0s autopkgtest [16:08:53]: starting date and time: 2024-11-14 16:08:53+0000 0s autopkgtest [16:08:53]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:08:53]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a5zett0k/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-37.secgroup --name adt-plucky-arm64-htseq-20241114-160852-juju-7f2275-prod-proposed-migration-environment-20-5867e842-adb5-41c0-af91-a0bb0a732878 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 80s autopkgtest [16:10:13]: testbed dpkg architecture: arm64 80s autopkgtest [16:10:13]: testbed apt version: 2.9.8 80s autopkgtest [16:10:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 81s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 81s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB] 81s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 81s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 81s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [138 kB] 81s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 81s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [724 kB] 81s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6012 B] 82s Fetched 2085 kB in 1s (2274 kB/s) 82s Reading package lists... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 85s Calculating upgrade... 85s The following packages will be upgraded: 85s pastebinit python3-systemd 86s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 61.6 kB of archives. 86s After this operation, 347 kB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 86s Fetched 61.6 kB in 0s (176 kB/s) 86s (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 ... 79925 files and directories currently installed.) 86s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 86s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 87s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 87s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 87s Setting up pastebinit (1.7.1-1) ... 87s Setting up python3-systemd (235-1build5) ... 87s Processing triggers for man-db (2.12.1-3) ... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 89s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 89s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 89s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 90s Reading package lists... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s Calculating upgrade... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s autopkgtest [16:10:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 96s autopkgtest [16:10:29]: @@@@@@@@@@@@@@@@@@@@ apt-source htseq 100s Get:1 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (dsc) [2158 B] 100s Get:2 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (tar) [36.8 MB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (diff) [11.2 kB] 100s gpgv: Signature made Fri Jun 14 16:08:34 2024 UTC 100s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 100s gpgv: issuer "tchet@debian.org" 100s gpgv: Can't check signature: No public key 100s dpkg-source: warning: cannot verify inline signature for ./htseq_2.0.5-2.dsc: no acceptable signature found 101s autopkgtest [16:10:34]: testing package htseq version 2.0.5-2 102s autopkgtest [16:10:35]: build not needed 106s autopkgtest [16:10:39]: test autodep8-python3: preparing testbed 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Starting pkgProblemResolver with broken count: 0 114s Starting 2 pkgProblemResolver with broken count: 0 114s Done 115s The following additional packages will be installed: 115s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 115s python3-all python3-htseq python3-numpy python3-pysam 115s Suggested packages: 115s gcc gfortran python-numpy-doc python3-dev python3-pytest 115s The following NEW packages will be installed: 115s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 115s libhtscodecs2 liblapack3 python3-all python3-htseq python3-numpy 115s python3-pysam 115s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 11.3 MB/11.3 MB of archives. 115s After this operation, 72.8 MB of additional disk space will be used. 115s Get:1 /tmp/autopkgtest.57Hvp3/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 116s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 116s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-htseq arm64 2.0.5-2 [303 kB] 117s Fetched 11.3 MB in 1s (10.4 MB/s) 117s Selecting previously unselected package libblas3:arm64. 117s (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 ... 79930 files and directories currently installed.) 117s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 117s Unpacking libblas3:arm64 (3.12.0-3build2) ... 117s Selecting previously unselected package libdeflate0:arm64. 117s Preparing to unpack .../01-libdeflate0_1.22-1_arm64.deb ... 117s Unpacking libdeflate0:arm64 (1.22-1) ... 117s Selecting previously unselected package libgfortran5:arm64. 117s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 117s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libhtscodecs2:arm64. 117s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_arm64.deb ... 117s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 117s Selecting previously unselected package libhts3t64:arm64. 117s Preparing to unpack .../04-libhts3t64_1.20+ds-1_arm64.deb ... 117s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 117s Selecting previously unselected package liblapack3:arm64. 117s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 117s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 117s Selecting previously unselected package python3-all. 117s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_arm64.deb ... 117s Unpacking python3-all (3.12.6-0ubuntu1) ... 117s Selecting previously unselected package python3-numpy. 117s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 117s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 117s Selecting previously unselected package python3-pysam. 117s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_arm64.deb ... 117s Unpacking python3-pysam (0.22.1+ds-2) ... 117s Selecting previously unselected package python3-htseq. 117s Preparing to unpack .../09-python3-htseq_2.0.5-2_arm64.deb ... 117s Unpacking python3-htseq (2.0.5-2) ... 117s Selecting previously unselected package autopkgtest-satdep. 117s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 117s Unpacking autopkgtest-satdep (0) ... 117s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 117s Setting up libdeflate0:arm64 (1.22-1) ... 117s Setting up python3-all (3.12.6-0ubuntu1) ... 117s Setting up libblas3:arm64 (3.12.0-3build2) ... 117s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 117s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 117s Setting up libhts3t64:arm64 (1.20+ds-1) ... 117s Setting up liblapack3:arm64 (3.12.0-3build2) ... 117s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 117s Setting up python3-pysam (0.22.1+ds-2) ... 118s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 120s Setting up python3-htseq (2.0.5-2) ... 120s /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\=' 120s _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$") 120s /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s' 120s _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)") 120s /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s' 120s _re_attr_empty = re.compile("^\s*$") 120s /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s' 120s _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)") 120s Setting up autopkgtest-satdep (0) ... 120s Processing triggers for man-db (2.12.1-3) ... 120s Processing triggers for libc-bin (2.40-1ubuntu3) ... 123s (Reading database ... 81271 files and directories currently installed.) 123s Removing autopkgtest-satdep (0) ... 124s autopkgtest [16:10:57]: 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 124s autopkgtest [16:10:57]: test autodep8-python3: [----------------------- 124s Testing with python3.12: 125s 125s autopkgtest [16:10:58]: test autodep8-python3: -----------------------] 125s autopkgtest [16:10:58]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 125s autodep8-python3 PASS (superficial) 126s autopkgtest [16:10:59]: @@@@@@@@@@@@@@@@@@@@ summary 126s autodep8-python3 PASS (superficial) 138s nova [W] Skipping flock in bos03-arm64 138s Creating nova instance adt-plucky-arm64-htseq-20241114-160852-juju-7f2275-prod-proposed-migration-environment-20-5867e842-adb5-41c0-af91-a0bb0a732878 from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...