0s autopkgtest [18:42:44]: starting date and time: 2024-11-14 18:42:44+0000 0s autopkgtest [18:42:44]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:42:44]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4o5d3ieh/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:numpy --apt-upgrade htseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- lxd -r lxd-armhf-10.145.243.229 lxd-armhf-10.145.243.229:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [18:43:37]: testbed dpkg architecture: armhf 55s autopkgtest [18:43:39]: testbed apt version: 2.9.8 55s autopkgtest [18:43:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.0 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [103 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [933 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [105 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [663 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3564 B] 64s Fetched 1903 kB in 1s (2005 kB/s) 64s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 109s The following packages will be upgraded: 109s libcap-ng0 pastebinit python3-systemd 109s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 72.8 kB of archives. 109s After this operation, 89.1 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-3build1 [13.8 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 110s Fetched 72.8 kB in 0s (173 kB/s) 110s (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 ... 59560 files and directories currently installed.) 110s Preparing to unpack .../libcap-ng0_0.8.5-3build1_armhf.deb ... 110s Unpacking libcap-ng0:armhf (0.8.5-3build1) over (0.8.5-1) ... 110s Setting up libcap-ng0:armhf (0.8.5-3build1) ... 110s (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 ... 59560 files and directories currently installed.) 110s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 110s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 110s Preparing to unpack .../python3-systemd_235-1build5_armhf.deb ... 110s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 110s Setting up pastebinit (1.7.1-1) ... 110s Setting up python3-systemd (235-1build5) ... 111s Processing triggers for man-db (2.12.1-3) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [18:44:41]: rebooting testbed after setup commands that affected boot 189s autopkgtest [18:45:53]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 217s autopkgtest [18:46:21]: @@@@@@@@@@@@@@@@@@@@ apt-source htseq 229s Get:1 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (dsc) [2158 B] 229s Get:2 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (tar) [36.8 MB] 229s Get:3 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (diff) [11.2 kB] 229s gpgv: Signature made Fri Jun 14 16:08:34 2024 UTC 229s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 229s gpgv: issuer "tchet@debian.org" 229s gpgv: Can't check signature: No public key 229s dpkg-source: warning: cannot verify inline signature for ./htseq_2.0.5-2.dsc: no acceptable signature found 230s autopkgtest [18:46:34]: testing package htseq version 2.0.5-2 233s autopkgtest [18:46:37]: build not needed 238s autopkgtest [18:46:42]: test autodep8-python3: preparing testbed 248s Reading package lists... 248s Building dependency tree... 248s Reading state information... 249s Starting pkgProblemResolver with broken count: 0 249s Starting 2 pkgProblemResolver with broken count: 0 249s Done 251s The following additional packages will be installed: 251s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 251s python3-all python3-htseq python3-numpy python3-pysam 251s Suggested packages: 251s gcc gfortran python-numpy-doc python3-dev python3-pytest 251s The following NEW packages will be installed: 251s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 251s libhtscodecs2 liblapack3 python3-all python3-htseq python3-numpy 251s python3-pysam 251s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 251s Need to get 10.7 MB/10.7 MB of archives. 251s After this operation, 61.8 MB of additional disk space will be used. 251s Get:1 /tmp/autopkgtest.ZpJQgy/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 252s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 252s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 252s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 252s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 252s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 252s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 252s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 252s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 252s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-htseq armhf 2.0.5-2 [299 kB] 253s Fetched 10.7 MB in 1s (10.2 MB/s) 253s Selecting previously unselected package libblas3:armhf. 253s (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 ... 59565 files and directories currently installed.) 253s Preparing to unpack .../00-libblas3_3.12.0-3build2_armhf.deb ... 253s Unpacking libblas3:armhf (3.12.0-3build2) ... 253s Selecting previously unselected package libdeflate0:armhf. 253s Preparing to unpack .../01-libdeflate0_1.22-1_armhf.deb ... 253s Unpacking libdeflate0:armhf (1.22-1) ... 253s Selecting previously unselected package libgfortran5:armhf. 253s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 253s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 253s Selecting previously unselected package libhtscodecs2:armhf. 253s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_armhf.deb ... 253s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 253s Selecting previously unselected package libhts3t64:armhf. 253s Preparing to unpack .../04-libhts3t64_1.20+ds-1_armhf.deb ... 253s Unpacking libhts3t64:armhf (1.20+ds-1) ... 253s Selecting previously unselected package liblapack3:armhf. 253s Preparing to unpack .../05-liblapack3_3.12.0-3build2_armhf.deb ... 253s Unpacking liblapack3:armhf (3.12.0-3build2) ... 253s Selecting previously unselected package python3-all. 253s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_armhf.deb ... 253s Unpacking python3-all (3.12.6-0ubuntu1) ... 253s Selecting previously unselected package python3-numpy. 254s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 254s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 254s Selecting previously unselected package python3-pysam. 254s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_armhf.deb ... 254s Unpacking python3-pysam (0.22.1+ds-2) ... 254s Selecting previously unselected package python3-htseq. 254s Preparing to unpack .../09-python3-htseq_2.0.5-2_armhf.deb ... 254s Unpacking python3-htseq (2.0.5-2) ... 254s Selecting previously unselected package autopkgtest-satdep. 254s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 254s Unpacking autopkgtest-satdep (0) ... 254s Setting up libhtscodecs2:armhf (1.6.1-1) ... 254s Setting up libdeflate0:armhf (1.22-1) ... 254s Setting up python3-all (3.12.6-0ubuntu1) ... 254s Setting up libblas3:armhf (3.12.0-3build2) ... 254s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 254s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 254s Setting up libhts3t64:armhf (1.20+ds-1) ... 254s Setting up liblapack3:armhf (3.12.0-3build2) ... 254s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 254s Setting up python3-pysam (0.22.1+ds-2) ... 255s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 258s Setting up python3-htseq (2.0.5-2) ... 258s /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\=' 258s _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$") 258s /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s' 258s _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)") 258s /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s' 258s _re_attr_empty = re.compile("^\s*$") 258s /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s' 258s _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)") 258s Setting up autopkgtest-satdep (0) ... 258s Processing triggers for man-db (2.12.1-3) ... 259s Processing triggers for libc-bin (2.40-1ubuntu3) ... 273s (Reading database ... 60907 files and directories currently installed.) 273s Removing autopkgtest-satdep (0) ... 279s autopkgtest [18:47:23]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import HTSeq; print(HTSeq)" ; done 279s autopkgtest [18:47:23]: test autodep8-python3: [----------------------- 281s Testing with python3.12: 281s 282s autopkgtest [18:47:26]: test autodep8-python3: -----------------------] 285s autopkgtest [18:47:29]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 285s autodep8-python3 PASS (superficial) 289s autopkgtest [18:47:33]: @@@@@@@@@@@@@@@@@@@@ summary 289s autodep8-python3 PASS (superficial)