0s autopkgtest [23:18:39]: starting date and time: 2024-11-13 23:18:39+0000 0s autopkgtest [23:18:39]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [23:18:39]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b0xxmaaa/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-pyfaidx --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-15@bos03-ppc64el-3.secgroup --name adt-plucky-ppc64el-python-pyfaidx-20241113-231839-juju-7f2275-prod-proposed-migration-environment-15-1352e1f7-9e1b-462d-92fe-131848143f90 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 140s autopkgtest [23:20:59]: testbed dpkg architecture: ppc64el 140s autopkgtest [23:20:59]: testbed apt version: 2.9.8 140s autopkgtest [23:20:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 142s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 142s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 142s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 142s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [692 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 142s Fetched 1993 kB in 1s (1740 kB/s) 142s Reading package lists... 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Calculating upgrade... 145s The following NEW packages will be installed: 145s python3.13-gdbm 145s The following packages will be upgraded: 145s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 145s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 145s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 145s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 4700 kB of archives. 145s After this operation, 215 kB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 145s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 145s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 146s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 146s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 146s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 146s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 146s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 146s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 146s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 146s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 146s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 146s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 146s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 147s Fetched 4700 kB in 1s (4077 kB/s) 147s (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.) 147s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 147s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 147s Setting up python3-minimal (3.12.7-1) ... 147s (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.) 147s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 147s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 147s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 147s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 147s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 147s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 147s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 147s (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.) 147s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 147s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 147s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 147s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 147s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 147s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 147s Selecting previously unselected package python3.13-gdbm. 147s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 147s Unpacking python3.13-gdbm (3.13.0-2) ... 147s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 147s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 147s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 147s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 147s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 148s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 148s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 148s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 148s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 148s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 148s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 148s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 148s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 148s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 148s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 148s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 148s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 148s Setting up libutempter0:ppc64el (1.2.1-4) ... 148s Setting up whiptail (0.52.24-2ubuntu4) ... 148s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 148s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 148s Setting up python3.13-gdbm (3.13.0-2) ... 148s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 148s Setting up bpftrace (0.21.2-2ubuntu2) ... 148s Setting up python3 (3.12.7-1) ... 148s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 148s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 148s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 148s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 148s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 148s Processing triggers for man-db (2.12.1-3) ... 149s Processing triggers for libc-bin (2.40-1ubuntu3) ... 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 150s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 150s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 151s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 151s Reading package lists... 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Calculating upgrade... 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s autopkgtest [23:21:14]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 155s autopkgtest [23:21:14]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pyfaidx 157s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.3-1 (dsc) [2544 B] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.3-1 (tar) [96.5 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.3-1 (diff) [7096 B] 157s gpgv: Signature made Wed Oct 16 19:20:44 2024 UTC 157s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 157s gpgv: issuer "emollier@debian.org" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./python-pyfaidx_0.8.1.3-1.dsc: no acceptable signature found 158s autopkgtest [23:21:17]: testing package python-pyfaidx version 0.8.1.3-1 158s autopkgtest [23:21:17]: build not needed 158s autopkgtest [23:21:17]: test run-unit-test: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 162s The following additional packages will be installed: 162s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 162s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 162s libgomp1 libgraphite2-3 libharfbuzz0b libhtscodecs2 libimagequant0 libjbig0 162s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 162s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 162s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 162s libxcb-shm0 libxrender1 python-pyfaidx-examples python3-all 162s python3-biopython python3-cairo python3-freetype python3-importlib-metadata 162s python3-iniconfig python3-numpy python3-packaging python3-pil python3-pluggy 162s python3-pyfaidx python3-pytest python3-reportlab python3-rlpycairo 162s python3.13 python3.13-minimal sgml-base tabix w3c-sgml-lib x11-common 162s xfonts-encodings xfonts-utils xml-core 162s Suggested packages: 162s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 162s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 162s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 162s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 162s gcc gfortran python-numpy-doc python3-dev python-pil-doc pdf-viewer 162s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 162s python3.13-venv python3.13-doc binfmt-support sgml-base-doc debhelper 162s Recommended packages: 162s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 162s The following NEW packages will be installed: 162s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 162s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 162s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhtscodecs2 162s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 162s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 162s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 162s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-pyfaidx-examples 162s python3-all python3-biopython python3-cairo python3-freetype 162s python3-importlib-metadata python3-iniconfig python3-numpy python3-packaging 162s python3-pil python3-pluggy python3-pyfaidx python3-pytest python3-reportlab 162s python3-rlpycairo python3.13 python3.13-minimal sgml-base tabix w3c-sgml-lib 162s x11-common xfonts-encodings xfonts-utils xml-core 162s 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 36.3 MB/36.3 MB of archives. 162s After this operation, 124 MB of additional disk space will be used. 162s Get:1 /tmp/autopkgtest.dmOVQJ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [752 B] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 163s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 163s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 163s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 163s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 163s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 163s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 163s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 163s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 163s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 165s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 165s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 165s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 165s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 165s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 165s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 165s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 165s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 166s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 166s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 166s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 166s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 166s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 166s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 166s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 166s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 166s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 166s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 166s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 166s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 166s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 167s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 167s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 167s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 167s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 167s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 167s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 167s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 167s Get:40 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-pyfaidx-examples all 0.8.1.3-1 [38.6 kB] 167s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 167s Get:42 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 167s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 168s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 168s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 168s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 168s Get:47 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 168s Get:48 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 168s Get:49 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 168s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 168s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 168s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB] 168s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-importlib-metadata all 8.5.0-1 [20.7 kB] 168s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 168s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 168s Get:56 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 168s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 168s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 168s Get:59 http://ftpmaster.internal/ubuntu plucky/universe ppc64el tabix ppc64el 1.20+ds-1 [715 kB] 169s Fetched 36.3 MB in 7s (5319 kB/s) 169s Selecting previously unselected package libpython3.13-minimal:ppc64el. 169s (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.) 169s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 169s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 169s Selecting previously unselected package python3.13-minimal. 169s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ... 169s Unpacking python3.13-minimal (3.13.0-2) ... 169s Selecting previously unselected package sgml-base. 169s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 169s Unpacking sgml-base (1.31) ... 169s Selecting previously unselected package fonts-dejavu-mono. 169s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 169s Unpacking fonts-dejavu-mono (2.37-8) ... 169s Selecting previously unselected package fonts-dejavu-core. 169s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 169s Unpacking fonts-dejavu-core (2.37-8) ... 169s Selecting previously unselected package libfontenc1:ppc64el. 169s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 169s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 169s Selecting previously unselected package x11-common. 169s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 169s Unpacking x11-common (1:7.7+23ubuntu3) ... 169s Selecting previously unselected package xfonts-encodings. 169s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 169s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 169s Selecting previously unselected package xfonts-utils. 169s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 169s Unpacking xfonts-utils (1:7.7+7) ... 169s Selecting previously unselected package fonts-urw-base35. 169s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 169s Unpacking fonts-urw-base35 (20200910-8) ... 169s Selecting previously unselected package fontconfig-config. 169s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 169s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 169s Selecting previously unselected package libblas3:ppc64el. 169s Preparing to unpack .../11-libblas3_3.12.0-3build2_ppc64el.deb ... 169s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 169s Selecting previously unselected package libfontconfig1:ppc64el. 169s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 169s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 169s Selecting previously unselected package libpixman-1-0:ppc64el. 169s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_ppc64el.deb ... 169s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 169s Selecting previously unselected package libxcb-render0:ppc64el. 169s Preparing to unpack .../14-libxcb-render0_1.17.0-2_ppc64el.deb ... 169s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 169s Selecting previously unselected package libxcb-shm0:ppc64el. 169s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_ppc64el.deb ... 169s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 170s Selecting previously unselected package libxrender1:ppc64el. 170s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 170s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 170s Selecting previously unselected package libcairo2:ppc64el. 170s Preparing to unpack .../17-libcairo2_1.18.2-2_ppc64el.deb ... 170s Unpacking libcairo2:ppc64el (1.18.2-2) ... 170s Selecting previously unselected package libdeflate0:ppc64el. 170s Preparing to unpack .../18-libdeflate0_1.22-1_ppc64el.deb ... 170s Unpacking libdeflate0:ppc64el (1.22-1) ... 170s Selecting previously unselected package libgfortran5:ppc64el. 170s Preparing to unpack .../19-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 170s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 170s Selecting previously unselected package libgomp1:ppc64el. 170s Preparing to unpack .../20-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 170s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 170s Selecting previously unselected package libgraphite2-3:ppc64el. 170s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 170s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 170s Selecting previously unselected package libharfbuzz0b:ppc64el. 170s Preparing to unpack .../22-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 170s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 170s Selecting previously unselected package libhtscodecs2:ppc64el. 170s Preparing to unpack .../23-libhtscodecs2_1.6.1-1_ppc64el.deb ... 170s Unpacking libhtscodecs2:ppc64el (1.6.1-1) ... 170s Selecting previously unselected package libimagequant0:ppc64el. 170s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_ppc64el.deb ... 170s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 170s Selecting previously unselected package libjpeg-turbo8:ppc64el. 170s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 170s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 170s Selecting previously unselected package libjpeg8:ppc64el. 170s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 170s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 170s Selecting previously unselected package liblapack3:ppc64el. 170s Preparing to unpack .../27-liblapack3_3.12.0-3build2_ppc64el.deb ... 170s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 170s Selecting previously unselected package liblcms2-2:ppc64el. 170s Preparing to unpack .../28-liblcms2-2_2.16-2_ppc64el.deb ... 170s Unpacking liblcms2-2:ppc64el (2.16-2) ... 170s Selecting previously unselected package liblerc4:ppc64el. 170s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 170s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 170s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 170s Preparing to unpack .../30-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ... 170s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ... 170s Selecting previously unselected package libraqm0:ppc64el. 170s Preparing to unpack .../31-libraqm0_0.10.1-1build1_ppc64el.deb ... 170s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 170s Selecting previously unselected package libsharpyuv0:ppc64el. 170s Preparing to unpack .../32-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 170s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 170s Selecting previously unselected package libjbig0:ppc64el. 170s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 170s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 170s Selecting previously unselected package libwebp7:ppc64el. 170s Preparing to unpack .../34-libwebp7_1.4.0-0.1_ppc64el.deb ... 170s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 170s Selecting previously unselected package libtiff6:ppc64el. 170s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 170s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 170s Selecting previously unselected package libwebpdemux2:ppc64el. 170s Preparing to unpack .../36-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 170s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 170s Selecting previously unselected package libwebpmux3:ppc64el. 170s Preparing to unpack .../37-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 170s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 170s Selecting previously unselected package python-pyfaidx-examples. 170s Preparing to unpack .../38-python-pyfaidx-examples_0.8.1.3-1_all.deb ... 170s Unpacking python-pyfaidx-examples (0.8.1.3-1) ... 170s Selecting previously unselected package python3.13. 170s Preparing to unpack .../39-python3.13_3.13.0-2_ppc64el.deb ... 170s Unpacking python3.13 (3.13.0-2) ... 170s Selecting previously unselected package python3-all. 170s Preparing to unpack .../40-python3-all_3.12.7-1_ppc64el.deb ... 170s Unpacking python3-all (3.12.7-1) ... 170s Selecting previously unselected package python3-numpy. 170s Preparing to unpack .../41-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 170s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 170s Selecting previously unselected package libopenjp2-7:ppc64el. 170s Preparing to unpack .../42-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 170s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 170s Selecting previously unselected package python3-pil:ppc64el. 170s Preparing to unpack .../43-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 170s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 170s Selecting previously unselected package python3-cairo. 170s Preparing to unpack .../44-python3-cairo_1.26.1-2_ppc64el.deb ... 170s Unpacking python3-cairo (1.26.1-2) ... 170s Selecting previously unselected package python3-freetype. 170s Preparing to unpack .../45-python3-freetype_2.5.1-1_all.deb ... 170s Unpacking python3-freetype (2.5.1-1) ... 170s Selecting previously unselected package python3-rlpycairo. 170s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ... 170s Unpacking python3-rlpycairo (0.3.0-3) ... 170s Selecting previously unselected package python3-reportlab. 170s Preparing to unpack .../47-python3-reportlab_4.2.5-1_all.deb ... 170s Unpacking python3-reportlab (4.2.5-1) ... 170s Selecting previously unselected package xml-core. 170s Preparing to unpack .../48-xml-core_0.19_all.deb ... 170s Unpacking xml-core (0.19) ... 170s Selecting previously unselected package w3c-sgml-lib. 170s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ... 170s Unpacking w3c-sgml-lib (1.3-3) ... 171s Selecting previously unselected package python3-biopython. 171s Preparing to unpack .../50-python3-biopython_1.84+dfsg-4_ppc64el.deb ... 171s Unpacking python3-biopython (1.84+dfsg-4) ... 171s Selecting previously unselected package python3-importlib-metadata. 171s Preparing to unpack .../51-python3-importlib-metadata_8.5.0-1_all.deb ... 171s Unpacking python3-importlib-metadata (8.5.0-1) ... 171s Selecting previously unselected package python3-iniconfig. 171s Preparing to unpack .../52-python3-iniconfig_1.1.1-2_all.deb ... 171s Unpacking python3-iniconfig (1.1.1-2) ... 171s Selecting previously unselected package python3-packaging. 171s Preparing to unpack .../53-python3-packaging_24.1-1_all.deb ... 171s Unpacking python3-packaging (24.1-1) ... 171s Selecting previously unselected package python3-pluggy. 171s Preparing to unpack .../54-python3-pluggy_1.5.0-1_all.deb ... 171s Unpacking python3-pluggy (1.5.0-1) ... 171s Selecting previously unselected package python3-pyfaidx. 171s Preparing to unpack .../55-python3-pyfaidx_0.8.1.3-1_all.deb ... 171s Unpacking python3-pyfaidx (0.8.1.3-1) ... 171s Selecting previously unselected package python3-pytest. 171s Preparing to unpack .../56-python3-pytest_8.3.3-1_all.deb ... 171s Unpacking python3-pytest (8.3.3-1) ... 171s Selecting previously unselected package tabix. 171s Preparing to unpack .../57-tabix_1.20+ds-1_ppc64el.deb ... 171s Unpacking tabix (1.20+ds-1) ... 171s Selecting previously unselected package autopkgtest-satdep. 171s Preparing to unpack .../58-1-autopkgtest-satdep.deb ... 171s Unpacking autopkgtest-satdep (0) ... 171s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 171s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 171s Setting up liblcms2-2:ppc64el (2.16-2) ... 171s Setting up python3-iniconfig (1.1.1-2) ... 171s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 171s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 171s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 171s Setting up python3-importlib-metadata (8.5.0-1) ... 171s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 171s Setting up python-pyfaidx-examples (0.8.1.3-1) ... 171s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 171s Setting up x11-common (1:7.7+23ubuntu3) ... 172s Setting up libdeflate0:ppc64el (1.22-1) ... 172s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 172s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 172s Setting up python3-freetype (2.5.1-1) ... 172s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 172s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ... 172s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 172s Setting up libblas3:ppc64el (3.12.0-3build2) ... 172s 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 172s Setting up python3-packaging (24.1-1) ... 172s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 172s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 172s Setting up fonts-dejavu-mono (2.37-8) ... 172s Setting up fonts-dejavu-core (2.37-8) ... 172s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 172s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 172s Setting up python3-pluggy (1.5.0-1) ... 172s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 172s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 172s Setting up python3.13-minimal (3.13.0-2) ... 173s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 173s Setting up sgml-base (1.31) ... 173s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 173s Setting up tabix (1.20+ds-1) ... 173s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 173s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 173s Setting up python3-pyfaidx (0.8.1.3-1) ... 173s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 173s 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 173s Setting up python3.13 (3.13.0-2) ... 175s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 175s Setting up python3-pytest (8.3.3-1) ... 175s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 175s Setting up python3-all (3.12.7-1) ... 175s Setting up xfonts-utils (1:7.7+7) ... 175s Setting up libraqm0:ppc64el (0.10.1-1build1) ... 175s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 180s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 180s Setting up xml-core (0.19) ... 180s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 180s Setting up fonts-urw-base35 (20200910-8) ... 180s Setting up libcairo2:ppc64el (1.18.2-2) ... 180s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ... 181s Setting up python3-cairo (1.26.1-2) ... 181s Setting up python3-rlpycairo (0.3.0-3) ... 181s Setting up python3-reportlab (4.2.5-1) ... 183s Processing triggers for libc-bin (2.40-1ubuntu3) ... 183s Processing triggers for systemd (256.5-2ubuntu4) ... 183s Processing triggers for man-db (2.12.1-3) ... 184s Processing triggers for sgml-base (1.31) ... 184s Setting up w3c-sgml-lib (1.3-3) ... 215s Setting up python3-biopython (1.84+dfsg-4) ... 218s Setting up autopkgtest-satdep (0) ... 221s (Reading database ... 77978 files and directories currently installed.) 221s Removing autopkgtest-satdep (0) ... 221s autopkgtest [23:22:20]: test run-unit-test: [----------------------- 222s Testing with python3.13 in /tmp/autopkgtest.dmOVQJ/build.U0D/src: 222s ============================= test session starts ============================== 222s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 222s cachedir: .pytest_cache 222s rootdir: /tmp/autopkgtest.dmOVQJ/build.U0D/src 222s configfile: pyproject.toml 222s plugins: typeguard-4.4.1 222s collecting ... collected 136 items 222s 222s tests/test_FastaRecord.py::test_sequence_uppercase PASSED [ 0%] 222s tests/test_FastaRecord.py::test_long_names PASSED [ 1%] 222s tests/test_FastaRecord.py::test_issue_62 PASSED [ 2%] 222s tests/test_FastaRecord.py::test_unpadded_length PASSED [ 2%] 222s tests/test_FastaRecord.py::test_numpy_array FAILED [ 3%] 222s tests/test_FastaRecord_iter.py::test_fetch_whole_fasta PASSED [ 4%] 222s tests/test_FastaRecord_iter.py::test_line_len PASSED [ 5%] 222s tests/test_FastaRecord_iter.py::test_reverse_iter PASSED [ 5%] 222s tests/test_FastaVariant.py::test_fetch_variant SKIPPED (pysam not in...) [ 6%] 222s tests/test_FastaVariant.py::test_fetch_hom_variant SKIPPED (pysam no...) [ 7%] 222s tests/test_FastaVariant.py::test_fetch_het_variant SKIPPED (pysam no...) [ 8%] 222s tests/test_FastaVariant.py::test_fetch_chr_not_in_vcf SKIPPED (pysam...) [ 8%] 222s tests/test_FastaVariant.py::test_all_pos SKIPPED (pysam not installed.) [ 9%] 222s tests/test_FastaVariant.py::test_all_diff SKIPPED (pysam not installed.) [ 10%] 222s tests/test_Fasta_bgzip.py::test_build_issue_126 SKIPPED (Biopython i...) [ 11%] 222s tests/test_Fasta_bgzip.py::test_integer_slice PASSED [ 11%] 222s tests/test_Fasta_bgzip.py::test_integer_index PASSED [ 12%] 222s tests/test_Fasta_bgzip.py::test_fetch_whole_fasta PASSED [ 13%] 222s tests/test_Fasta_bgzip.py::test_line_len PASSED [ 13%] 222s tests/test_Fasta_bgzip.py::test_mutable_bgzf PASSED [ 14%] 222s tests/test_Fasta_bgzip.py::test_long_names XFAIL [ 15%] 222s tests/test_Fasta_bgzip.py::test_fetch_whole_entry PASSED [ 16%] 222s tests/test_Fasta_bgzip.py::test_fetch_middle PASSED [ 16%] 222s tests/test_Fasta_bgzip.py::test_fetch_end PASSED [ 17%] 222s tests/test_Fasta_bgzip.py::test_fetch_border PASSED [ 18%] 222s tests/test_Fasta_bgzip.py::test_rev PASSED [ 19%] 222s tests/test_Fasta_bgzip.py::test_fetch_past_bounds PASSED [ 19%] 222s tests/test_Fasta_bgzip.py::test_fetch_negative PASSED [ 20%] 222s tests/test_Fasta_bgzip.py::test_fetch_reversed_coordinates PASSED [ 21%] 222s tests/test_Fasta_bgzip.py::test_fetch_keyerror PASSED [ 22%] 222s tests/test_Fasta_bgzip.py::test_blank_string PASSED [ 22%] 222s tests/test_Fasta_bgzip.py::test_slice_from_beginning PASSED [ 23%] 222s tests/test_Fasta_bgzip.py::test_slice_from_end PASSED [ 24%] 222s tests/test_Fasta_bgzip.py::test_issue_74_start PASSED [ 25%] 222s tests/test_Fasta_bgzip.py::test_issue_74_consistency PASSED [ 25%] 222s tests/test_Fasta_bgzip.py::test_issue_74_end_faidx PASSED [ 26%] 222s tests/test_Fasta_bgzip.py::test_issue_74_end_fasta PASSED [ 27%] 222s tests/test_Fasta_bgzip.py::test_issue_79_fix PASSED [ 27%] 222s tests/test_Fasta_bgzip.py::test_issue_79_fix_negate PASSED [ 28%] 222s tests/test_Fasta_bgzip.py::test_issue_79_fix_one_based_false PASSED [ 29%] 222s tests/test_Fasta_bgzip.py::test_issue_79_fix_one_based_false_negate PASSED [ 30%] 222s tests/test_Fasta_bgzip.py::test_fetch_border_padded PASSED [ 30%] 222s tests/test_Fasta_integer_index.py::test_integer_slice PASSED [ 31%] 222s tests/test_Fasta_integer_index.py::test_integer_index PASSED [ 32%] 223s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_reads PASSED [ 33%] 223s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_reads_and_writes PASSED [ 33%] 223s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_writes PASSED [ 34%] 223s tests/test_Path.py::test_Faidx PASSED [ 35%] 223s tests/test_Path.py::test_Fasta PASSED [ 36%] 223s tests/test_bio_seqio.py::test_fetch_whole_entry SKIPPED (Biopython i...) [ 36%] 223s tests/test_bio_seqio.py::test_slice_whole_entry SKIPPED (Biopython i...) [ 37%] 223s tests/test_bio_seqio.py::test_revcomp_whole_entry SKIPPED (Biopython...) [ 38%] 223s tests/test_faidx.py::test_short_line_lengths PASSED [ 38%] 223s tests/test_faidx.py::test_fetch_whole_file PASSED [ 39%] 223s tests/test_faidx.py::test_split_entry PASSED [ 40%] 223s tests/test_faidx.py::test_fetch_error PASSED [ 41%] 223s tests/test_faidx.py::test_key_warning PASSED [ 41%] 223s tests/test_faidx.py::test_auto_strand PASSED [ 42%] 223s tests/test_faidx.py::test_regexp PASSED [ 43%] 223s tests/test_faidx.py::test_not_regexp PASSED [ 44%] 223s tests/test_faidx.py::test_not_regexp_multi PASSED [ 44%] 223s tests/test_feature_bounds_check.py::test_index_zero_length PASSED [ 45%] 223s tests/test_feature_bounds_check.py::test_fetch_zero_length PASSED [ 46%] 223s tests/test_feature_bounds_check.py::test_as_raw_zero_length_subsequence PASSED [ 47%] 223s tests/test_feature_bounds_check.py::test_zero_length_subsequence PASSED [ 47%] 223s tests/test_feature_bounds_check.py::test_fetch_whole_entry PASSED [ 48%] 223s tests/test_feature_bounds_check.py::test_fetch_middle PASSED [ 49%] 223s tests/test_feature_bounds_check.py::test_fetch_end PASSED [ 50%] 223s tests/test_feature_bounds_check.py::test_fetch_border PASSED [ 50%] 223s tests/test_feature_bounds_check.py::test_rev PASSED [ 51%] 223s tests/test_feature_bounds_check.py::test_fetch_past_bounds PASSED [ 52%] 223s tests/test_feature_bounds_check.py::test_fetch_negative PASSED [ 52%] 223s tests/test_feature_bounds_check.py::test_fetch_reversed_coordinates PASSED [ 53%] 223s tests/test_feature_bounds_check.py::test_fetch_keyerror PASSED [ 54%] 223s tests/test_feature_bounds_check.py::test_blank_string PASSED [ 55%] 223s tests/test_feature_bounds_check.py::test_slice_from_beginning PASSED [ 55%] 223s tests/test_feature_bounds_check.py::test_slice_from_end PASSED [ 56%] 223s tests/test_feature_bounds_check.py::test_issue_74_start PASSED [ 57%] 223s tests/test_feature_bounds_check.py::test_issue_74_consistency PASSED [ 58%] 223s tests/test_feature_bounds_check.py::test_issue_74_end_faidx PASSED [ 58%] 223s tests/test_feature_bounds_check.py::test_issue_74_end_fasta PASSED [ 59%] 223s tests/test_feature_bounds_check.py::test_issue_79_fix PASSED [ 60%] 223s tests/test_feature_bounds_check.py::test_issue_79_fix_negate PASSED [ 61%] 223s tests/test_feature_bounds_check.py::test_issue_79_fix_one_based_false PASSED [ 61%] 223s tests/test_feature_bounds_check.py::test_issue_79_fix_one_based_false_negate PASSED [ 62%] 223s tests/test_feature_default_seq.py::test_fetch_border_padded PASSED [ 63%] 223s tests/test_feature_indexing.py::test_version_issue_206 PASSED [ 63%] 223s tests/test_feature_indexing.py::test_build PASSED [ 64%] 223s tests/test_feature_indexing.py::test_build_issue_141 PASSED [ 65%] 223s tests/test_feature_indexing.py::test_build_issue_111 PASSED [ 66%] 223s tests/test_feature_indexing.py::test_order PASSED [ 66%] 228s tests/test_feature_indexing.py::test_valgrind_short_lines PASSED [ 67%] 232s tests/test_feature_indexing.py::test_valgrind_long_lines PASSED [ 68%] 237s tests/test_feature_indexing.py::test_valgrind_blank_lines PASSED [ 69%] 239s tests/test_feature_indexing.py::test_reindex_on_modification PASSED [ 69%] 239s tests/test_feature_indexing.py::test_build_issue_83 PASSED [ 70%] 239s tests/test_feature_indexing.py::test_build_issue_96_fail_build_faidx PASSED [ 71%] 239s tests/test_feature_indexing.py::test_build_issue_96_fail_read_malformed_index_duplicate_key PASSED [ 72%] 239s tests/test_feature_indexing.py::test_read_back_index PASSED [ 72%] 239s tests/test_feature_indexing.py::test_issue_134_no_build_index PASSED [ 73%] 239s tests/test_feature_indexing.py::test_issue_144_no_defline PASSED [ 74%] 239s tests/test_feature_key_function.py::test_keys PASSED [ 75%] 239s tests/test_feature_key_function.py::test_key_function_by_dictionary_get_key PASSED [ 75%] 239s tests/test_feature_key_function.py::test_key_function_by_fetch PASSED [ 76%] 239s tests/test_feature_key_function.py::test_duplicated_keys PASSED [ 77%] 239s tests/test_feature_key_function.py::test_duplicated_keys_shortest PASSED [ 77%] 239s tests/test_feature_key_function.py::test_duplicated_keys_longest PASSED [ 78%] 239s tests/test_feature_read_ahead_buffer.py::test_buffer_false PASSED [ 79%] 239s tests/test_feature_read_ahead_buffer.py::test_buffer_true PASSED [ 80%] 239s tests/test_feature_read_ahead_buffer.py::test_buffer_exceed PASSED [ 80%] 239s tests/test_feature_read_ahead_buffer.py::test_bounds_error PASSED [ 81%] 239s tests/test_feature_read_ahead_buffer.py::test_buffer_value PASSED [ 82%] 239s tests/test_feature_sequence_as_raw.py::test_as_raw_false PASSED [ 83%] 239s tests/test_feature_sequence_as_raw.py::test_as_raw_true PASSED [ 83%] 239s tests/test_feature_sequence_as_raw.py::test_as_raw_false_error PASSED [ 84%] 239s tests/test_feature_sequence_as_raw.py::test_as_raw_true_error PASSED [ 85%] 239s tests/test_feature_sequence_as_raw.py::test_as_raw_type_when_blen_lt_0 PASSED [ 86%] 239s tests/test_feature_spliced_seq.py::test_split_seq PASSED [ 86%] 239s tests/test_feature_spliced_seq.py::test_get_seq_rc PASSED [ 87%] 239s tests/test_feature_split_char.py::test_keys PASSED [ 88%] 239s tests/test_feature_split_char.py::test_key_function_by_dictionary_get_key PASSED [ 88%] 239s tests/test_feature_split_char.py::test_key_function_by_fetch PASSED [ 89%] 239s tests/test_feature_split_char.py::test_stop PASSED [ 90%] 239s tests/test_fsspec.py::test_fsspec_fetch_whole_file SKIPPED (uncondit...) [ 91%] 239s tests/test_fsspec.py::test_fsspec_default_index SKIPPED (uncondition...) [ 91%] 239s tests/test_fsspec.py::test_fsspec_local_index SKIPPED (unconditional...) [ 92%] 239s tests/test_fsspec.py::test_fsspec_remote_index SKIPPED (unconditiona...) [ 93%] 239s tests/test_sequence_class.py::test_negate PASSED [ 94%] 239s tests/test_sequence_class.py::test_negate_metadata PASSED [ 94%] 239s tests/test_sequence_class.py::test_seq_invalid PASSED [ 95%] 239s tests/test_sequence_class.py::test_integer_index PASSED [ 96%] 239s tests/test_sequence_class.py::test_slice_index PASSED [ 97%] 239s tests/test_sequence_class.py::test_comp_invalid PASSED [ 97%] 239s tests/test_sequence_class.py::test_check_coordinates PASSED [ 98%] 239s tests/test_sequence_class.py::test_comp_valid PASSED [ 99%] 239s tests/test_sequence_class.py::test_comp_empty PASSED [100%] 239s 239s =================================== FAILURES =================================== 239s _______________________________ test_numpy_array _______________________________ 239s 239s """ 239s Contains the core of NumPy: ndarray, ufuncs, dtypes, etc. 239s 239s Please note that this module is private. All functions and objects 239s are available in the main ``numpy`` namespace - use that instead. 239s 239s """ 239s 239s import os 239s import warnings 239s 239s from numpy.version import version as __version__ 239s 239s 239s # disables OpenBLAS affinity setting of the main thread that limits 239s # python threads or processes to one core 239s env_added = [] 239s for envkey in ['OPENBLAS_MAIN_FREE', 'GOTOBLAS_MAIN_FREE']: 239s if envkey not in os.environ: 239s os.environ[envkey] = '1' 239s env_added.append(envkey) 239s 239s try: 239s > from . import multiarray 239s 239s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: 239s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 239s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 239s from . import overrides 239s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 239s 239s """Implementation of __array_function__ overrides from NEP-18.""" 239s import collections 239s import functools 239s import os 239s 239s from .._utils import set_module 239s from .._utils._inspect import getargspec 239s > from numpy.core._multiarray_umath import ( 239s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 239s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 239s 239s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: ModuleNotFoundError 239s 239s During handling of the above exception, another exception occurred: 239s 239s """ 239s NumPy 239s ===== 239s 239s Provides 239s 1. An array object of arbitrary homogeneous items 239s 2. Fast mathematical operations over arrays 239s 3. Linear Algebra, Fourier Transforms, Random Number Generation 239s 239s How to use the documentation 239s ---------------------------- 239s Documentation is available in two forms: docstrings provided 239s with the code, and a loose standing reference guide, available from 239s `the NumPy homepage `_. 239s 239s We recommend exploring the docstrings using 239s `IPython `_, an advanced Python shell with 239s TAB-completion and introspection capabilities. See below for further 239s instructions. 239s 239s The docstring examples assume that `numpy` has been imported as ``np``:: 239s 239s >>> import numpy as np 239s 239s Code snippets are indicated by three greater-than signs:: 239s 239s >>> x = 42 239s >>> x = x + 1 239s 239s Use the built-in ``help`` function to view a function's docstring:: 239s 239s >>> help(np.sort) 239s ... # doctest: +SKIP 239s 239s For some objects, ``np.info(obj)`` may provide additional help. This is 239s particularly true if you see the line "Help on ufunc object:" at the top 239s of the help() page. Ufuncs are implemented in C, not Python, for speed. 239s The native Python help() does not know how to view their help, but our 239s np.info() function does. 239s 239s To search for documents containing a keyword, do:: 239s 239s >>> np.lookfor('keyword') 239s ... # doctest: +SKIP 239s 239s General-purpose documents like a glossary and help on the basic concepts 239s of numpy are available under the ``doc`` sub-module:: 239s 239s >>> from numpy import doc 239s >>> help(doc) 239s ... # doctest: +SKIP 239s 239s Available subpackages 239s --------------------- 239s lib 239s Basic functions used by several sub-packages. 239s random 239s Core Random Tools 239s linalg 239s Core Linear Algebra Tools 239s fft 239s Core FFT routines 239s polynomial 239s Polynomial tools 239s testing 239s NumPy testing tools 239s distutils 239s Enhancements to distutils with support for 239s Fortran compilers support and more (for Python <= 3.11). 239s 239s Utilities 239s --------- 239s test 239s Run numpy unittests 239s show_config 239s Show numpy build configuration 239s matlib 239s Make everything matrices. 239s __version__ 239s NumPy version string 239s 239s Viewing documentation using IPython 239s ----------------------------------- 239s 239s Start IPython and import `numpy` usually under the alias ``np``: `import 239s numpy as np`. Then, directly past or use the ``%cpaste`` magic to paste 239s examples into the shell. To see which functions are available in `numpy`, 239s type ``np.`` (where ```` refers to the TAB key), or use 239s ``np.*cos*?`` (where ```` refers to the ENTER key) to narrow 239s down the list. To view the docstring for a function, use 239s ``np.cos?`` (to view the docstring) and ``np.cos??`` (to view 239s the source code). 239s 239s Copies vs. in-place operation 239s ----------------------------- 239s Most of the functions in `numpy` return a copy of the array argument 239s (e.g., `np.sort`). In-place versions of these functions are often 239s available as array methods, i.e. ``x = np.array([1,2,3]); x.sort()``. 239s Exceptions to this rule are documented. 239s 239s """ 239s import sys 239s import warnings 239s 239s from ._globals import _NoValue, _CopyMode 239s # These exceptions were moved in 1.25 and are hidden from __dir__() 239s from .exceptions import ( 239s ComplexWarning, ModuleDeprecationWarning, VisibleDeprecationWarning, 239s TooHardError, AxisError) 239s 239s 239s # If a version with git hash was stored, use that instead 239s from . import version 239s from .version import __version__ 239s 239s # We first need to detect if we're being called as part of the numpy setup 239s # procedure itself in a reliable manner. 239s try: 239s __NUMPY_SETUP__ 239s except NameError: 239s __NUMPY_SETUP__ = False 239s 239s if __NUMPY_SETUP__: 239s sys.stderr.write('Running from numpy source directory.\n') 239s else: 239s # Allow distributors to run custom init code before importing numpy.core 239s from . import _distributor_init 239s 239s try: 239s > from numpy.__config__ import show as show_config 239s 239s /usr/lib/python3/dist-packages/numpy/__init__.py:130: 239s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 239s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 239s from numpy.core._multiarray_umath import ( 239s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 239s 239s """ 239s Contains the core of NumPy: ndarray, ufuncs, dtypes, etc. 239s 239s Please note that this module is private. All functions and objects 239s are available in the main ``numpy`` namespace - use that instead. 239s 239s """ 239s 239s import os 239s import warnings 239s 239s from numpy.version import version as __version__ 239s 239s 239s # disables OpenBLAS affinity setting of the main thread that limits 239s # python threads or processes to one core 239s env_added = [] 239s for envkey in ['OPENBLAS_MAIN_FREE', 'GOTOBLAS_MAIN_FREE']: 239s if envkey not in os.environ: 239s os.environ[envkey] = '1' 239s env_added.append(envkey) 239s 239s try: 239s from . import multiarray 239s except ImportError as exc: 239s import sys 239s msg = """ 239s 239s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 239s 239s Importing the numpy C-extensions failed. This error can happen for 239s many reasons, often due to issues with your setup or how NumPy was 239s installed. 239s 239s We have compiled some common reasons and troubleshooting tips at: 239s 239s https://numpy.org/devdocs/user/troubleshooting-importerror.html 239s 239s Please note and check the following: 239s 239s * The Python version is: Python%d.%d from "%s" 239s * The NumPy version is: "%s" 239s 239s and make sure that they are the versions you expect. 239s Please carefully study the documentation linked above for further help. 239s 239s Original error was: %s 239s """ % (sys.version_info[0], sys.version_info[1], sys.executable, 239s __version__, exc) 239s > raise ImportError(msg) 239s E ImportError: 239s E 239s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 239s E 239s E Importing the numpy C-extensions failed. This error can happen for 239s E many reasons, often due to issues with your setup or how NumPy was 239s E installed. 239s E 239s E We have compiled some common reasons and troubleshooting tips at: 239s E 239s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 239s E 239s E Please note and check the following: 239s E 239s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 239s E * The NumPy version is: "1.26.4" 239s E 239s E and make sure that they are the versions you expect. 239s E Please carefully study the documentation linked above for further help. 239s E 239s E Original error was: No module named 'numpy.core._multiarray_umath' 239s 239s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: ImportError 239s 239s The above exception was the direct cause of the following exception: 239s 239s remove_index = None 239s 239s def test_numpy_array(remove_index): 239s """ Test the __array_interface__ """ 239s > import numpy 239s 239s /tmp/autopkgtest.dmOVQJ/build.U0D/src/tests/test_FastaRecord.py:103: 239s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 239s 239s """ 239s NumPy 239s ===== 239s 239s Provides 239s 1. An array object of arbitrary homogeneous items 239s 2. Fast mathematical operations over arrays 239s 3. Linear Algebra, Fourier Transforms, Random Number Generation 239s 239s How to use the documentation 239s ---------------------------- 239s Documentation is available in two forms: docstrings provided 239s with the code, and a loose standing reference guide, available from 239s `the NumPy homepage `_. 239s 239s We recommend exploring the docstrings using 239s `IPython `_, an advanced Python shell with 239s TAB-completion and introspection capabilities. See below for further 239s instructions. 239s 239s The docstring examples assume that `numpy` has been imported as ``np``:: 239s 239s >>> import numpy as np 239s 239s Code snippets are indicated by three greater-than signs:: 239s 239s >>> x = 42 239s >>> x = x + 1 239s 239s Use the built-in ``help`` function to view a function's docstring:: 239s 239s >>> help(np.sort) 239s ... # doctest: +SKIP 239s 239s For some objects, ``np.info(obj)`` may provide additional help. This is 239s particularly true if you see the line "Help on ufunc object:" at the top 239s of the help() page. Ufuncs are implemented in C, not Python, for speed. 239s The native Python help() does not know how to view their help, but our 239s np.info() function does. 239s 239s To search for documents containing a keyword, do:: 239s 239s >>> np.lookfor('keyword') 239s ... # doctest: +SKIP 239s 239s General-purpose documents like a glossary and help on the basic concepts 239s of numpy are available under the ``doc`` sub-module:: 239s 239s >>> from numpy import doc 239s >>> help(doc) 239s ... # doctest: +SKIP 239s 239s Available subpackages 239s --------------------- 239s lib 239s Basic functions used by several sub-packages. 239s random 239s Core Random Tools 239s linalg 239s Core Linear Algebra Tools 239s fft 239s Core FFT routines 239s polynomial 239s Polynomial tools 239s testing 239s NumPy testing tools 239s distutils 239s Enhancements to distutils with support for 239s Fortran compilers support and more (for Python <= 3.11). 239s 239s Utilities 239s --------- 239s test 239s Run numpy unittests 239s show_config 239s Show numpy build configuration 239s matlib 239s Make everything matrices. 239s __version__ 239s NumPy version string 239s 239s Viewing documentation using IPython 239s ----------------------------------- 239s 239s Start IPython and import `numpy` usually under the alias ``np``: `import 239s numpy as np`. Then, directly past or use the ``%cpaste`` magic to paste 239s examples into the shell. To see which functions are available in `numpy`, 239s type ``np.`` (where ```` refers to the TAB key), or use 239s ``np.*cos*?`` (where ```` refers to the ENTER key) to narrow 239s down the list. To view the docstring for a function, use 239s ``np.cos?`` (to view the docstring) and ``np.cos??`` (to view 239s the source code). 239s 239s Copies vs. in-place operation 239s ----------------------------- 239s Most of the functions in `numpy` return a copy of the array argument 239s (e.g., `np.sort`). In-place versions of these functions are often 239s available as array methods, i.e. ``x = np.array([1,2,3]); x.sort()``. 239s Exceptions to this rule are documented. 239s 239s """ 239s import sys 239s import warnings 239s 239s from ._globals import _NoValue, _CopyMode 239s # These exceptions were moved in 1.25 and are hidden from __dir__() 239s from .exceptions import ( 239s ComplexWarning, ModuleDeprecationWarning, VisibleDeprecationWarning, 239s TooHardError, AxisError) 239s 239s 239s # If a version with git hash was stored, use that instead 239s from . import version 239s from .version import __version__ 239s 239s # We first need to detect if we're being called as part of the numpy setup 239s # procedure itself in a reliable manner. 239s try: 239s __NUMPY_SETUP__ 239s except NameError: 239s __NUMPY_SETUP__ = False 239s 239s if __NUMPY_SETUP__: 239s sys.stderr.write('Running from numpy source directory.\n') 239s else: 239s # Allow distributors to run custom init code before importing numpy.core 239s from . import _distributor_init 239s 239s try: 239s from numpy.__config__ import show as show_config 239s except ImportError as e: 239s msg = """Error importing numpy: you should not try to import numpy from 239s its source directory; please exit the numpy source tree, and relaunch 239s your python interpreter from there.""" 239s > raise ImportError(msg) from e 239s E ImportError: Error importing numpy: you should not try to import numpy from 239s E its source directory; please exit the numpy source tree, and relaunch 239s E your python interpreter from there. 239s 239s /usr/lib/python3/dist-packages/numpy/__init__.py:135: ImportError 239s =========================== short test summary info ============================ 239s FAILED tests/test_FastaRecord.py::test_numpy_array - ImportError: Error impor... 239s ============ 1 failed, 120 passed, 14 skipped, 1 xfailed in 16.83s ============= 239s autopkgtest [23:22:38]: test run-unit-test: -----------------------] 240s autopkgtest [23:22:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 240s run-unit-test FAIL non-zero exit status 1 240s autopkgtest [23:22:39]: test autodep8-python3: preparing testbed 365s autopkgtest [23:24:44]: testbed dpkg architecture: ppc64el 365s autopkgtest [23:24:44]: testbed apt version: 2.9.8 365s autopkgtest [23:24:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 366s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 366s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 367s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 367s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 367s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 367s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB] 367s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [692 kB] 367s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 367s Fetched 1993 kB in 1s (2112 kB/s) 367s Reading package lists... 369s Reading package lists... 370s Building dependency tree... 370s Reading state information... 370s Calculating upgrade... 370s The following NEW packages will be installed: 370s python3.13-gdbm 370s The following packages will be upgraded: 370s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 370s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 370s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 370s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 370s Need to get 4700 kB of archives. 370s After this operation, 215 kB of additional disk space will be used. 370s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 370s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 370s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 370s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 371s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 371s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 371s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 371s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 371s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 371s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 371s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 371s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 371s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 371s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 371s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 371s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 371s Fetched 4700 kB in 1s (6227 kB/s) 371s (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.) 371s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 371s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 372s Setting up python3-minimal (3.12.7-1) ... 372s (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.) 372s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 372s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 372s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 372s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 372s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 372s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 372s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 372s (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.) 372s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 372s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 372s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 372s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 372s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 372s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 372s Selecting previously unselected package python3.13-gdbm. 372s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 372s Unpacking python3.13-gdbm (3.13.0-2) ... 372s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 372s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 372s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 372s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 372s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 372s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 372s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 372s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 373s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 373s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 373s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 373s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 373s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 373s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 373s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 373s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 373s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 373s Setting up libutempter0:ppc64el (1.2.1-4) ... 373s Setting up whiptail (0.52.24-2ubuntu4) ... 373s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 373s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 373s Setting up python3.13-gdbm (3.13.0-2) ... 373s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 373s Setting up bpftrace (0.21.2-2ubuntu2) ... 373s Setting up python3 (3.12.7-1) ... 373s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 373s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 373s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 374s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 374s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 374s Processing triggers for man-db (2.12.1-3) ... 375s Processing triggers for libc-bin (2.40-1ubuntu3) ... 375s Reading package lists... 376s Building dependency tree... 376s Reading state information... 376s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 376s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 376s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 377s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 377s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 378s Reading package lists... 378s Reading package lists... 378s Building dependency tree... 378s Reading state information... 378s Calculating upgrade... 379s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 379s Reading package lists... 379s Building dependency tree... 379s Reading state information... 379s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 383s Reading package lists... 383s Building dependency tree... 383s Reading state information... 384s Starting pkgProblemResolver with broken count: 0 384s Starting 2 pkgProblemResolver with broken count: 0 384s Done 384s The following additional packages will be installed: 384s libpython3.13-minimal libpython3.13-stdlib python3-all 384s python3-importlib-metadata python3-packaging python3-pyfaidx python3.13 384s python3.13-minimal 384s Suggested packages: 384s python3.13-venv python3.13-doc binfmt-support 384s Recommended packages: 384s python3-biopython 384s The following NEW packages will be installed: 384s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 384s python3-importlib-metadata python3-packaging python3-pyfaidx python3.13 384s python3.13-minimal 385s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 385s Need to get 6143 kB/6143 kB of archives. 385s After this operation, 26.2 MB of additional disk space will be used. 385s Get:1 /tmp/autopkgtest.dmOVQJ/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 385s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 385s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 385s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 385s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 385s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 385s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-importlib-metadata all 8.5.0-1 [20.7 kB] 385s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 385s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 386s Fetched 6143 kB in 1s (5860 kB/s) 386s Selecting previously unselected package libpython3.13-minimal:ppc64el. 386s (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.) 386s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 386s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 386s Selecting previously unselected package python3.13-minimal. 386s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_ppc64el.deb ... 386s Unpacking python3.13-minimal (3.13.0-2) ... 386s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 386s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ... 386s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ... 386s Selecting previously unselected package python3.13. 386s Preparing to unpack .../3-python3.13_3.13.0-2_ppc64el.deb ... 386s Unpacking python3.13 (3.13.0-2) ... 386s Selecting previously unselected package python3-all. 386s Preparing to unpack .../4-python3-all_3.12.7-1_ppc64el.deb ... 386s Unpacking python3-all (3.12.7-1) ... 386s Selecting previously unselected package python3-importlib-metadata. 386s Preparing to unpack .../5-python3-importlib-metadata_8.5.0-1_all.deb ... 386s Unpacking python3-importlib-metadata (8.5.0-1) ... 386s Selecting previously unselected package python3-packaging. 386s Preparing to unpack .../6-python3-packaging_24.1-1_all.deb ... 386s Unpacking python3-packaging (24.1-1) ... 386s Selecting previously unselected package python3-pyfaidx. 386s Preparing to unpack .../7-python3-pyfaidx_0.8.1.3-1_all.deb ... 386s Unpacking python3-pyfaidx (0.8.1.3-1) ... 386s Selecting previously unselected package autopkgtest-satdep. 386s Preparing to unpack .../8-2-autopkgtest-satdep.deb ... 386s Unpacking autopkgtest-satdep (0) ... 386s Setting up python3-importlib-metadata (8.5.0-1) ... 387s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ... 387s Setting up python3-packaging (24.1-1) ... 387s Setting up python3.13-minimal (3.13.0-2) ... 388s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 388s Setting up python3-pyfaidx (0.8.1.3-1) ... 388s Setting up python3.13 (3.13.0-2) ... 390s Setting up python3-all (3.12.7-1) ... 390s Setting up autopkgtest-satdep (0) ... 390s Processing triggers for man-db (2.12.1-3) ... 390s Processing triggers for systemd (256.5-2ubuntu4) ... 392s (Reading database ... 74570 files and directories currently installed.) 392s Removing autopkgtest-satdep (0) ... 394s autopkgtest [23:25:13]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pyfaidx; print(pyfaidx)" ; done 394s autopkgtest [23:25:13]: test autodep8-python3: [----------------------- 394s Testing with python3.13: 394s 394s Testing with python3.12: 394s 395s autopkgtest [23:25:14]: test autodep8-python3: -----------------------] 395s autodep8-python3 PASS (superficial) 395s autopkgtest [23:25:14]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 396s autopkgtest [23:25:15]: @@@@@@@@@@@@@@@@@@@@ summary 396s run-unit-test FAIL non-zero exit status 1 396s autodep8-python3 PASS (superficial) 407s nova [W] Using flock in prodstack6-ppc64el 407s Creating nova instance adt-plucky-ppc64el-python-pyfaidx-20241113-231839-juju-7f2275-prod-proposed-migration-environment-15-1352e1f7-9e1b-462d-92fe-131848143f90 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)... 407s nova [W] Using flock in prodstack6-ppc64el 407s flock: timeout while waiting to get lock 407s Creating nova instance adt-plucky-ppc64el-python-pyfaidx-20241113-231839-juju-7f2275-prod-proposed-migration-environment-15-1352e1f7-9e1b-462d-92fe-131848143f90 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...