualityIO ... ok 310s test_SeqIO_SeqXML ... ok 310s test_SeqIO_SnapGene ... ok 311s test_SeqIO_TwoBitIO ... ok 311s test_SeqIO_Xdna ... ok 312s test_SeqIO_features ... ok 337s test_SeqIO_index ... ok 337s test_SeqIO_online ... skipping. internet not available 337s test_SeqIO_write ... ok 337s test_SeqRecord ... ok 337s test_SeqUtils ... ok 339s test_Seq_objs ... ok 340s test_SffIO ... ok 340s test_SwissProt ... ok 340s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 340s test_TogoWS ... skipping. internet not available 340s test_TreeConstruction ... ok 341s test_UniGene ... ok 341s test_UniProt ... skipping. internet not available 341s test_UniProt_GOA ... ok 341s test_UniProt_Parser ... ok 341s test_align ... ok 341s test_align_substitution_matrices ... ok 344s test_bgzf ... ok 344s test_cellosaurus ... ok 352s test_codonalign ... ok 352s test_geo ... ok 352s test_kNN ... ok 352s test_motifs ... ok 353s test_motifs_online ... skipping. internet not available 353s 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. 353s warnings.warn( 353s ok 353s test_pairwise2_no_C ... ok 353s test_pairwise_aligner ... ok 353s test_pairwise_alignment_map ... ok 362s test_phenotype ... ok 362s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 362s 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. 362s test_prodoc ... ok 362s test_prosite ... ok 362s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 362s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 362s test_seq ... ok 363s test_translate ... ok 363s ---------------------------------------------------------------------- 363s Ran 217 tests in 164.356 seconds 363s 363s Skipping any tests requiring internet access 363s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 363s Operating system: posix linux 363s autopkgtest [21:24:40]: test dependencies: -----------------------] 364s autopkgtest [21:24:41]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 364s dependencies PASS 364s autopkgtest [21:24:41]: test full_suite: preparing testbed 477s autopkgtest [21:26:34]: testbed dpkg architecture: ppc64el 477s autopkgtest [21:26:34]: testbed apt version: 2.9.8 477s autopkgtest [21:26:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 478s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 478s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 478s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 478s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 479s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 479s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB] 479s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [679 kB] 479s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 479s Fetched 1978 kB in 1s (1958 kB/s) 479s Reading package lists... 481s Reading package lists... 482s Building dependency tree... 482s Reading state information... 482s Calculating upgrade... 482s The following NEW packages will be installed: 482s python3.13-gdbm 482s The following packages will be upgraded: 482s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 482s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 482s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 482s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 482s Need to get 4700 kB of archives. 482s After this operation, 215 kB of additional disk space will be used. 482s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 482s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 482s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 482s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 482s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 482s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 482s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 482s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 482s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 482s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 483s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 483s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 483s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 483s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 483s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 483s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 483s Fetched 4700 kB in 1s (6249 kB/s) 483s (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 ... 73767 files and directories currently installed.) 483s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 483s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 483s Setting up python3-minimal (3.12.7-1) ... 484s (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 ... 73767 files and directories currently installed.) 484s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 484s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 484s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 484s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 484s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 484s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 484s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 484s (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 ... 73767 files and directories currently installed.) 484s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 484s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 484s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 484s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 484s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 484s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 484s Selecting previously unselected package python3.13-gdbm. 484s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 484s Unpacking python3.13-gdbm (3.13.0-2) ... 484s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 484s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 484s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 484s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 484s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 484s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 484s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 484s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 484s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 484s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 484s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 484s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 484s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 484s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 484s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 484s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 484s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 484s Setting up libutempter0:ppc64el (1.2.1-4) ... 484s Setting up whiptail (0.52.24-2ubuntu4) ... 484s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 484s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 484s Setting up python3.13-gdbm (3.13.0-2) ... 484s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 484s Setting up bpftrace (0.21.2-2ubuntu2) ... 484s Setting up python3 (3.12.7-1) ... 485s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 485s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 485s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 485s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 485s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 485s Processing triggers for man-db (2.12.1-3) ... 486s Processing triggers for libc-bin (2.40-1ubuntu3) ... 487s Reading package lists... 487s Building dependency tree... 487s Reading state information... 487s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 487s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 487s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 487s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 488s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 488s Reading package lists... 488s Reading package lists... 489s Building dependency tree... 489s Reading state information... 489s Calculating upgrade... 489s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 489s Reading package lists... 489s Building dependency tree... 489s Reading state information... 490s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 493s Reading package lists... 493s Building dependency tree... 493s Reading state information... 494s Starting pkgProblemResolver with broken count: 0 494s Starting 2 pkgProblemResolver with broken count: 0 494s Done 494s The following additional packages will be installed: 494s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 494s cpp cpp-14 cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper 494s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 494s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 494s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 494s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 494s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 494s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext ghostscript 494s hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 494s intltool-debian libaom3 libapache-pom-java libarchive-zip-perl 494s libargtable2-0 libasan8 libavahi-client3 libavahi-common-data 494s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 494s libcommons-logging-java libcommons-parent-java libcups2t64 libde265-0 494s libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 494s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 494s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 494s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 494s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libice6 libidn12 libijs-0.35 494s libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 494s libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore 494s libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 494s liblqr-1-0 liblsan0 libltdl7 libmagickcore-6.q16-7t64 494s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 494s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 494s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libpq5 libptexenc1 494s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.13 494s libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 494s libquadmath0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 494s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 494s libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 494s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 494s libxt6t64 libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm 494s phylip po-debconf poppler-data prank preview-latex-style probcons 494s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 494s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 494s python3-brotli python3-cairo python3-contourpy python3-cycler 494s python3-dateutil python3-decorator python3-defusedxml python3-dev 494s python3-docutils python3-fonttools python3-freetype python3-fs 494s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 494s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 494s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 494s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 494s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 494s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 494s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 494s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 494s python3.13-dev python3.13-minimal python3.13-tk sgml-base sphinx-common 494s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 494s texlive-binaries texlive-fonts-recommended texlive-latex-base 494s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 494s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 494s xfonts-encodings xfonts-utils xml-core zlib1g-dev 494s Suggested packages: 494s autoconf-archive gnu-standards autoconf-doc blt-demo samtools cpp-doc 494s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 494s python3-wheel emboss-doc emboss-test embassy clustalw bison flex-doc 494s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-14-doc 494s gcc-multilib manpages-dev gdb gcc-doc gdb-powerpc64le-linux-gnu gettext-doc 494s libasprintf-dev libgettextpo-dev hevea-doc imagemagick-6-doc autotrace 494s cups-bsd | lpr | lprng enscript ffmpeg gimp gnuplot grads graphviz hp2xx 494s html2ps libwmf-bin mplayer povray radiance sane-utils transfig libraw-bin 494s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 494s cups-common libfftw3-bin libfftw3-dev libgd-tools libheif-plugin-x265 494s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 494s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 494s libheif-plugin-rav1e libheif-plugin-svtenc libjs-jquery-ui-docs 494s liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc libstdc++-14-doc 494s tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 494s phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho 494s | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic 494s fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra muscle3 494s phyml python3-psycopg2 raxml python-cycler-doc docutils-doc 494s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 494s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 494s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 494s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 494s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 494s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 494s gfortran python-numpy-doc python3-pytest python-pil-doc python-rdflib-doc 494s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 494s rl-renderpm python-scipy-doc python3-stemmer dvisvgm fonts-freefont-otf 494s latexmk libjs-mathjax sphinx-doc tex-gyre texlive-fonts-extra 494s texlive-plain-generic python-sympy-doc tix python3-tk-dbg python3.13-venv 494s python3.13-doc binfmt-support sgml-base-doc boxshade seaview 494s t-coffee-examples perl-tk xpdf | pdf-viewer xzdec hintview 494s texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex icc-profiles 494s libfile-which-perl texlive-latex-extra-doc texlive-science 494s texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex 494s texlive-pictures-doc vprerex wise-doc 494s Recommended packages: 494s primer3 libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 494s fonts-droid-fallback libheif-plugin-aomenc javascript-common libjson-xs-perl 494s libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 494s python3-cssselect python3-html5lib python3-olefile python3-sparqlwrapper 494s fonts-dejavu-extra isympy-common amap-align clustalw dialign-tx fsa kalign 494s libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align 494s lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 494s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 494s libx11-protocol-perl x11-utils x11-xserver-utils 494s The following NEW packages will be installed: 494s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 494s build-essential bwa clustalo cpp cpp-14 cpp-14-powerpc64le-linux-gnu 494s cpp-powerpc64le-linux-gnu debhelper debugedit dh-autoreconf dh-python 494s dh-strip-nondeterminism dialign docutils-common dssp dwz emboss emboss-data 494s emboss-lib fasttree flex fontconfig-config fonts-dejavu-core 494s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 494s fonts-urw-base35 g++ g++-14 g++-14-powerpc64le-linux-gnu 494s g++-powerpc64le-linux-gnu gcc gcc-14 gcc-14-powerpc64le-linux-gnu 494s gcc-powerpc64le-linux-gnu gettext ghostscript hevea hicolor-icon-theme 494s imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 494s libapache-pom-java libarchive-zip-perl libargtable2-0 libasan8 494s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcairo2 494s libcc1-0 libcifpp-data libcifpp7 libcommons-logging-java 494s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 494s libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 494s libfontbox-java libfontconfig1 libfontenc1 libgcc-14-dev libgd3 libgfortran5 494s libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b 494s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libice6 494s libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 494s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 494s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 494s liblerc4 liblqr-1-0 liblsan0 libltdl7 libmagickcore-6.q16-7t64 494s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 494s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 494s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libpq5 libptexenc1 494s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.13 494s libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 494s libquadmath0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 494s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 494s libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 494s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 494s libxt6t64 libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm 494s phylip po-debconf poppler-data prank preview-latex-style probcons 494s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 494s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 494s python3-brotli python3-cairo python3-contourpy python3-cycler 494s python3-dateutil python3-decorator python3-defusedxml python3-dev 494s python3-docutils python3-fonttools python3-freetype python3-fs 494s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 494s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 494s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 494s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 494s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 494s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 494s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 494s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 494s python3.13-dev python3.13-minimal python3.13-tk sgml-base sphinx-common 494s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 494s texlive-binaries texlive-fonts-recommended texlive-latex-base 494s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 494s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 494s xfonts-encodings xfonts-utils xml-core zlib1g-dev 494s 0 upgraded, 260 newly installed, 0 to remove and 0 not upgraded. 494s Need to get 419 MB/419 MB of archives. 494s After this operation, 1907 MB of additional disk space will be used. 494s Get:1 /tmp/autopkgtest.KHTw7M/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [1004 B] 494s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB] 495s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el flex ppc64el 2.6.4-8.2build1 [303 kB] 495s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-lato all 2.015-1 [2781 kB] 495s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 495s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfftw3-double3 ppc64el 3.3.10-1ubuntu4 [443 kB] 495s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 495s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 495s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 495s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 495s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 495s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 495s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 495s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 495s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 495s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 495s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libaom3 ppc64el 3.11.0~rc1-1 [3022 kB] 496s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif-plugin-aomdec ppc64el 1.18.1-2 [11.2 kB] 496s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libde265-0 ppc64el 1.0.15-1build4 [284 kB] 496s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif-plugin-libde265 ppc64el 1.18.1-2 [9068 B] 496s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif1 ppc64el 1.18.1-2 [340 kB] 496s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 496s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 496s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 496s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 496s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblqr-1-0 ppc64el 0.4.2-2.1build2 [43.4 kB] 496s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libltdl7 ppc64el 2.4.7-7build1 [48.2 kB] 496s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 496s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraw23t64 ppc64el 0.21.3-1 [510 kB] 496s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 496s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 496s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 496s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 496s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 496s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 496s Get:36 http://ftpmaster.internal/ubuntu plucky/universe ppc64el imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 496s Get:37 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmagickcore-6.q16-7t64 ppc64el 8:6.9.13.12+dfsg1-1build1 [2252 kB] 496s Get:38 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmagickwand-6.q16-7t64 ppc64el 8:6.9.13.12+dfsg1-1build1 [291 kB] 496s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el poppler-data all 0.4.12-1 [2060 kB] 496s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 496s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 496s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 496s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el autoconf all 2.72-3 [382 kB] 496s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 496s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 496s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el autopoint all 0.22.5-2 [616 kB] 496s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB] 496s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 496s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 496s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 496s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB] 496s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB] 496s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B] 496s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 496s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 496s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [10.5 MB] 497s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-8ubuntu1 [1034 B] 497s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [5456 B] 497s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.1.0-2ubuntu1 [22.5 kB] 497s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 14.2.0-8ubuntu1 [48.1 kB] 497s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 14.2.0-8ubuntu1 [31.9 kB] 497s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 14.2.0-8ubuntu1 [2945 kB] 497s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 14.2.0-8ubuntu1 [1322 kB] 497s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 14.2.0-8ubuntu1 [2695 kB] 497s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 14.2.0-8ubuntu1 [1191 kB] 497s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 14.2.0-8ubuntu1 [158 kB] 497s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-8ubuntu1 [1619 kB] 497s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [20.6 MB] 498s Get:69 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-8ubuntu1 [528 kB] 498s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [1222 B] 498s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.1.0-2ubuntu1 [5006 B] 498s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-8ubuntu1 [2673 kB] 498s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [12.0 MB] 499s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-8ubuntu1 [19.9 kB] 499s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [968 B] 499s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.1.0-2ubuntu1 [1090 B] 499s Get:77 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 499s Get:78 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bwa ppc64el 0.7.18-1 [231 kB] 499s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libargtable2-0 ppc64el 13-2 [18.9 kB] 499s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el clustalo ppc64el 1.2.4-8build1 [246 kB] 499s Get:81 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 499s Get:82 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtool all 2.4.7-7build1 [166 kB] 499s Get:83 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-autoreconf all 20 [16.1 kB] 499s Get:84 http://ftpmaster.internal/ubuntu plucky/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 499s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 499s Get:86 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-strip-nondeterminism all 1.14.0-1 [5058 B] 499s Get:87 http://ftpmaster.internal/ubuntu plucky/main ppc64el debugedit ppc64el 1:5.1-1 [52.1 kB] 499s Get:88 http://ftpmaster.internal/ubuntu plucky/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] 499s Get:89 http://ftpmaster.internal/ubuntu plucky/main ppc64el gettext ppc64el 0.22.5-2 [1082 kB] 499s Get:90 http://ftpmaster.internal/ubuntu plucky/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 499s Get:91 http://ftpmaster.internal/ubuntu plucky/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 499s Get:92 http://ftpmaster.internal/ubuntu plucky/main ppc64el debhelper all 13.20ubuntu1 [893 kB] 499s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dh-python all 6.20241024 [112 kB] 499s Get:94 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dialign ppc64el 2.2.1-13 [158 kB] 499s Get:95 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 499s Get:96 http://ftpmaster.internal/ubuntu plucky/main ppc64el docutils-common all 0.21.2+dfsg-2 [131 kB] 499s Get:97 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcifpp-data all 7.0.7-3 [480 kB] 499s Get:98 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcifpp7 ppc64el 7.0.7-3 [1123 kB] 499s Get:99 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dssp ppc64el 4.4.10-1 [793 kB] 499s Get:100 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 499s Get:101 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 499s Get:102 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 499s Get:103 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 499s Get:104 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxpm4 ppc64el 1:3.5.17-1build2 [49.9 kB] 499s Get:105 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgd3 ppc64el 2.3.3-12ubuntu3 [165 kB] 499s Get:106 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhpdf-2.3.0 ppc64el 2.3.0+dfsg-1build3 [460 kB] 500s Get:107 http://ftpmaster.internal/ubuntu plucky/main ppc64el mysql-common all 5.8+1.1.1 [6800 B] 500s Get:108 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmysqlclient21 ppc64el 8.0.40-1 [1294 kB] 500s Get:109 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpq5 ppc64el 17.0-1 [280 kB] 500s Get:110 http://ftpmaster.internal/ubuntu plucky/universe ppc64el emboss-lib ppc64el 6.6.0+dfsg-12ubuntu2 [3460 kB] 500s Get:111 http://ftpmaster.internal/ubuntu plucky/universe ppc64el emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 502s Get:112 http://ftpmaster.internal/ubuntu plucky/universe ppc64el emboss ppc64el 6.6.0+dfsg-12ubuntu2 [1041 kB] 502s Get:113 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 502s Get:114 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lmodern all 2.005-1 [4799 kB] 503s Get:115 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB] 503s Get:116 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 503s Get:117 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 503s Get:118 http://ftpmaster.internal/ubuntu plucky/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu6 [29.7 kB] 503s Get:119 http://ftpmaster.internal/ubuntu plucky/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu6 [26.3 kB] 503s Get:120 http://ftpmaster.internal/ubuntu plucky/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu6 [30.8 kB] 503s Get:121 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcups2t64 ppc64el 2.4.10-1ubuntu2 [345 kB] 503s Get:122 http://ftpmaster.internal/ubuntu plucky/main ppc64el libidn12 ppc64el 1.42-2 [61.8 kB] 503s Get:123 http://ftpmaster.internal/ubuntu plucky/main ppc64el libijs-0.35 ppc64el 0.35-15.1build1 [16.9 kB] 503s Get:124 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig2dec0 ppc64el 0.20-1build3 [90.9 kB] 503s Get:125 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper1 ppc64el 1.1.29build1 [13.7 kB] 503s Get:126 http://ftpmaster.internal/ubuntu plucky/main ppc64el libice6 ppc64el 2:1.1.1-1 [49.9 kB] 503s Get:127 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsm6 ppc64el 2:1.2.4-1 [18.4 kB] 503s Get:128 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB] 503s Get:129 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgs10 ppc64el 10.03.1~dfsg1-0ubuntu2 [4946 kB] 503s Get:130 http://ftpmaster.internal/ubuntu plucky/main ppc64el ghostscript ppc64el 10.03.1~dfsg1-0ubuntu2 [43.6 kB] 503s Get:131 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libnetpbm11t64 ppc64el 2:11.08.01-1 [142 kB] 503s Get:132 http://ftpmaster.internal/ubuntu plucky/universe ppc64el netpbm ppc64el 2:11.08.01-1 [2573 kB] 503s Get:133 http://ftpmaster.internal/ubuntu plucky/universe ppc64el tex-common all 6.18 [32.8 kB] 503s Get:134 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper-utils ppc64el 1.1.29build1 [8742 B] 503s Get:135 http://ftpmaster.internal/ubuntu plucky/main ppc64el libkpathsea6 ppc64el 2024.20240313.70630+ds-5 [72.1 kB] 503s Get:136 http://ftpmaster.internal/ubuntu plucky/main ppc64el libptexenc1 ppc64el 2024.20240313.70630+ds-5 [44.9 kB] 503s Get:137 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsynctex2 ppc64el 2024.20240313.70630+ds-5 [68.1 kB] 503s Get:138 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtexlua53-5 ppc64el 2024.20240313.70630+ds-5 [163 kB] 503s Get:139 http://ftpmaster.internal/ubuntu plucky/main ppc64el t1utils ppc64el 1.41-4build3 [69.7 kB] 503s Get:140 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 503s Get:141 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 503s Get:142 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 503s Get:143 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 503s Get:144 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmpfi0 ppc64el 1.5.4+ds-4 [38.6 kB] 503s Get:145 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpotrace0 ppc64el 1.16-2build1 [23.0 kB] 503s Get:146 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libteckit0 ppc64el 2.5.12+ds1-1 [399 kB] 503s Get:147 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxmu6 ppc64el 2:1.1.3-3build2 [56.8 kB] 503s Get:148 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxaw7 ppc64el 2:1.0.16-1 [230 kB] 503s Get:149 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxi6 ppc64el 2:1.8.2-1 [37.9 kB] 503s Get:150 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libzzip-0-13t64 ppc64el 0.13.72+dfsg.1-1.2build1 [32.2 kB] 503s Get:151 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-binaries ppc64el 2024.20240313.70630+ds-5 [12.4 MB] 504s Get:152 http://ftpmaster.internal/ubuntu plucky/main ppc64el xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 504s Get:153 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-base all 2024.20241102-1 [22.5 MB] 506s Get:154 http://ftpmaster.internal/ubuntu plucky/main ppc64el hicolor-icon-theme all 0.18-1 [13.5 kB] 506s Get:155 http://ftpmaster.internal/ubuntu plucky/universe ppc64el imagemagick-6.q16 ppc64el 8:6.9.13.12+dfsg1-1build1 [254 kB] 506s Get:156 http://ftpmaster.internal/ubuntu plucky/universe ppc64el imagemagick ppc64el 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 506s Get:157 http://ftpmaster.internal/ubuntu plucky/universe ppc64el hevea ppc64el 2.36-2 [2153 kB] 506s Get:158 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libapache-pom-java all 33-2 [5874 B] 506s Get:159 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 506s Get:160 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB] 506s Get:161 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 506s Get:162 http://ftpmaster.internal/ubuntu plucky/main ppc64el libexpat1-dev ppc64el 2.6.2-2 [149 kB] 506s Get:163 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 506s Get:164 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 506s Get:165 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 506s Get:166 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 506s Get:167 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB] 506s Get:168 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] 506s Get:169 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 506s Get:170 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 506s Get:171 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmbedcrypto7t64 ppc64el 2.28.8-1 [267 kB] 506s Get:172 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmbedx509-1t64 ppc64el 2.28.8-1 [51.7 kB] 506s Get:173 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmbedtls14t64 ppc64el 2.28.8-1 [90.6 kB] 506s Get:174 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 507s Get:175 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.12-dev ppc64el 3.12.7-3 [6136 kB] 507s Get:176 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-dev ppc64el 3.12.7-1 [10.3 kB] 507s Get:177 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 507s Get:178 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13 ppc64el 3.13.0-2 [2527 kB] 507s Get:179 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-dev ppc64el 3.13.0-2 [5958 kB] 508s Get:180 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-all-dev ppc64el 3.12.7-1 [916 B] 508s Get:181 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 508s Get:182 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB] 508s Get:183 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mafft ppc64el 7.505-1 [990 kB] 508s Get:184 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 508s Get:185 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ncbi-blast+ ppc64el 2.16.0+ds-6 [16.1 MB] 509s Get:186 http://ftpmaster.internal/ubuntu plucky/universe ppc64el phylip ppc64el 1:3.697+dfsg-4build1 [952 kB] 509s Get:187 http://ftpmaster.internal/ubuntu plucky/universe ppc64el prank ppc64el 0.0.170427+dfsg-3 [353 kB] 509s Get:188 http://ftpmaster.internal/ubuntu plucky/universe ppc64el preview-latex-style all 13.2-1 [347 kB] 509s Get:189 http://ftpmaster.internal/ubuntu plucky/universe ppc64el probcons ppc64el 1.12-14 [174 kB] 509s Get:190 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 510s Get:191 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-3 [2928 kB] 510s Get:192 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 510s Get:193 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 510s Get:194 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-dev ppc64el 3.12.7-3 [505 kB] 511s Get:195 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-dev ppc64el 3.12.7-1 [26.7 kB] 511s Get:196 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-dev ppc64el 3.13.0-2 [507 kB] 511s Get:197 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all-dev ppc64el 3.12.7-1 [912 B] 511s Get:198 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 511s Get:199 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 511s Get:200 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB] 511s Get:201 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-tk ppc64el 3.13.0-2 [107 kB] 511s Get:202 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-tk ppc64el 3.12.7-1 [9752 B] 511s Get:203 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu1 [9810 B] 511s Get:204 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 511s Get:205 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 511s Get:206 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 511s Get:207 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 511s Get:208 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 511s Get:209 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 511s Get:210 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB] 512s Get:211 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 512s Get:212 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build2 [413 kB] 512s Get:213 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2 [217 kB] 512s Get:214 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 512s Get:215 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB] 512s Get:216 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB] 512s Get:217 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 512s Get:218 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-defusedxml all 0.7.1-2 [42.0 kB] 512s Get:219 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-roman all 4.2-1 [10.0 kB] 512s Get:220 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-docutils all 0.21.2+dfsg-2 [409 kB] 512s Get:221 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 513s Get:222 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 513s Get:223 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 513s Get:224 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB] 513s Get:225 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 513s Get:226 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-4 [91.3 kB] 513s Get:227 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB] 513s Get:228 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build4 [27.8 kB] 513s Get:229 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 513s Get:230 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.46.0-1build2 [1473 kB] 513s Get:231 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-imagesize all 1.4.1-1 [6844 B] 513s Get:232 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-isodate all 0.6.1-3 [24.3 kB] 513s Get:233 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2 [59.2 kB] 513s Get:234 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 513s Get:235 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-3 [4610 kB] 513s Get:236 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-msgpack ppc64el 1.0.3-3build2 [86.9 kB] 513s Get:237 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mmtf all 1.1.3-1 [16.2 kB] 513s Get:238 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-mysqldb ppc64el 1.4.6-2build3 [49.6 kB] 513s Get:239 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 513s Get:240 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-common all 7.4.7-4 [775 kB] 514s Get:241 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-alabaster all 0.7.16-0.1 [18.5 kB] 514s Get:242 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 514s Get:243 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sphinx all 7.4.7-4 [593 kB] 514s Get:244 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tabulate all 0.9.0-1 [45.3 kB] 514s Get:245 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-numpydoc all 1.6.0-2 [50.5 kB] 514s Get:246 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rdflib all 7.0.0-1 [405 kB] 514s Get:247 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 514s Get:248 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 514s Get:249 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 514s Get:250 http://ftpmaster.internal/ubuntu plucky/universe ppc64el t-coffee ppc64el 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1022 kB] 514s Get:251 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 514s Get:252 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-latex-base all 2024.20241102-1 [1260 kB] 514s Get:253 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfontbox-java all 1:1.8.16-5 [208 kB] 514s Get:254 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpdfbox-java all 1:1.8.16-5 [5521 kB] 514s Get:255 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-latex-recommended all 2024.20241102-1 [8739 kB] 515s Get:256 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-pictures all 2024.20241102-1 [17.0 MB] 515s Get:257 http://ftpmaster.internal/ubuntu plucky/universe ppc64el texlive-latex-extra all 2024.20241102-1 [24.2 MB] 516s Get:258 http://ftpmaster.internal/ubuntu plucky/universe ppc64el wise-data all 2.4.1-25 [83.0 kB] 516s Get:259 http://ftpmaster.internal/ubuntu plucky/universe ppc64el wise ppc64el 2.4.1-25 [1081 kB] 516s Get:260 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fasttree ppc64el 2.1.11-2 [218 kB] 517s Preconfiguring packages ... 517s Fetched 419 MB in 22s (19.0 MB/s) 517s Selecting previously unselected package m4. 517s (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 ... 73775 files and directories currently installed.) 517s Preparing to unpack .../000-m4_1.4.19-4build1_ppc64el.deb ... 517s Unpacking m4 (1.4.19-4build1) ... 517s Selecting previously unselected package flex. 517s Preparing to unpack .../001-flex_2.6.4-8.2build1_ppc64el.deb ... 517s Unpacking flex (2.6.4-8.2build1) ... 517s Selecting previously unselected package fonts-lato. 517s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 517s Unpacking fonts-lato (2.015-1) ... 517s Selecting previously unselected package libgomp1:ppc64el. 517s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 517s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libfftw3-double3:ppc64el. 517s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_ppc64el.deb ... 517s Unpacking libfftw3-double3:ppc64el (3.3.10-1ubuntu4) ... 518s Selecting previously unselected package fonts-dejavu-mono. 518s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 518s Unpacking fonts-dejavu-mono (2.37-8) ... 518s Selecting previously unselected package fonts-dejavu-core. 518s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 518s Unpacking fonts-dejavu-core (2.37-8) ... 518s Selecting previously unselected package libfontenc1:ppc64el. 518s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 518s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 518s Selecting previously unselected package x11-common. 518s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu3_all.deb ... 518s Unpacking x11-common (1:7.7+23ubuntu3) ... 518s Selecting previously unselected package xfonts-encodings. 518s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 518s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 518s Selecting previously unselected package xfonts-utils. 518s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 518s Unpacking xfonts-utils (1:7.7+7) ... 518s Selecting previously unselected package fonts-urw-base35. 518s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 518s Unpacking fonts-urw-base35 (20200910-8) ... 518s Selecting previously unselected package fontconfig-config. 518s Preparing to unpack .../012-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 518s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 518s Selecting previously unselected package libfontconfig1:ppc64el. 518s Preparing to unpack .../013-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 518s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 518s Selecting previously unselected package libsharpyuv0:ppc64el. 518s Preparing to unpack .../014-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 518s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 518s Selecting previously unselected package libaom3:ppc64el. 518s Preparing to unpack .../015-libaom3_3.11.0~rc1-1_ppc64el.deb ... 518s Unpacking libaom3:ppc64el (3.11.0~rc1-1) ... 518s Selecting previously unselected package libheif-plugin-aomdec:ppc64el. 518s Preparing to unpack .../016-libheif-plugin-aomdec_1.18.1-2_ppc64el.deb ... 518s Unpacking libheif-plugin-aomdec:ppc64el (1.18.1-2) ... 518s Selecting previously unselected package libde265-0:ppc64el. 518s Preparing to unpack .../017-libde265-0_1.0.15-1build4_ppc64el.deb ... 518s Unpacking libde265-0:ppc64el (1.0.15-1build4) ... 518s Selecting previously unselected package libheif-plugin-libde265:ppc64el. 518s Preparing to unpack .../018-libheif-plugin-libde265_1.18.1-2_ppc64el.deb ... 518s Unpacking libheif-plugin-libde265:ppc64el (1.18.1-2) ... 518s Selecting previously unselected package libheif1:ppc64el. 519s Preparing to unpack .../019-libheif1_1.18.1-2_ppc64el.deb ... 519s Unpacking libheif1:ppc64el (1.18.1-2) ... 519s Selecting previously unselected package libjbig0:ppc64el. 519s Preparing to unpack .../020-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 519s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 519s Selecting previously unselected package libjpeg-turbo8:ppc64el. 519s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 519s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 519s Selecting previously unselected package libjpeg8:ppc64el. 519s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 519s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 519s Selecting previously unselected package liblcms2-2:ppc64el. 519s Preparing to unpack .../023-liblcms2-2_2.16-2_ppc64el.deb ... 519s Unpacking liblcms2-2:ppc64el (2.16-2) ... 519s Selecting previously unselected package liblqr-1-0:ppc64el. 519s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_ppc64el.deb ... 519s Unpacking liblqr-1-0:ppc64el (0.4.2-2.1build2) ... 519s Selecting previously unselected package libltdl7:ppc64el. 519s Preparing to unpack .../025-libltdl7_2.4.7-7build1_ppc64el.deb ... 519s Unpacking libltdl7:ppc64el (2.4.7-7build1) ... 519s Selecting previously unselected package libopenjp2-7:ppc64el. 519s Preparing to unpack .../026-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 519s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 519s Selecting previously unselected package libraw23t64:ppc64el. 519s Preparing to unpack .../027-libraw23t64_0.21.3-1_ppc64el.deb ... 519s Unpacking libraw23t64:ppc64el (0.21.3-1) ... 519s Selecting previously unselected package libdeflate0:ppc64el. 519s Preparing to unpack .../028-libdeflate0_1.22-1_ppc64el.deb ... 519s Unpacking libdeflate0:ppc64el (1.22-1) ... 519s Selecting previously unselected package liblerc4:ppc64el. 519s Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 519s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 519s Selecting previously unselected package libwebp7:ppc64el. 519s Preparing to unpack .../030-libwebp7_1.4.0-0.1_ppc64el.deb ... 519s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 519s Selecting previously unselected package libtiff6:ppc64el. 519s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 519s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 519s Selecting previously unselected package libwebpdemux2:ppc64el. 519s Preparing to unpack .../032-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 519s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 519s Selecting previously unselected package libwebpmux3:ppc64el. 519s Preparing to unpack .../033-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 519s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 519s Selecting previously unselected package imagemagick-6-common. 519s Preparing to unpack .../034-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 519s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 519s Selecting previously unselected package libmagickcore-6.q16-7t64:ppc64el. 519s Preparing to unpack .../035-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_ppc64el.deb ... 519s Unpacking libmagickcore-6.q16-7t64:ppc64el (8:6.9.13.12+dfsg1-1build1) ... 519s Selecting previously unselected package libmagickwand-6.q16-7t64:ppc64el. 519s Preparing to unpack .../036-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_ppc64el.deb ... 519s Unpacking libmagickwand-6.q16-7t64:ppc64el (8:6.9.13.12+dfsg1-1build1) ... 519s Selecting previously unselected package poppler-data. 519s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 519s Unpacking poppler-data (0.4.12-1) ... 519s Selecting previously unselected package libpython3.13-minimal:ppc64el. 519s Preparing to unpack .../038-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 519s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 519s Selecting previously unselected package python3.13-minimal. 519s Preparing to unpack .../039-python3.13-minimal_3.13.0-2_ppc64el.deb ... 519s Unpacking python3.13-minimal (3.13.0-2) ... 519s Selecting previously unselected package sgml-base. 519s Preparing to unpack .../040-sgml-base_1.31_all.deb ... 519s Unpacking sgml-base (1.31) ... 519s Selecting previously unselected package autoconf. 519s Preparing to unpack .../041-autoconf_2.72-3_all.deb ... 519s Unpacking autoconf (2.72-3) ... 519s Selecting previously unselected package autotools-dev. 519s Preparing to unpack .../042-autotools-dev_20220109.1_all.deb ... 519s Unpacking autotools-dev (20220109.1) ... 520s Selecting previously unselected package automake. 520s Preparing to unpack .../043-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 520s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 520s Selecting previously unselected package autopoint. 520s Preparing to unpack .../044-autopoint_0.22.5-2_all.deb ... 520s Unpacking autopoint (0.22.5-2) ... 520s Selecting previously unselected package libtcl8.6:ppc64el. 520s Preparing to unpack .../045-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ... 520s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 520s Selecting previously unselected package libxrender1:ppc64el. 520s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 520s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 520s Selecting previously unselected package libxft2:ppc64el. 520s Preparing to unpack .../047-libxft2_2.3.6-1build1_ppc64el.deb ... 520s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 520s Selecting previously unselected package libxss1:ppc64el. 520s Preparing to unpack .../048-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 520s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 520s Selecting previously unselected package libtk8.6:ppc64el. 520s Preparing to unpack .../049-libtk8.6_8.6.15-1_ppc64el.deb ... 520s Unpacking libtk8.6:ppc64el (8.6.15-1) ... 520s Selecting previously unselected package tk8.6-blt2.5. 520s Preparing to unpack .../050-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ... 520s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 520s Selecting previously unselected package blt. 520s Preparing to unpack .../051-blt_2.5.3+dfsg-7build1_ppc64el.deb ... 520s Unpacking blt (2.5.3+dfsg-7build1) ... 520s Selecting previously unselected package libisl23:ppc64el. 520s Preparing to unpack .../052-libisl23_0.27-1_ppc64el.deb ... 520s Unpacking libisl23:ppc64el (0.27-1) ... 520s Selecting previously unselected package libmpc3:ppc64el. 520s Preparing to unpack .../053-libmpc3_1.3.1-1build2_ppc64el.deb ... 520s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 520s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 520s Preparing to unpack .../054-cpp-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package cpp-14. 520s Preparing to unpack .../055-cpp-14_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 520s Preparing to unpack .../056-cpp-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 520s Unpacking cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 520s Selecting previously unselected package cpp. 520s Preparing to unpack .../057-cpp_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 520s Unpacking cpp (4:14.1.0-2ubuntu1) ... 520s Selecting previously unselected package libcc1-0:ppc64el. 520s Preparing to unpack .../058-libcc1-0_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking libcc1-0:ppc64el (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package libitm1:ppc64el. 520s Preparing to unpack .../059-libitm1_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking libitm1:ppc64el (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package libasan8:ppc64el. 520s Preparing to unpack .../060-libasan8_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking libasan8:ppc64el (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package liblsan0:ppc64el. 520s Preparing to unpack .../061-liblsan0_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking liblsan0:ppc64el (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package libtsan2:ppc64el. 520s Preparing to unpack .../062-libtsan2_14.2.0-8ubuntu1_ppc64el.deb ... 520s Unpacking libtsan2:ppc64el (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package libubsan1:ppc64el. 521s Preparing to unpack .../063-libubsan1_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking libubsan1:ppc64el (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package libquadmath0:ppc64el. 521s Preparing to unpack .../064-libquadmath0_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking libquadmath0:ppc64el (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package libgcc-14-dev:ppc64el. 521s Preparing to unpack .../065-libgcc-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 521s Preparing to unpack .../066-gcc-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package gcc-14. 521s Preparing to unpack .../067-gcc-14_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 521s Preparing to unpack .../068-gcc-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 521s Unpacking gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 521s Selecting previously unselected package gcc. 521s Preparing to unpack .../069-gcc_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 521s Unpacking gcc (4:14.1.0-2ubuntu1) ... 521s Selecting previously unselected package libstdc++-14-dev:ppc64el. 521s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking libstdc++-14-dev:ppc64el (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package g++-14-powerpc64le-linux-gnu. 521s Preparing to unpack .../071-g++-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 521s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 522s Selecting previously unselected package g++-14. 522s Preparing to unpack .../072-g++-14_14.2.0-8ubuntu1_ppc64el.deb ... 522s Unpacking g++-14 (14.2.0-8ubuntu1) ... 522s Selecting previously unselected package g++-powerpc64le-linux-gnu. 522s Preparing to unpack .../073-g++-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 522s Unpacking g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 522s Selecting previously unselected package g++. 522s Preparing to unpack .../074-g++_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 522s Unpacking g++ (4:14.1.0-2ubuntu1) ... 522s Selecting previously unselected package build-essential. 522s Preparing to unpack .../075-build-essential_12.10ubuntu1_ppc64el.deb ... 522s Unpacking build-essential (12.10ubuntu1) ... 522s Selecting previously unselected package bwa. 522s Preparing to unpack .../076-bwa_0.7.18-1_ppc64el.deb ... 522s Unpacking bwa (0.7.18-1) ... 522s Selecting previously unselected package libargtable2-0. 522s Preparing to unpack .../077-libargtable2-0_13-2_ppc64el.deb ... 522s Unpacking libargtable2-0 (13-2) ... 522s Selecting previously unselected package clustalo. 522s Preparing to unpack .../078-clustalo_1.2.4-8build1_ppc64el.deb ... 522s Unpacking clustalo (1.2.4-8build1) ... 522s Selecting previously unselected package libdebhelper-perl. 522s Preparing to unpack .../079-libdebhelper-perl_13.20ubuntu1_all.deb ... 522s Unpacking libdebhelper-perl (13.20ubuntu1) ... 522s Selecting previously unselected package libtool. 522s Preparing to unpack .../080-libtool_2.4.7-7build1_all.deb ... 522s Unpacking libtool (2.4.7-7build1) ... 522s Selecting previously unselected package dh-autoreconf. 522s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 522s Unpacking dh-autoreconf (20) ... 522s Selecting previously unselected package libarchive-zip-perl. 522s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 522s Unpacking libarchive-zip-perl (1.68-1) ... 522s Selecting previously unselected package libfile-stripnondeterminism-perl. 522s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 522s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 522s Selecting previously unselected package dh-strip-nondeterminism. 522s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.0-1_all.deb ... 522s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 522s Selecting previously unselected package debugedit. 522s Preparing to unpack .../085-debugedit_1%3a5.1-1_ppc64el.deb ... 522s Unpacking debugedit (1:5.1-1) ... 522s Selecting previously unselected package dwz. 522s Preparing to unpack .../086-dwz_0.15-1build6_ppc64el.deb ... 522s Unpacking dwz (0.15-1build6) ... 522s Selecting previously unselected package gettext. 522s Preparing to unpack .../087-gettext_0.22.5-2_ppc64el.deb ... 522s Unpacking gettext (0.22.5-2) ... 522s Selecting previously unselected package intltool-debian. 522s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 522s Unpacking intltool-debian (0.35.0+20060710.6) ... 522s Selecting previously unselected package po-debconf. 522s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 522s Unpacking po-debconf (1.0.21+nmu1) ... 522s Selecting previously unselected package debhelper. 522s Preparing to unpack .../090-debhelper_13.20ubuntu1_all.deb ... 522s Unpacking debhelper (13.20ubuntu1) ... 522s Selecting previously unselected package dh-python. 522s Preparing to unpack .../091-dh-python_6.20241024_all.deb ... 522s Unpacking dh-python (6.20241024) ... 522s Selecting previously unselected package dialign. 522s Preparing to unpack .../092-dialign_2.2.1-13_ppc64el.deb ... 522s Unpacking dialign (2.2.1-13) ... 522s Selecting previously unselected package xml-core. 522s Preparing to unpack .../093-xml-core_0.19_all.deb ... 522s Unpacking xml-core (0.19) ... 522s Selecting previously unselected package docutils-common. 522s Preparing to unpack .../094-docutils-common_0.21.2+dfsg-2_all.deb ... 522s Unpacking docutils-common (0.21.2+dfsg-2) ... 522s Selecting previously unselected package libcifpp-data. 522s Preparing to unpack .../095-libcifpp-data_7.0.7-3_all.deb ... 522s Unpacking libcifpp-data (7.0.7-3) ... 522s Selecting previously unselected package libcifpp7:ppc64el. 522s Preparing to unpack .../096-libcifpp7_7.0.7-3_ppc64el.deb ... 522s Unpacking libcifpp7:ppc64el (7.0.7-3) ... 522s Selecting previously unselected package dssp. 522s Preparing to unpack .../097-dssp_4.4.10-1_ppc64el.deb ... 522s Unpacking dssp (4.4.10-1) ... 523s Selecting previously unselected package libimagequant0:ppc64el. 523s Preparing to unpack .../098-libimagequant0_2.18.0-1build1_ppc64el.deb ... 523s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 523s Selecting previously unselected package libgraphite2-3:ppc64el. 523s Preparing to unpack .../099-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 523s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 523s Selecting previously unselected package libharfbuzz0b:ppc64el. 523s Preparing to unpack .../100-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 523s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 523s Selecting previously unselected package libraqm0:ppc64el. 523s Preparing to unpack .../101-libraqm0_0.10.1-1build1_ppc64el.deb ... 523s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 523s Selecting previously unselected package libxpm4:ppc64el. 523s Preparing to unpack .../102-libxpm4_1%3a3.5.17-1build2_ppc64el.deb ... 523s Unpacking libxpm4:ppc64el (1:3.5.17-1build2) ... 523s Selecting previously unselected package libgd3:ppc64el. 523s Preparing to unpack .../103-libgd3_2.3.3-12ubuntu3_ppc64el.deb ... 523s Unpacking libgd3:ppc64el (2.3.3-12ubuntu3) ... 523s Selecting previously unselected package libhpdf-2.3.0:ppc64el. 523s Preparing to unpack .../104-libhpdf-2.3.0_2.3.0+dfsg-1build3_ppc64el.deb ... 523s Unpacking libhpdf-2.3.0:ppc64el (2.3.0+dfsg-1build3) ... 523s Selecting previously unselected package mysql-common. 523s Preparing to unpack .../105-mysql-common_5.8+1.1.1_all.deb ... 523s Unpacking mysql-common (5.8+1.1.1) ... 523s Selecting previously unselected package libmysqlclient21:ppc64el. 523s Preparing to unpack .../106-libmysqlclient21_8.0.40-1_ppc64el.deb ... 523s Unpacking libmysqlclient21:ppc64el (8.0.40-1) ... 523s Selecting previously unselected package libpq5:ppc64el. 523s Preparing to unpack .../107-libpq5_17.0-1_ppc64el.deb ... 523s Unpacking libpq5:ppc64el (17.0-1) ... 523s Selecting previously unselected package emboss-lib. 523s Preparing to unpack .../108-emboss-lib_6.6.0+dfsg-12ubuntu2_ppc64el.deb ... 523s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 523s Selecting previously unselected package emboss-data. 523s Preparing to unpack .../109-emboss-data_6.6.0+dfsg-12ubuntu2_all.deb ... 523s Unpacking emboss-data (6.6.0+dfsg-12ubuntu2) ... 527s Selecting previously unselected package emboss. 527s Preparing to unpack .../110-emboss_6.6.0+dfsg-12ubuntu2_ppc64el.deb ... 527s Unpacking emboss (6.6.0+dfsg-12ubuntu2) ... 528s Selecting previously unselected package fonts-font-awesome. 528s Preparing to unpack .../111-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 528s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 528s Selecting previously unselected package fonts-lmodern. 528s Preparing to unpack .../112-fonts-lmodern_2.005-1_all.deb ... 528s Unpacking fonts-lmodern (2.005-1) ... 528s Selecting previously unselected package fonts-lyx. 528s Preparing to unpack .../113-fonts-lyx_2.4.2.1-1_all.deb ... 528s Unpacking fonts-lyx (2.4.2.1-1) ... 528s Selecting previously unselected package libgs-common. 528s Preparing to unpack .../114-libgs-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 528s Unpacking libgs-common (10.03.1~dfsg1-0ubuntu2) ... 528s Selecting previously unselected package libgs10-common. 528s Preparing to unpack .../115-libgs10-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 528s Unpacking libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 528s Selecting previously unselected package libavahi-common-data:ppc64el. 528s Preparing to unpack .../116-libavahi-common-data_0.8-13ubuntu6_ppc64el.deb ... 528s Unpacking libavahi-common-data:ppc64el (0.8-13ubuntu6) ... 528s Selecting previously unselected package libavahi-common3:ppc64el. 528s Preparing to unpack .../117-libavahi-common3_0.8-13ubuntu6_ppc64el.deb ... 528s Unpacking libavahi-common3:ppc64el (0.8-13ubuntu6) ... 528s Selecting previously unselected package libavahi-client3:ppc64el. 528s Preparing to unpack .../118-libavahi-client3_0.8-13ubuntu6_ppc64el.deb ... 528s Unpacking libavahi-client3:ppc64el (0.8-13ubuntu6) ... 528s Selecting previously unselected package libcups2t64:ppc64el. 528s Preparing to unpack .../119-libcups2t64_2.4.10-1ubuntu2_ppc64el.deb ... 528s Unpacking libcups2t64:ppc64el (2.4.10-1ubuntu2) ... 528s Selecting previously unselected package libidn12:ppc64el. 528s Preparing to unpack .../120-libidn12_1.42-2_ppc64el.deb ... 528s Unpacking libidn12:ppc64el (1.42-2) ... 528s Selecting previously unselected package libijs-0.35:ppc64el. 528s Preparing to unpack .../121-libijs-0.35_0.35-15.1build1_ppc64el.deb ... 528s Unpacking libijs-0.35:ppc64el (0.35-15.1build1) ... 528s Selecting previously unselected package libjbig2dec0:ppc64el. 528s Preparing to unpack .../122-libjbig2dec0_0.20-1build3_ppc64el.deb ... 528s Unpacking libjbig2dec0:ppc64el (0.20-1build3) ... 528s Selecting previously unselected package libpaper1:ppc64el. 528s Preparing to unpack .../123-libpaper1_1.1.29build1_ppc64el.deb ... 528s Unpacking libpaper1:ppc64el (1.1.29build1) ... 528s Selecting previously unselected package libice6:ppc64el. 528s Preparing to unpack .../124-libice6_2%3a1.1.1-1_ppc64el.deb ... 528s Unpacking libice6:ppc64el (2:1.1.1-1) ... 528s Selecting previously unselected package libsm6:ppc64el. 528s Preparing to unpack .../125-libsm6_2%3a1.2.4-1_ppc64el.deb ... 528s Unpacking libsm6:ppc64el (2:1.2.4-1) ... 528s Selecting previously unselected package libxt6t64:ppc64el. 528s Preparing to unpack .../126-libxt6t64_1%3a1.2.1-1.2build1_ppc64el.deb ... 528s Unpacking libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 528s Selecting previously unselected package libgs10:ppc64el. 528s Preparing to unpack .../127-libgs10_10.03.1~dfsg1-0ubuntu2_ppc64el.deb ... 528s Unpacking libgs10:ppc64el (10.03.1~dfsg1-0ubuntu2) ... 528s Selecting previously unselected package ghostscript. 528s Preparing to unpack .../128-ghostscript_10.03.1~dfsg1-0ubuntu2_ppc64el.deb ... 528s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu2) ... 528s Selecting previously unselected package libnetpbm11t64:ppc64el. 528s Preparing to unpack .../129-libnetpbm11t64_2%3a11.08.01-1_ppc64el.deb ... 528s Unpacking libnetpbm11t64:ppc64el (2:11.08.01-1) ... 528s Selecting previously unselected package netpbm. 528s Preparing to unpack .../130-netpbm_2%3a11.08.01-1_ppc64el.deb ... 528s Unpacking netpbm (2:11.08.01-1) ... 529s Selecting previously unselected package tex-common. 529s Preparing to unpack .../131-tex-common_6.18_all.deb ... 529s Unpacking tex-common (6.18) ... 529s Selecting previously unselected package libpaper-utils. 529s Preparing to unpack .../132-libpaper-utils_1.1.29build1_ppc64el.deb ... 529s Unpacking libpaper-utils (1.1.29build1) ... 529s Selecting previously unselected package libkpathsea6:ppc64el. 529s Preparing to unpack .../133-libkpathsea6_2024.20240313.70630+ds-5_ppc64el.deb ... 529s Unpacking libkpathsea6:ppc64el (2024.20240313.70630+ds-5) ... 529s Selecting previously unselected package libptexenc1:ppc64el. 529s Preparing to unpack .../134-libptexenc1_2024.20240313.70630+ds-5_ppc64el.deb ... 529s Unpacking libptexenc1:ppc64el (2024.20240313.70630+ds-5) ... 529s Selecting previously unselected package libsynctex2:ppc64el. 529s Preparing to unpack .../135-libsynctex2_2024.20240313.70630+ds-5_ppc64el.deb ... 529s Unpacking libsynctex2:ppc64el (2024.20240313.70630+ds-5) ... 529s Selecting previously unselected package libtexlua53-5:ppc64el. 529s Preparing to unpack .../136-libtexlua53-5_2024.20240313.70630+ds-5_ppc64el.deb ... 529s Unpacking libtexlua53-5:ppc64el (2024.20240313.70630+ds-5) ... 529s Selecting previously unselected package t1utils. 529s Preparing to unpack .../137-t1utils_1.41-4build3_ppc64el.deb ... 529s Unpacking t1utils (1.41-4build3) ... 529s Selecting previously unselected package libpixman-1-0:ppc64el. 529s Preparing to unpack .../138-libpixman-1-0_0.44.0-3_ppc64el.deb ... 529s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 529s Selecting previously unselected package libxcb-render0:ppc64el. 529s Preparing to unpack .../139-libxcb-render0_1.17.0-2_ppc64el.deb ... 529s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 529s Selecting previously unselected package libxcb-shm0:ppc64el. 529s Preparing to unpack .../140-libxcb-shm0_1.17.0-2_ppc64el.deb ... 529s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 529s Selecting previously unselected package libcairo2:ppc64el. 529s Preparing to unpack .../141-libcairo2_1.18.2-2_ppc64el.deb ... 529s Unpacking libcairo2:ppc64el (1.18.2-2) ... 529s Selecting previously unselected package libmpfi0:ppc64el. 529s Preparing to unpack .../142-libmpfi0_1.5.4+ds-4_ppc64el.deb ... 529s Unpacking libmpfi0:ppc64el (1.5.4+ds-4) ... 529s Selecting previously unselected package libpotrace0:ppc64el. 529s Preparing to unpack .../143-libpotrace0_1.16-2build1_ppc64el.deb ... 529s Unpacking libpotrace0:ppc64el (1.16-2build1) ... 529s Selecting previously unselected package libteckit0:ppc64el. 529s Preparing to unpack .../144-libteckit0_2.5.12+ds1-1_ppc64el.deb ... 529s Unpacking libteckit0:ppc64el (2.5.12+ds1-1) ... 529s Selecting previously unselected package libxmu6:ppc64el. 529s Preparing to unpack .../145-libxmu6_2%3a1.1.3-3build2_ppc64el.deb ... 529s Unpacking libxmu6:ppc64el (2:1.1.3-3build2) ... 529s Selecting previously unselected package libxaw7:ppc64el. 529s Preparing to unpack .../146-libxaw7_2%3a1.0.16-1_ppc64el.deb ... 529s Unpacking libxaw7:ppc64el (2:1.0.16-1) ... 529s Selecting previously unselected package libxi6:ppc64el. 529s Preparing to unpack .../147-libxi6_2%3a1.8.2-1_ppc64el.deb ... 529s Unpacking libxi6:ppc64el (2:1.8.2-1) ... 529s Selecting previously unselected package libzzip-0-13t64:ppc64el. 529s Preparing to unpack .../148-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_ppc64el.deb ... 529s Unpacking libzzip-0-13t64:ppc64el (0.13.72+dfsg.1-1.2build1) ... 529s Selecting previously unselected package texlive-binaries. 529s Preparing to unpack .../149-texlive-binaries_2024.20240313.70630+ds-5_ppc64el.deb ... 529s Unpacking texlive-binaries (2024.20240313.70630+ds-5) ... 529s Selecting previously unselected package xdg-utils. 529s Preparing to unpack .../150-xdg-utils_1.2.1-0ubuntu1_all.deb ... 529s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 530s Selecting previously unselected package texlive-base. 530s Preparing to unpack .../151-texlive-base_2024.20241102-1_all.deb ... 530s Unpacking texlive-base (2024.20241102-1) ... 531s Selecting previously unselected package hicolor-icon-theme. 531s Preparing to unpack .../152-hicolor-icon-theme_0.18-1_all.deb ... 531s Unpacking hicolor-icon-theme (0.18-1) ... 531s Selecting previously unselected package imagemagick-6.q16. 531s Preparing to unpack .../153-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_ppc64el.deb ... 531s Unpacking imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 531s Selecting previously unselected package imagemagick. 531s Preparing to unpack .../154-imagemagick_8%3a6.9.13.12+dfsg1-1build1_ppc64el.deb ... 531s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 531s Selecting previously unselected package hevea. 531s Preparing to unpack .../155-hevea_2.36-2_ppc64el.deb ... 531s Unpacking hevea (2.36-2) ... 531s Selecting previously unselected package libapache-pom-java. 531s Preparing to unpack .../156-libapache-pom-java_33-2_all.deb ... 531s Unpacking libapache-pom-java (33-2) ... 531s Selecting previously unselected package libblas3:ppc64el. 531s Preparing to unpack .../157-libblas3_3.12.0-3build2_ppc64el.deb ... 531s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 531s Selecting previously unselected package libcommons-parent-java. 531s Preparing to unpack .../158-libcommons-parent-java_56-1_all.deb ... 531s Unpacking libcommons-parent-java (56-1) ... 531s Selecting previously unselected package libcommons-logging-java. 531s Preparing to unpack .../159-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 531s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 531s Selecting previously unselected package libexpat1-dev:ppc64el. 531s Preparing to unpack .../160-libexpat1-dev_2.6.2-2_ppc64el.deb ... 531s Unpacking libexpat1-dev:ppc64el (2.6.2-2) ... 531s Selecting previously unselected package libgfortran5:ppc64el. 531s Preparing to unpack .../161-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 531s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 531s Selecting previously unselected package libjs-jquery. 531s Preparing to unpack .../162-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 531s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 531s Selecting previously unselected package libjs-jquery-ui. 531s Preparing to unpack .../163-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 531s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 531s Selecting previously unselected package libjs-underscore. 531s Preparing to unpack .../164-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 531s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 531s Selecting previously unselected package libjs-sphinxdoc. 531s Preparing to unpack .../165-libjs-sphinxdoc_7.4.7-4_all.deb ... 531s Unpacking libjs-sphinxdoc (7.4.7-4) ... 531s Selecting previously unselected package libjson-perl. 531s Preparing to unpack .../166-libjson-perl_4.10000-1_all.deb ... 531s Unpacking libjson-perl (4.10000-1) ... 532s Selecting previously unselected package liblapack3:ppc64el. 532s Preparing to unpack .../167-liblapack3_3.12.0-3build2_ppc64el.deb ... 532s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 532s Selecting previously unselected package liblbfgsb0:ppc64el. 532s Preparing to unpack .../168-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 532s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 532s Selecting previously unselected package libmbedcrypto7t64:ppc64el. 532s Preparing to unpack .../169-libmbedcrypto7t64_2.28.8-1_ppc64el.deb ... 532s Unpacking libmbedcrypto7t64:ppc64el (2.28.8-1) ... 532s Selecting previously unselected package libmbedx509-1t64:ppc64el. 532s Preparing to unpack .../170-libmbedx509-1t64_2.28.8-1_ppc64el.deb ... 532s Unpacking libmbedx509-1t64:ppc64el (2.28.8-1) ... 532s Selecting previously unselected package libmbedtls14t64:ppc64el. 532s Preparing to unpack .../171-libmbedtls14t64_2.28.8-1_ppc64el.deb ... 532s Unpacking libmbedtls14t64:ppc64el (2.28.8-1) ... 532s Selecting previously unselected package zlib1g-dev:ppc64el. 532s Preparing to unpack .../172-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 532s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 532s Selecting previously unselected package libpython3.12-dev:ppc64el. 532s Preparing to unpack .../173-libpython3.12-dev_3.12.7-3_ppc64el.deb ... 532s Unpacking libpython3.12-dev:ppc64el (3.12.7-3) ... 532s Selecting previously unselected package libpython3-dev:ppc64el. 532s Preparing to unpack .../174-libpython3-dev_3.12.7-1_ppc64el.deb ... 532s Unpacking libpython3-dev:ppc64el (3.12.7-1) ... 532s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 532s Preparing to unpack .../175-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ... 532s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ... 532s Selecting previously unselected package libpython3.13:ppc64el. 532s Preparing to unpack .../176-libpython3.13_3.13.0-2_ppc64el.deb ... 532s Unpacking libpython3.13:ppc64el (3.13.0-2) ... 532s Selecting previously unselected package libpython3.13-dev:ppc64el. 532s Preparing to unpack .../177-libpython3.13-dev_3.13.0-2_ppc64el.deb ... 532s Unpacking libpython3.13-dev:ppc64el (3.13.0-2) ... 532s Selecting previously unselected package libpython3-all-dev:ppc64el. 532s Preparing to unpack .../178-libpython3-all-dev_3.12.7-1_ppc64el.deb ... 532s Unpacking libpython3-all-dev:ppc64el (3.12.7-1) ... 532s Selecting previously unselected package libqhull-r8.0:ppc64el. 532s Preparing to unpack .../179-libqhull-r8.0_2020.2-6build1_ppc64el.deb ... 532s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ... 532s Selecting previously unselected package libxslt1.1:ppc64el. 532s Preparing to unpack .../180-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ... 532s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 532s Selecting previously unselected package mafft. 532s Preparing to unpack .../181-mafft_7.505-1_ppc64el.deb ... 532s Unpacking mafft (7.505-1) ... 533s Selecting previously unselected package ncbi-data. 533s Preparing to unpack .../182-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 533s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 533s Selecting previously unselected package ncbi-blast+. 533s Preparing to unpack .../183-ncbi-blast+_2.16.0+ds-6_ppc64el.deb ... 533s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 533s Selecting previously unselected package phylip. 533s Preparing to unpack .../184-phylip_1%3a3.697+dfsg-4build1_ppc64el.deb ... 533s Unpacking phylip (1:3.697+dfsg-4build1) ... 533s Selecting previously unselected package prank. 533s Preparing to unpack .../185-prank_0.0.170427+dfsg-3_ppc64el.deb ... 533s Unpacking prank (0.0.170427+dfsg-3) ... 533s Selecting previously unselected package preview-latex-style. 533s Preparing to unpack .../186-preview-latex-style_13.2-1_all.deb ... 533s Unpacking preview-latex-style (13.2-1) ... 533s Selecting previously unselected package probcons. 533s Preparing to unpack .../187-probcons_1.12-14_ppc64el.deb ... 533s Unpacking probcons (1.12-14) ... 533s Selecting previously unselected package python-biopython-doc. 533s Preparing to unpack .../188-python-biopython-doc_1.84+dfsg-4_all.deb ... 533s Unpacking python-biopython-doc (1.84+dfsg-4) ... 534s Selecting previously unselected package python-matplotlib-data. 534s Preparing to unpack .../189-python-matplotlib-data_3.8.3-3_all.deb ... 534s Unpacking python-matplotlib-data (3.8.3-3) ... 534s Selecting previously unselected package python3.13. 534s Preparing to unpack .../190-python3.13_3.13.0-2_ppc64el.deb ... 534s Unpacking python3.13 (3.13.0-2) ... 534s Selecting previously unselected package python3-all. 534s Preparing to unpack .../191-python3-all_3.12.7-1_ppc64el.deb ... 534s Unpacking python3-all (3.12.7-1) ... 534s Selecting previously unselected package python3.12-dev. 534s Preparing to unpack .../192-python3.12-dev_3.12.7-3_ppc64el.deb ... 534s Unpacking python3.12-dev (3.12.7-3) ... 534s Selecting previously unselected package python3-dev. 534s Preparing to unpack .../193-python3-dev_3.12.7-1_ppc64el.deb ... 534s Unpacking python3-dev (3.12.7-1) ... 534s Selecting previously unselected package python3.13-dev. 534s Preparing to unpack .../194-python3.13-dev_3.13.0-2_ppc64el.deb ... 534s Unpacking python3.13-dev (3.13.0-2) ... 534s Selecting previously unselected package python3-all-dev. 534s Preparing to unpack .../195-python3-all-dev_3.12.7-1_ppc64el.deb ... 534s Unpacking python3-all-dev (3.12.7-1) ... 534s Selecting previously unselected package python3-appdirs. 534s Preparing to unpack .../196-python3-appdirs_1.4.4-4_all.deb ... 534s Unpacking python3-appdirs (1.4.4-4) ... 534s Selecting previously unselected package python3-numpy. 534s Preparing to unpack .../197-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 534s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 534s Selecting previously unselected package python3.12-tk. 534s Preparing to unpack .../198-python3.12-tk_3.12.7-3_ppc64el.deb ... 534s Unpacking python3.12-tk (3.12.7-3) ... 534s Selecting previously unselected package python3.13-tk. 534s Preparing to unpack .../199-python3.13-tk_3.13.0-2_ppc64el.deb ... 534s Unpacking python3.13-tk (3.13.0-2) ... 534s Selecting previously unselected package python3-tk:ppc64el. 534s Preparing to unpack .../200-python3-tk_3.12.7-1_ppc64el.deb ... 534s Unpacking python3-tk:ppc64el (3.12.7-1) ... 534s Selecting previously unselected package python3-pil.imagetk:ppc64el. 534s Preparing to unpack .../201-python3-pil.imagetk_10.4.0-1ubuntu1_ppc64el.deb ... 534s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 534s Selecting previously unselected package python3-pil:ppc64el. 534s Preparing to unpack .../202-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 534s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 534s Selecting previously unselected package python3-cairo. 534s Preparing to unpack .../203-python3-cairo_1.26.1-2_ppc64el.deb ... 534s Unpacking python3-cairo (1.26.1-2) ... 535s Selecting previously unselected package python3-freetype. 535s Preparing to unpack .../204-python3-freetype_2.5.1-1_all.deb ... 535s Unpacking python3-freetype (2.5.1-1) ... 535s Selecting previously unselected package python3-rlpycairo. 535s Preparing to unpack .../205-python3-rlpycairo_0.3.0-3_all.deb ... 535s Unpacking python3-rlpycairo (0.3.0-3) ... 535s Selecting previously unselected package python3-reportlab. 535s Preparing to unpack .../206-python3-reportlab_4.2.5-1_all.deb ... 535s Unpacking python3-reportlab (4.2.5-1) ... 535s Selecting previously unselected package w3c-sgml-lib. 535s Preparing to unpack .../207-w3c-sgml-lib_1.3-3_all.deb ... 535s Unpacking w3c-sgml-lib (1.3-3) ... 535s Selecting previously unselected package python3-biopython. 535s Preparing to unpack .../208-python3-biopython_1.84+dfsg-4_ppc64el.deb ... 535s Unpacking python3-biopython (1.84+dfsg-4) ... 535s Selecting previously unselected package python3-biopython-sql. 535s Preparing to unpack .../209-python3-biopython-sql_1.84+dfsg-4_all.deb ... 535s Unpacking python3-biopython-sql (1.84+dfsg-4) ... 535s Selecting previously unselected package python3-brotli. 535s Preparing to unpack .../210-python3-brotli_1.1.0-2build2_ppc64el.deb ... 535s Unpacking python3-brotli (1.1.0-2build2) ... 535s Selecting previously unselected package python3-contourpy. 535s Preparing to unpack .../211-python3-contourpy_1.3.0-2_ppc64el.deb ... 535s Unpacking python3-contourpy (1.3.0-2) ... 535s Selecting previously unselected package python3-cycler. 535s Preparing to unpack .../212-python3-cycler_0.12.1-1_all.deb ... 535s Unpacking python3-cycler (0.12.1-1) ... 535s Selecting previously unselected package python3-six. 535s Preparing to unpack .../213-python3-six_1.16.0-7_all.deb ... 535s Unpacking python3-six (1.16.0-7) ... 535s Selecting previously unselected package python3-dateutil. 535s Preparing to unpack .../214-python3-dateutil_2.9.0-2_all.deb ... 535s Unpacking python3-dateutil (2.9.0-2) ... 535s Selecting previously unselected package python3-decorator. 535s Preparing to unpack .../215-python3-decorator_5.1.1-5_all.deb ... 535s Unpacking python3-decorator (5.1.1-5) ... 535s Selecting previously unselected package python3-defusedxml. 535s Preparing to unpack .../216-python3-defusedxml_0.7.1-2_all.deb ... 535s Unpacking python3-defusedxml (0.7.1-2) ... 535s Selecting previously unselected package python3-roman. 535s Preparing to unpack .../217-python3-roman_4.2-1_all.deb ... 535s Unpacking python3-roman (4.2-1) ... 535s Selecting previously unselected package python3-docutils. 535s Preparing to unpack .../218-python3-docutils_0.21.2+dfsg-2_all.deb ... 535s Unpacking python3-docutils (0.21.2+dfsg-2) ... 535s Selecting previously unselected package python3-scipy. 535s Preparing to unpack .../219-python3-scipy_1.13.1-5_ppc64el.deb ... 535s Unpacking python3-scipy (1.13.1-5) ... 536s Selecting previously unselected package python3-ufolib2. 536s Preparing to unpack .../220-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 536s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 536s Selecting previously unselected package python3-mpmath. 536s Preparing to unpack .../221-python3-mpmath_1.3.0-1_all.deb ... 536s Unpacking python3-mpmath (1.3.0-1) ... 536s Selecting previously unselected package python3-sympy. 536s Preparing to unpack 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libfftw3-double3:ppc64el (3.3.10-1ubuntu4) ... 553s Setting up libcifpp-data (7.0.7-3) ... 553s Setting up libkpathsea6:ppc64el (2024.20240313.70630+ds-5) ... 553s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 553s Setting up autoconf (2.72-3) ... 553s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 553s Setting up libubsan1:ppc64el (14.2.0-8ubuntu1) ... 553s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 553s Setting up dwz (0.15-1build6) ... 553s Setting up liblqr-1-0:ppc64el (0.4.2-2.1build2) ... 553s Setting up python3-rdflib (7.0.0-1) ... 554s Setting up libasan8:ppc64el (14.2.0-8ubuntu1) ... 554s Setting up libjson-perl (4.10000-1) ... 554s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 554s Setting up debugedit (1:5.1-1) ... 554s Setting up fonts-lmodern (2.005-1) ... 554s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 554s Setting up python3.13-minimal (3.13.0-2) ... 555s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 555s Setting up python3-dateutil (2.9.0-2) ... 555s Setting up fasttree (2.1.11-2) ... 555s Setting up sgml-base (1.31) ... 555s Setting up python3-msgpack (1.0.3-3build2) ... 556s Setting up libxss1:ppc64el (1:1.2.3-1build3) ... 556s Setting up libtsan2:ppc64el (14.2.0-8ubuntu1) ... 556s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 556s Setting up python3-mpmath (1.3.0-1) ... 557s Setting up libisl23:ppc64el (0.27-1) ... 557s Setting up libde265-0:ppc64el (1.0.15-1build4) ... 557s Setting up python-matplotlib-data (3.8.3-3) ... 557s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 557s Setting up python3-appdirs (1.4.4-4) ... 557s Setting up dialign (2.2.1-13) ... 557s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 557s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 557s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 557s Setting up xdg-utils (1.2.1-0ubuntu1) ... 557s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 557s 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572s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 572s Setting up gettext (0.22.5-2) ... 572s Setting up libmbedx509-1t64:ppc64el (2.28.8-1) ... 572s Setting up libpdfbox-java (1:1.8.16-5) ... 572s Setting up python3.13 (3.13.0-2) ... 574s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 574s Setting up wise (2.4.1-25) ... 574s Setting up preview-latex-style (13.2-1) ... 574s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 574s Setting up libcommons-parent-java (56-1) ... 574s Setting up libavahi-common3:ppc64el (0.8-13ubuntu6) ... 574s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 574s Setting up python3-all (3.12.7-1) ... 574s Setting up libcifpp7:ppc64el (7.0.7-3) ... 574s Setting up libpython3.12-dev:ppc64el (3.12.7-3) ... 574s Setting up clustalo (1.2.4-8build1) ... 574s Setting up dssp (4.4.10-1) ... 574s Setting up 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(1.18.1-2) ... 595s Setting up libheif1:ppc64el (1.18.1-2) ... 595s Setting up libmagickcore-6.q16-7t64:ppc64el (8:6.9.13.12+dfsg1-1build1) ... 595s Setting up python3-fonttools (4.46.0-1build2) ... 597s Setting up libmagickwand-6.q16-7t64:ppc64el (8:6.9.13.12+dfsg1-1build1) ... 597s Setting up libgd3:ppc64el (2.3.3-12ubuntu3) ... 597s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 597s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 597s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 597s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 597s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 597s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 597s update-alternatives: using 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update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 597s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 597s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 597s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 597s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 597s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 597s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 597s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 597s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 597s Setting up python3-matplotlib (3.8.3-3) ... 600s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 600s Setting up hevea (2.36-2) ... 600s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 600s Processing triggers for install-info (7.1.1-1) ... 600s Processing triggers for libc-bin (2.40-1ubuntu3) ... 600s Processing triggers for systemd (256.5-2ubuntu4) ... 601s Processing triggers for man-db (2.12.1-3) ... 604s Processing triggers for shared-mime-info (2.4-5) ... 605s Processing triggers for sgml-base (1.31) ... 605s Setting up w3c-sgml-lib (1.3-3) ... 640s Setting up docutils-common (0.21.2+dfsg-2) ... 640s Setting up python3-biopython (1.84+dfsg-4) ... 643s Setting up python3-biopython-sql (1.84+dfsg-4) ... 643s Processing triggers for sgml-base (1.31) ... 643s Setting up python3-docutils (0.21.2+dfsg-2) ... 644s Setting up python3-sphinx (7.4.7-4) ... 646s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 646s Setting up python3-numpydoc (1.6.0-2) ... 647s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 647s Setting up autopkgtest-satdep (0) ... 647s Processing triggers for tex-common (6.18) ... 647s Running updmap-sys. This may take some time... done. 647s Running mktexlsr /var/lib/texmf ... done. 647s Building format(s) --all. 731s This may take some time... done. 740s (Reading database ... 121732 files and directories currently installed.) 740s Removing autopkgtest-satdep (0) ... 754s autopkgtest [21:31:11]: test full_suite: sh debian/tests/run-unit-test 754s autopkgtest [21:31:11]: test full_suite: [----------------------- 755s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 755s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 757s mkdir: created directory 'Bio' 757s mkdir: created directory 'Bio/Align' 757s mkdir: created directory 'Bio/Align/substitution_matrices' 757s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 757s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 757s Remove test test_Tutorial.py which is bound to fail 758s test_Ace ... ok 758s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 758s 758s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 758s 758s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 758s 758s test_Align_a2m ... loading tests failed: 758s Failed to import test module: test_Align_a2m 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 758s test_Align_bed ... loading tests failed: 758s Failed to import test module: test_Align_bed 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 758s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_Align_bigmaf ... loading tests failed: 758s Failed to import test module: test_Align_bigmaf 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 758s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_Align_clustal ... loading tests failed: 758s Failed to import test module: test_Align_clustal 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 758s test_Align_codonalign ... loading tests failed: 758s Failed to import test module: test_Align_codonalign 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 758s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 758s 758s test_Align_fasta ... loading tests failed: 758s Failed to import test module: test_Align_fasta 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 758s test_Align_hhr ... loading tests failed: 758s Failed to import test module: test_Align_hhr 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 758s from . import multiarray 758s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 758s from . import overrides 758s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 758s from numpy.core._multiarray_umath import ( 758s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 758s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 758s 758s During handling of the above exception, another exception occurred: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 758s from numpy.__config__ import show as show_config 758s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 758s from numpy.core._multiarray_umath import ( 758s ...<3 lines>... 758s ) 758s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 758s raise ImportError(msg) 758s ImportError: 758s 758s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 758s 758s Importing the numpy C-extensions failed. This error can happen for 758s many reasons, often due to issues with your setup or how NumPy was 758s installed. 758s 758s We have compiled some common reasons and troubleshooting tips at: 758s 758s https://numpy.org/devdocs/user/troubleshooting-importerror.html 758s 758s Please note and check the following: 758s 758s * The Python version is: Python3.13 from "/usr/bin/python3.13" 758s * The NumPy version is: "1.26.4" 758s 758s and make sure that they are the versions you expect. 758s Please carefully study the documentation linked above for further help. 758s 758s Original error was: No module named 'numpy.core._multiarray_umath' 758s 758s 758s The above exception was the direct cause of the following exception: 758s 758s Traceback (most recent call last): 758s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 758s module = __import__(module_name) 758s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 758s import numpy as np 758s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 758s raise ImportError(msg) from e 758s ImportError: Error importing numpy: you should not try to import numpy from 758s its source directory; please exit the numpy source tree, and relaunch 758s your python interpreter from there. 758s 759s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Application ... ok 759s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Blast_Record ... loading tests failed: 759s Failed to import test module: test_Blast_Record 759s Traceback (most recent call last): 759s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 759s from . import multiarray 759s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 759s from . import overrides 759s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 759s from numpy.core._multiarray_umath import ( 759s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 759s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 759s 759s During handling of the above exception, another exception occurred: 759s 759s Traceback (most recent call last): 759s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 759s from numpy.__config__ import show as show_config 759s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 759s from numpy.core._multiarray_umath import ( 759s ...<3 lines>... 759s ) 759s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 759s raise ImportError(msg) 759s ImportError: 759s 759s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 759s 759s Importing the numpy C-extensions failed. This error can happen for 759s many reasons, often due to issues with your setup or how NumPy was 759s installed. 759s 759s We have compiled some common reasons and troubleshooting tips at: 759s 759s https://numpy.org/devdocs/user/troubleshooting-importerror.html 759s 759s Please note and check the following: 759s 759s * The Python version is: Python3.13 from "/usr/bin/python3.13" 759s * The NumPy version is: "1.26.4" 759s 759s and make sure that they are the versions you expect. 759s Please carefully study the documentation linked above for further help. 759s 759s Original error was: No module named 'numpy.core._multiarray_umath' 759s 759s 759s The above exception was the direct cause of the following exception: 759s 759s Traceback (most recent call last): 759s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 759s module = __import__(module_name) 759s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 759s from Bio.Blast.NCBIXML import HSP 759s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 759s import numpy as np 759s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 759s raise ImportError(msg) from e 759s ImportError: Error importing numpy: you should not try to import numpy from 759s its source directory; please exit the numpy source tree, and relaunch 759s your python interpreter from there. 759s 759s test_Blast_parser ... loading tests failed: 759s Failed to import test module: test_Blast_parser 759s Traceback (most recent call last): 759s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 759s from . import multiarray 759s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 759s from . import overrides 759s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 759s from numpy.core._multiarray_umath import ( 759s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 759s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 759s 759s During handling of the above exception, another exception occurred: 759s 759s Traceback (most recent call last): 759s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 759s from numpy.__config__ import show as show_config 759s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 759s from numpy.core._multiarray_umath import ( 759s ...<3 lines>... 759s ) 759s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 759s raise ImportError(msg) 759s ImportError: 759s 759s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 759s 759s Importing the numpy C-extensions failed. This error can happen for 759s many reasons, often due to issues with your setup or how NumPy was 759s installed. 759s 759s We have compiled some common reasons and troubleshooting tips at: 759s 759s https://numpy.org/devdocs/user/troubleshooting-importerror.html 759s 759s Please note and check the following: 759s 759s * The Python version is: Python3.13 from "/usr/bin/python3.13" 759s * The NumPy version is: "1.26.4" 759s 759s and make sure that they are the versions you expect. 759s Please carefully study the documentation linked above for further help. 759s 759s Original error was: No module named 'numpy.core._multiarray_umath' 759s 759s 759s The above exception was the direct cause of the following exception: 759s 759s Traceback (most recent call last): 759s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 759s module = __import__(module_name) 759s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 759s import numpy as np 759s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 759s raise ImportError(msg) from e 759s ImportError: Error importing numpy: you should not try to import numpy from 759s its source directory; please exit the numpy source tree, and relaunch 759s your python interpreter from there. 759s 759s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s 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 759s warnings.warn( 759s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 759s 759s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 759s 759s test_CodonTable ... ok 759s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 759s 759s test_Compass ... ok 760s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 760s 760s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 760s 760s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 760s 760s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 760s 760s test_EmbossPrimer ... ok 764s test_Entrez ... ok 764s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 764s 765s test_Entrez_parser ... ok 765s test_Enzyme ... ok 765s test_ExPASy ... skipping. internet not available 765s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 765s 765s test_File ... ok 765s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 765s 765s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 765s 765s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 765s 765s test_GraphicsDistribution ... loading tests failed: 765s Failed to import test module: test_GraphicsDistribution 765s Traceback (most recent call last): 765s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 765s module = __import__(module_name) 765s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 765s from Bio.Graphics.Distribution import BarChartDistribution 765s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 765s from reportlab.graphics.charts.barcharts import BarChartProperties 765s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 765s from reportlab.lib import colors 765s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 765s from reportlab.lib.rl_accel import fp_str 765s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 765s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 765s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 765s from PIL import Image 765s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 765s from . import _imaging as core 765s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 765s 765s test_GraphicsGeneral ... loading tests failed: 765s Failed to import test module: test_GraphicsGeneral 765s Traceback (most recent call last): 765s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 765s module = __import__(module_name) 765s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 765s from Bio.Graphics.Comparative import ComparativeScatterPlot 765s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 765s from reportlab.graphics.charts.lineplots import LinePlot 765s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 765s from reportlab.lib import colors 765s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 765s from reportlab.lib.rl_accel import fp_str 765s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 765s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 765s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 765s from PIL import Image 765s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 765s from . import _imaging as core 765s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 765s 765s test_HMMCasino ... ok 765s test_HMMGeneral ... ok 765s test_KEGG ... ok 765s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 765s 765s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 766s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 766s test_KGML_nographics ... ok 766s test_KeyWList ... ok 766s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 766s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 766s 766s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 766s 766s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 766s 766s test_Medline ... ok 766s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 766s 767s test_NCBIXML ... loading tests failed: 767s Failed to import test module: test_NCBIXML 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 767s from . import multiarray 767s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 767s from . import overrides 767s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 767s from numpy.core._multiarray_umath import ( 767s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 767s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 767s 767s During handling of the above exception, another exception occurred: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 767s from numpy.__config__ import show as show_config 767s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 767s from numpy.core._multiarray_umath import ( 767s ...<3 lines>... 767s ) 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 767s raise ImportError(msg) 767s ImportError: 767s 767s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 767s 767s Importing the numpy C-extensions failed. This error can happen for 767s many reasons, often due to issues with your setup or how NumPy was 767s installed. 767s 767s We have compiled some common reasons and troubleshooting tips at: 767s 767s https://numpy.org/devdocs/user/troubleshooting-importerror.html 767s 767s Please note and check the following: 767s 767s * The Python version is: Python3.13 from "/usr/bin/python3.13" 767s * The NumPy version is: "1.26.4" 767s 767s and make sure that they are the versions you expect. 767s Please carefully study the documentation linked above for further help. 767s 767s Original error was: No module named 'numpy.core._multiarray_umath' 767s 767s 767s The above exception was the direct cause of the following exception: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 767s module = __import__(module_name) 767s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 767s from Bio.Blast import NCBIXML 767s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 767s import numpy as np 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 767s raise ImportError(msg) from e 767s ImportError: Error importing numpy: you should not try to import numpy from 767s its source directory; please exit the numpy source tree, and relaunch 767s your python interpreter from there. 767s 767s test_NCBI_BLAST_tools ... loading tests failed: 767s Failed to import test module: test_NCBI_BLAST_tools 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 767s from . import multiarray 767s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 767s from . import overrides 767s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 767s from numpy.core._multiarray_umath import ( 767s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 767s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 767s 767s During handling of the above exception, another exception occurred: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 767s from numpy.__config__ import show as show_config 767s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 767s from numpy.core._multiarray_umath import ( 767s ...<3 lines>... 767s ) 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 767s raise ImportError(msg) 767s ImportError: 767s 767s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 767s 767s Importing the numpy C-extensions failed. This error can happen for 767s many reasons, often due to issues with your setup or how NumPy was 767s installed. 767s 767s We have compiled some common reasons and troubleshooting tips at: 767s 767s https://numpy.org/devdocs/user/troubleshooting-importerror.html 767s 767s Please note and check the following: 767s 767s * The Python version is: Python3.13 from "/usr/bin/python3.13" 767s * The NumPy version is: "1.26.4" 767s 767s and make sure that they are the versions you expect. 767s Please carefully study the documentation linked above for further help. 767s 767s Original error was: No module named 'numpy.core._multiarray_umath' 767s 767s 767s The above exception was the direct cause of the following exception: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 767s module = __import__(module_name) 767s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 767s from Bio.Blast import Applications 767s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 767s import numpy as np 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 767s raise ImportError(msg) from e 767s ImportError: Error importing numpy: you should not try to import numpy from 767s its source directory; please exit the numpy source tree, and relaunch 767s your python interpreter from there. 767s 767s test_NCBI_qblast ... loading tests failed: 767s Failed to import test module: test_NCBI_qblast 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 767s from . import multiarray 767s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 767s from . import overrides 767s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 767s from numpy.core._multiarray_umath import ( 767s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 767s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 767s 767s During handling of the above exception, another exception occurred: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 767s from numpy.__config__ import show as show_config 767s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 767s from numpy.core._multiarray_umath import ( 767s ...<3 lines>... 767s ) 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 767s raise ImportError(msg) 767s ImportError: 767s 767s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 767s 767s Importing the numpy C-extensions failed. This error can happen for 767s many reasons, often due to issues with your setup or how NumPy was 767s installed. 767s 767s We have compiled some common reasons and troubleshooting tips at: 767s 767s https://numpy.org/devdocs/user/troubleshooting-importerror.html 767s 767s Please note and check the following: 767s 767s * The Python version is: Python3.13 from "/usr/bin/python3.13" 767s * The NumPy version is: "1.26.4" 767s 767s and make sure that they are the versions you expect. 767s Please carefully study the documentation linked above for further help. 767s 767s Original error was: No module named 'numpy.core._multiarray_umath' 767s 767s 767s The above exception was the direct cause of the following exception: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 767s module = __import__(module_name) 767s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 767s from Bio.Blast import NCBIWWW 767s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 767s import numpy as np 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 767s raise ImportError(msg) from e 767s ImportError: Error importing numpy: you should not try to import numpy from 767s its source directory; please exit the numpy source tree, and relaunch 767s your python interpreter from there. 767s 767s test_NMR ... ok 767s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 767s 767s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 767s 767s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_Disordered ... loading tests failed: 767s Failed to import test module: test_PDB_Disordered 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 767s from . import multiarray 767s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 767s from . import overrides 767s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 767s from numpy.core._multiarray_umath import ( 767s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 767s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 767s 767s During handling of the above exception, another exception occurred: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 767s from numpy.__config__ import show as show_config 767s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 767s from numpy.core._multiarray_umath import ( 767s ...<3 lines>... 767s ) 767s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 767s raise ImportError(msg) 767s ImportError: 767s 767s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 767s 767s Importing the numpy C-extensions failed. This error can happen for 767s many reasons, often due to issues with your setup or how NumPy was 767s installed. 767s 767s We have compiled some common reasons and troubleshooting tips at: 767s 767s https://numpy.org/devdocs/user/troubleshooting-importerror.html 767s 767s Please note and check the following: 767s 767s * The Python version is: Python3.13 from "/usr/bin/python3.13" 767s * The NumPy version is: "1.26.4" 767s 767s and make sure that they are the versions you expect. 767s Please carefully study the documentation linked above for further help. 767s 767s Original error was: No module named 'numpy.core._multiarray_umath' 767s 767s 767s The above exception was the direct cause of the following exception: 767s 767s Traceback (most recent call last): 767s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 767s module = __import__(module_name) 767s File "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 767s import numpy as np 767s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 767s raise ImportError(msg) from e 767s ImportError: Error importing numpy: you should not try to import numpy from 767s its source directory; please exit the numpy source tree, and relaunch 767s your python interpreter from there. 767s 767s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 767s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 767s 767s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 767s 767s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 767s 767s test_Pathway ... ok 767s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 767s 767s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_PopGen_GenePop_nodepend ... ok 767s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 767s 767s test_ProtParam ... ok 768s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 768s 768s test_Restriction ... ok 768s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 768s 768s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 768s 768s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 768s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 768s 769s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 769s 769s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 769s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 769s 769s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 769s 770s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 770s 770s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 770s 770s test_UniGene ... ok 770s test_UniProt ... skipping. internet not available 770s test_UniProt_GOA ... ok 770s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 770s 770s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 770s 770s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 773s test_bgzf ... ok 773s test_cellosaurus ... ok 773s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 773s 773s test_geo ... ok 773s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 773s 773s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 773s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 773s 773s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 773s 773s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 773s 773s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 773s 773s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 773s 773s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 773s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 773s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 773s 773s test_prodoc ... ok 773s test_prosite ... ok 773s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 773s 773s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 773s test_seq ... ok 773s test_translate ... ok 773s Skipping any tests requiring internet access 773s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 773s Operating system: posix linux 773s ---------------------------------------------------------------------- 773s Ran 217 tests in 15.909 seconds 773s 773s FAILED (failures = 15) 774s test_Ace ... ok 774s test_Affy ... ok 779s test_AlignIO ... ok 779s test_AlignIO_ClustalIO ... ok 779s test_AlignIO_EmbossIO ... ok 779s test_AlignIO_FastaIO ... ok 779s test_AlignIO_MauveIO ... ok 779s test_AlignIO_PhylipIO ... ok 779s test_AlignIO_convert ... ok 779s test_AlignInfo ... ok 779s test_Align_Alignment ... ok 780s test_Align_a2m ... ok 780s test_Align_bed ... ok 780s test_Align_bigbed ... ok 781s test_Align_bigmaf ... ok 781s test_Align_bigpsl ... ok 781s test_Align_chain ... ok 781s test_Align_clustal ... ok 789s test_Align_codonalign ... ok 789s test_Align_emboss ... ok 789s test_Align_exonerate ... ok 789s test_Align_fasta ... ok 789s test_Align_hhr ... ok 791s test_Align_maf ... ok 791s test_Align_mauve ... ok 791s test_Align_msf ... ok 791s test_Align_nexus ... ok 791s test_Align_phylip ... ok 792s test_Align_psl ... ok 792s test_Align_sam ... ok 795s test_Align_stockholm ... ok 795s test_Align_tabular ... ok 795s test_Application ... ok 796s test_BioSQL_MySQLdb_online ... skipping. internet not available 796s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 796s test_BioSQL_mysql_connector_online ... skipping. internet not available 796s test_BioSQL_psycopg2_online ... skipping. internet not available 803s test_BioSQL_sqlite3 ... ok 803s test_BioSQL_sqlite3_online ... skipping. internet not available 803s test_Blast_Record ... ok 804s test_Blast_parser ... ok 804s test_CAPS ... ok 804s test_Chi2 ... ok 805s test_ClustalOmega_tool ... ok 805s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 805s test_Cluster ... ok 805s test_CodonTable ... ok 805s test_ColorSpiral ... ok 805s test_Compass ... ok 807s test_Consensus ... ok 808s test_Dialign_tool ... ok 808s test_EMBL_unittest ... ok 815s test_Emboss ... ok 815s test_EmbossPrimer ... ok 819s test_Entrez ... ok 819s test_Entrez_online ... skipping. internet not available 820s test_Entrez_parser ... ok 820s test_Enzyme ... ok 820s test_ExPASy ... skipping. internet not available 820s test_Fasttree_tool ... ok 820s test_File ... ok 820s test_GenBank ... ok 823s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 826s ok 827s test_GraphicsChromosome ... ok 827s test_GraphicsDistribution ... ok 829s test_GraphicsGeneral ... ok 829s test_HMMCasino ... ok 829s test_HMMGeneral ... ok 829s test_KEGG ... ok 829s test_KEGG_online ... skipping. internet not available 836s test_KGML_graphics ... ok 836s test_KGML_graphics_online ... skipping. internet not available 837s test_KGML_nographics ... ok 837s test_KeyWList ... ok 837s test_LogisticRegression ... ok 839s test_MafIO_index ... ok 840s test_Mafft_tool ... ok 840s test_MarkovModel ... ok 840s test_Medline ... ok 840s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 841s test_NCBIXML ... ok 843s test_NCBI_BLAST_tools ... ok 843s test_NCBI_qblast ... ok 843s test_NMR ... ok 843s test_NaiveBayes ... ok 844s test_Nexus ... ok 844s test_PAML_baseml ... ok 845s test_PAML_codeml ... ok 845s test_PAML_yn00 ... ok 848s test_PDB_CEAligner ... ok 850s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 850s Configuration error: 850s 850s The attempt to retrieve compound information for "SO4" failed. 850s 850s This information is searched for in a CCD file called components.cif or 850s components.cif.gz which should be located in one of the following directories: 850s 850s "/usr/share/libcifpp" 850s "/var/cache/libcifpp" 850s "/tmp/autopkgtest.KHTw7M/autopkgtest_tmp/libcifpp-data" 850s "/usr/share/libcifpp" 850s "/usr/share/libcifpp" 850s 850s (Note that you can add a directory to the search paths by setting the 850s LIBCIFPP_DATA_DIR environmental variable) 850s 850s On Linux an optional cron script might have been installed that automatically updates 850s components.cif and mmCIF dictionary files. This script only works when the file 850s libcifpp.conf contains an uncommented line with the text: 850s 850s update=true 850s 850s If you do not have a working cron script, you can manually update the files 850s in /var/cache/libcifpp using the following commands: 850s 850s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 850s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 850s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 850s 850s The current order of compound factory objects is: 850s 850s CCD components.cif resource 850s CCD components.cif resource 850s Unknown compound: SO4 850s Missing compound information for SO4 850s 850s warnings.warn(err) 851s ok 851s test_PDB_Dice ... ok 851s test_PDB_Disordered ... ok 851s test_PDB_Exposure ... ok 851s test_PDB_FragmentMapper ... ok 854s test_PDB_KDTree ... ok 854s test_PDB_MMCIF2Dict ... ok 855s test_PDB_MMCIFIO ... ok 856s test_PDB_MMCIFParser ... ok 856s test_PDB_NACCESS ... ok 856s test_PDB_PDBIO ... ok 856s test_PDB_PDBList ... skipping. internet not available 865s test_PDB_PDBMLParser ... ok 865s test_PDB_PDBParser ... ok 866s 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 866s test_PDB_Polypeptide ... ok 866s test_PDB_QCPSuperimposer ... ok 870s test_PDB_SASA ... ok 871s test_PDB_SMCRA ... ok 871s test_PDB_Selection ... ok 871s test_PDB_StructureAlignment ... ok 871s test_PDB_Superimposer ... ok 871s test_PDB_alphafold_db ... skipping. internet not available 877s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 877s warnings.warn( 877s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 877s warnings.warn( 877s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 877s warnings.warn( 877s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 877s warnings.warn( 877s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 877s warnings.warn( 877s ok 888s test_PDB_internal_coords ... ok 889s test_PDB_parse_pdb_header ... ok 889s test_PDB_vectors ... ok 889s test_PQR ... ok 889s test_Pathway ... ok 889s test_Phd ... ok 890s test_Phylo ... ok 890s test_PhyloXML ... ok 891s test_Phylo_CDAO ... ok 891s test_Phylo_NeXML ... ok 891s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 895s test_Phylo_matplotlib ... ok 896s test_Phylo_networkx ... ok 896s test_PopGen_GenePop_nodepend ... ok 898s test_Prank_tool ... ok 898s test_Probcons_tool ... ok 899s test_ProtParam ... ok 900s test_RCSBFormats ... ok 900s test_Restriction ... ok 900s test_SCOP_Astral ... ok 901s test_SCOP_Cla ... ok 901s test_SCOP_Des ... ok 901s test_SCOP_Dom ... ok 902s test_SCOP_Hie ... ok 902s test_SCOP_Raf ... ok 902s test_SCOP_Residues ... ok 902s test_SCOP_Scop ... ok 903s test_SVDSuperimposer ... ok 903s test_SearchIO_blast_tab ... ok 904s test_SearchIO_blast_tab_index ... ok 904s test_SearchIO_blast_xml ... ok 906s test_SearchIO_blast_xml_index ... ok 906s test_SearchIO_blat_psl ... ok 906s test_SearchIO_blat_psl_index ... ok 907s test_SearchIO_exonerate ... ok 907s test_SearchIO_exonerate_text_index ... ok 908s test_SearchIO_exonerate_vulgar_index ... ok 908s test_SearchIO_fasta_m10 ... ok 908s test_SearchIO_fasta_m10_index ... ok 909s test_SearchIO_hhsuite2_text ... ok 909s test_SearchIO_hmmer2_text ... ok 910s test_SearchIO_hmmer2_text_index ... ok 910s test_SearchIO_hmmer3_domtab ... ok 911s test_SearchIO_hmmer3_domtab_index ... ok 911s test_SearchIO_hmmer3_tab ... ok 911s test_SearchIO_hmmer3_tab_index ... ok 912s test_SearchIO_hmmer3_text ... ok 912s test_SearchIO_hmmer3_text_index ... ok 912s test_SearchIO_interproscan_xml ... ok 913s test_SearchIO_model ... ok 913s test_SearchIO_write ... ok 914s test_SeqFeature ... ok 935s test_SeqIO ... ok 936s test_SeqIO_AbiIO ... ok 936s test_SeqIO_FastaIO ... ok 936s test_SeqIO_Gck ... ok 937s test_SeqIO_Gfa ... ok 937s test_SeqIO_Insdc ... ok 937s test_SeqIO_NibIO ... ok 941s test_SeqIO_PdbIO ... ok 942s test_SeqIO_QualityIO ... ok 942s test_SeqIO_SeqXML ... ok 942s test_SeqIO_SnapGene ... ok 944s test_SeqIO_TwoBitIO ... ok 945s test_SeqIO_Xdna ... ok 946s test_SeqIO_features ... ok 970s test_SeqIO_index ... ok 970s test_SeqIO_online ... skipping. internet not available 971s test_SeqIO_write ... ok 971s test_SeqRecord ... ok 972s test_SeqUtils ... ok 974s test_Seq_objs ... ok 974s test_SffIO ... ok 975s test_SwissProt ... ok 976s test_TCoffee_tool ... ok 976s test_TogoWS ... skipping. internet not available 977s test_TreeConstruction ... ok 978s test_UniGene ... ok 978s test_UniProt ... skipping. internet not available 978s test_UniProt_GOA ... ok 979s test_UniProt_Parser ... ok 979s test_align ... ok 980s test_align_substitution_matrices ... ok 983s test_bgzf ... ok 983s test_cellosaurus ... ok 992s test_codonalign ... ok 993s test_geo ... ok 993s test_kNN ... ok 994s test_motifs ... ok 994s test_motifs_online ... skipping. internet not available 994s 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. 994s warnings.warn( 994s ok 995s test_pairwise2_no_C ... ok 995s test_pairwise_aligner ... ok 996s test_pairwise_alignment_map ... ok 1005s test_phenotype ... ok 1005s test_phenotype_fit ... ok 1005s 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. 1006s test_prodoc ... ok 1006s test_prosite ... ok 1006s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1007s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1007s test_seq ... ok 1007s test_translate ... ok 1008s ---------------------------------------------------------------------- 1008s Ran 217 tests in 233.631 seconds 1008s 1008s Skipping any tests requiring internet access 1008s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 1008s Operating system: posix linux 1009s autopkgtest [21:35:26]: test full_suite: -----------------------] 1009s autopkgtest [21:35:26]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1009s full_suite PASS 1010s autopkgtest [21:35:27]: @@@@@@@@@@@@@@@@@@@@ summary 1010s dependencies PASS 1010s full_suite PASS 1014s virt: nova [W] Using flock in prodstack6-ppc64el 1014s virt: Creating nova instance adt-plucky-ppc64el-python-biopython-20241113-211837-juju-7f2275-prod-proposed-migration-environment-2-62acb108-b152-42e3-8330-d78f3f674de7 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)... 1014s virt: nova [W] Using flock in prodstack6-ppc64el 1014s virt: flock: timeout while waiting to get lock 1014s virt: Creating nova instance adt-plucky-ppc64el-python-biopython-20241113-211837-juju-7f2275-prod-proposed-migration-environment-2-62acb108-b152-42e3-8330-d78f3f674de7 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...