0s autopkgtest [02:50:13]: starting date and time: 2024-11-15 02:50:13+0000 0s autopkgtest [02:50:13]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [02:50:13]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vdrr3heu/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-28.secgroup --name adt-plucky-amd64-htseq-20241115-025013-juju-7f2275-prod-proposed-migration-environment-15-fd9bfde0-327d-4df3-9870-76b634c286b9 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/ 46s autopkgtest [02:50:59]: testbed dpkg architecture: amd64 46s autopkgtest [02:50:59]: testbed apt version: 2.9.8 46s autopkgtest [02:50:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 47s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 47s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 47s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 47s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [166 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [101 kB] 47s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [293 kB] 47s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [800 kB] 47s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 47s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B] 48s Fetched 2630 kB in 1s (3178 kB/s) 48s Reading package lists... 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s Calculating upgrade... 51s The following packages will be upgraded: 51s firmware-sof-signed libcap-ng0 libexpat1 lxd-installer man-db pastebinit 51s python3-systemd xfsprogs 51s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 9537 kB of archives. 51s After this operation, 441 kB of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 52s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 52s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 52s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 52s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 52s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 52s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 52s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 52s Preconfiguring packages ... 52s Fetched 9537 kB in 1s (10.0 MB/s) 52s (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 ... 75542 files and directories currently installed.) 52s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 52s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 52s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 52s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 52s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 53s (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 ... 75568 files and directories currently installed.) 53s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 53s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 53s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 53s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 53s Preparing to unpack .../2-lxd-installer_9_all.deb ... 53s Unpacking lxd-installer (9) over (8) ... 53s Preparing to unpack .../3-pastebinit_1.7.1-1_all.deb ... 53s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 53s Preparing to unpack .../4-python3-systemd_235-1build5_amd64.deb ... 53s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 53s Preparing to unpack .../5-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 53s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 53s Setting up libexpat1:amd64 (2.6.4-1) ... 53s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 53s Setting up pastebinit (1.7.1-1) ... 53s Setting up man-db (2.13.0-1) ... 53s Updating database of manual pages ... 55s man-db.service is a disabled or a static unit not running, not starting it. 55s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 55s update-initramfs: deferring update (trigger activated) 55s Setting up lxd-installer (9) ... 56s Setting up python3-systemd (235-1build5) ... 56s Processing triggers for libc-bin (2.40-1ubuntu3) ... 56s Processing triggers for initramfs-tools (0.142ubuntu34) ... 56s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 56s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 65s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 66s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s autopkgtest [02:51:20]: rebooting testbed after setup commands that affected boot 84s autopkgtest [02:51:37]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 87s autopkgtest [02:51:40]: @@@@@@@@@@@@@@@@@@@@ apt-source htseq 90s Get:1 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (dsc) [2158 B] 90s Get:2 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (tar) [36.8 MB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky/universe htseq 2.0.5-2 (diff) [11.2 kB] 91s gpgv: Signature made Fri Jun 14 16:08:34 2024 UTC 91s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 91s gpgv: issuer "tchet@debian.org" 91s gpgv: Can't check signature: No public key 91s dpkg-source: warning: cannot verify inline signature for ./htseq_2.0.5-2.dsc: no acceptable signature found 91s autopkgtest [02:51:44]: testing package htseq version 2.0.5-2 93s autopkgtest [02:51:46]: build not needed 99s autopkgtest [02:51:52]: test autodep8-python3: preparing testbed 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Starting pkgProblemResolver with broken count: 0 102s Starting 2 pkgProblemResolver with broken count: 0 102s Done 102s The following additional packages will be installed: 102s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 102s python3-all python3-htseq python3-numpy python3-pysam 102s Suggested packages: 102s gcc gfortran python-numpy-doc python3-dev python3-pytest 102s The following NEW packages will be installed: 102s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 102s libhtscodecs2 liblapack3 python3-all python3-htseq python3-numpy 102s python3-pysam 102s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 13.6 MB/13.6 MB of archives. 102s After this operation, 88.1 MB of additional disk space will be used. 102s Get:1 /tmp/autopkgtest.h5D00e/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 103s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 103s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-htseq amd64 2.0.5-2 [319 kB] 104s Fetched 13.6 MB in 1s (10.1 MB/s) 104s Selecting previously unselected package libblas3:amd64. 104s (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 ... 75574 files and directories currently installed.) 104s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 104s Unpacking libblas3:amd64 (3.12.0-3build2) ... 104s Selecting previously unselected package libdeflate0:amd64. 104s Preparing to unpack .../01-libdeflate0_1.22-1_amd64.deb ... 104s Unpacking libdeflate0:amd64 (1.22-1) ... 104s Selecting previously unselected package libgfortran5:amd64. 104s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 104s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 104s Selecting previously unselected package libhtscodecs2:amd64. 104s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_amd64.deb ... 104s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 104s Selecting previously unselected package libhts3t64:amd64. 104s Preparing to unpack .../04-libhts3t64_1.20+ds-1_amd64.deb ... 104s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 104s Selecting previously unselected package liblapack3:amd64. 104s Preparing to unpack .../05-liblapack3_3.12.0-3build2_amd64.deb ... 104s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 104s Selecting previously unselected package python3-all. 104s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_amd64.deb ... 104s Unpacking python3-all (3.12.6-0ubuntu1) ... 104s Selecting previously unselected package python3-numpy. 104s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 104s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 104s Selecting previously unselected package python3-pysam. 104s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_amd64.deb ... 104s Unpacking python3-pysam (0.22.1+ds-2) ... 104s Selecting previously unselected package python3-htseq. 104s Preparing to unpack .../09-python3-htseq_2.0.5-2_amd64.deb ... 104s Unpacking python3-htseq (2.0.5-2) ... 105s Selecting previously unselected package autopkgtest-satdep. 105s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 105s Unpacking autopkgtest-satdep (0) ... 105s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 105s Setting up libdeflate0:amd64 (1.22-1) ... 105s Setting up python3-all (3.12.6-0ubuntu1) ... 105s Setting up libblas3:amd64 (3.12.0-3build2) ... 105s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 105s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 105s Setting up libhts3t64:amd64 (1.20+ds-1) ... 105s Setting up liblapack3:amd64 (3.12.0-3build2) ... 105s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 105s Setting up python3-pysam (0.22.1+ds-2) ... 105s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 106s Setting up python3-htseq (2.0.5-2) ... 106s /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\=' 106s _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$") 106s /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s' 106s _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)") 106s /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s' 106s _re_attr_empty = re.compile("^\s*$") 106s /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s' 106s _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)") 106s Setting up autopkgtest-satdep (0) ... 106s Processing triggers for man-db (2.13.0-1) ... 107s Processing triggers for libc-bin (2.40-1ubuntu3) ... 109s (Reading database ... 76915 files and directories currently installed.) 109s Removing autopkgtest-satdep (0) ... 110s autopkgtest [02:52:03]: 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 110s autopkgtest [02:52:03]: test autodep8-python3: [----------------------- 110s Testing with python3.12: 110s 110s autopkgtest [02:52:03]: test autodep8-python3: -----------------------] 111s autopkgtest [02:52:04]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 111s autodep8-python3 PASS (superficial) 111s autopkgtest [02:52:04]: @@@@@@@@@@@@@@@@@@@@ summary 111s autodep8-python3 PASS (superficial) 124s nova [W] Skipping flock for amd64 124s Creating nova instance adt-plucky-amd64-htseq-20241115-025013-juju-7f2275-prod-proposed-migration-environment-15-fd9bfde0-327d-4df3-9870-76b634c286b9 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...