0s autopkgtest [03:10:28]: starting date and time: 2024-03-24 03:10:28+0000 0s autopkgtest [03:10:28]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:10:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u93ub9pl/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade python-pybedtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-2.secgroup --name adt-noble-arm64-python-pybedtools-20240324-025130-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 68s autopkgtest [03:11:36]: testbed dpkg architecture: arm64 68s autopkgtest [03:11:36]: testbed apt version: 2.7.12 68s autopkgtest [03:11:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 69s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 69s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 69s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 69s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 69s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [707 kB] 69s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 69s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 69s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 69s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 69s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 69s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 69s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 71s Fetched 9845 kB in 2s (5723 kB/s) 71s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s sh: Attempting to set up Debian/Ubuntu apt sources automatically 76s sh: Distribution appears to be Ubuntu 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s eatmydata is already the newest version (131-1). 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s dbus is already the newest version (1.14.10-4ubuntu1). 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s rng-tools-debian is already the newest version (2.4). 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s The following packages will be REMOVED: 80s cloud-init* python3-configobj* python3-debconf* 80s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 80s After this operation, 3256 kB disk space will be freed. 81s (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 ... 74819 files and directories currently installed.) 81s Removing cloud-init (24.1.2-0ubuntu1) ... 81s Removing python3-configobj (5.0.8-3) ... 81s Removing python3-debconf (1.5.86) ... 81s Processing triggers for man-db (2.12.0-3) ... 82s (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 ... 74430 files and directories currently installed.) 82s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 83s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 83s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 83s invoke-rc.d: policy-rc.d denied execution of try-restart. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 84s linux-generic is already the newest version (6.8.0-11.11+1). 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 84s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 84s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 86s Reading package lists... 86s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s autopkgtest [03:11:56]: rebooting testbed after setup commands that affected boot 116s autopkgtest [03:12:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 118s autopkgtest [03:12:26]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pybedtools 123s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-pybedtools 0.9.1-1 (dsc) [2520 B] 123s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-pybedtools 0.9.1-1 (tar) [12.0 MB] 123s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-pybedtools 0.9.1-1 (diff) [29.9 kB] 123s gpgv: Signature made Wed Nov 1 06:51:36 2023 UTC 123s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 123s gpgv: issuer "tille@debian.org" 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.9.1-1.dsc: no acceptable signature found 123s autopkgtest [03:12:31]: testing package python-pybedtools version 0.9.1-1 124s autopkgtest [03:12:32]: build not needed 125s autopkgtest [03:12:33]: test autodep8-python3: preparing testbed 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 138s The following additional packages will be installed: 138s libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 liblapack3 138s libpython3.11-minimal libpython3.11-stdlib python3-all python3-distutils 138s python3-lib2to3 python3-numpy python3-pybedtools python3-pysam python3.11 138s python3.11-minimal 138s Suggested packages: 138s gcc gfortran python3-dev python3-pytest python-pybedtools-doc 138s python3.11-venv python3.11-doc binfmt-support 139s The following NEW packages will be installed: 139s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 139s liblapack3 libpython3.11-minimal libpython3.11-stdlib python3-all 139s python3-distutils python3-lib2to3 python3-numpy python3-pybedtools 139s python3-pysam python3.11 python3.11-minimal 139s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 30.3 MB/30.3 MB of archives. 139s After this operation, 119 MB of additional disk space will be used. 139s Get:1 /tmp/autopkgtest.Zew2on/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 139s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 139s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 140s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 140s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 140s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 140s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 140s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 140s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 140s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 140s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 140s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 140s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 140s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 140s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 140s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybedtools arm64 0.9.1-1 [12.3 MB] 141s Fetched 30.3 MB in 2s (14.6 MB/s) 141s Selecting previously unselected package libpython3.11-minimal:arm64. 141s (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 ... 74375 files and directories currently installed.) 142s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 142s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 142s Selecting previously unselected package python3.11-minimal. 142s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 142s Unpacking python3.11-minimal (3.11.8-1) ... 142s Selecting previously unselected package libpython3.11-stdlib:arm64. 142s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 142s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 142s Selecting previously unselected package python3.11. 142s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ... 142s Unpacking python3.11 (3.11.8-1) ... 142s Selecting previously unselected package libblas3:arm64. 142s Preparing to unpack .../04-libblas3_3.12.0-3_arm64.deb ... 142s Unpacking libblas3:arm64 (3.12.0-3) ... 142s Selecting previously unselected package libdeflate0:arm64. 142s Preparing to unpack .../05-libdeflate0_1.19-1_arm64.deb ... 142s Unpacking libdeflate0:arm64 (1.19-1) ... 142s Selecting previously unselected package libgfortran5:arm64. 142s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 142s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 142s Selecting previously unselected package libhtscodecs2:arm64. 142s Preparing to unpack .../07-libhtscodecs2_1.6.0-1_arm64.deb ... 142s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 142s Selecting previously unselected package libhts3:arm64. 142s Preparing to unpack .../08-libhts3_1.18+ds-1_arm64.deb ... 142s Unpacking libhts3:arm64 (1.18+ds-1) ... 142s Selecting previously unselected package liblapack3:arm64. 142s Preparing to unpack .../09-liblapack3_3.12.0-3_arm64.deb ... 142s Unpacking liblapack3:arm64 (3.12.0-3) ... 142s Selecting previously unselected package python3-lib2to3. 142s Preparing to unpack .../10-python3-lib2to3_3.11.5-1_all.deb ... 142s Unpacking python3-lib2to3 (3.11.5-1) ... 142s Selecting previously unselected package python3-distutils. 142s Preparing to unpack .../11-python3-distutils_3.11.5-1_all.deb ... 142s Unpacking python3-distutils (3.11.5-1) ... 142s Selecting previously unselected package python3-all. 142s Preparing to unpack .../12-python3-all_3.12.1-0ubuntu2_arm64.deb ... 142s Unpacking python3-all (3.12.1-0ubuntu2) ... 142s Selecting previously unselected package python3-numpy. 142s Preparing to unpack .../13-python3-numpy_1%3a1.24.2-2_arm64.deb ... 142s Unpacking python3-numpy (1:1.24.2-2) ... 142s Selecting previously unselected package python3-pysam. 142s Preparing to unpack .../14-python3-pysam_0.22.0+ds-1_arm64.deb ... 142s Unpacking python3-pysam (0.22.0+ds-1) ... 143s Selecting previously unselected package python3-pybedtools. 143s Preparing to unpack .../15-python3-pybedtools_0.9.1-1_arm64.deb ... 143s Unpacking python3-pybedtools (0.9.1-1) ... 143s Selecting previously unselected package autopkgtest-satdep. 143s Preparing to unpack .../16-1-autopkgtest-satdep.deb ... 143s Unpacking autopkgtest-satdep (0) ... 143s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 143s Setting up libdeflate0:arm64 (1.19-1) ... 143s Setting up libblas3:arm64 (3.12.0-3) ... 143s 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 143s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 143s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 143s Setting up python3-lib2to3 (3.11.5-1) ... 143s Setting up python3-distutils (3.11.5-1) ... 143s python3.12: can't get files for byte-compilation 143s Setting up python3.11-minimal (3.11.8-1) ... 144s Setting up liblapack3:arm64 (3.12.0-3) ... 144s 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 144s Setting up libhts3:arm64 (1.18+ds-1) ... 144s Setting up python3-pysam (0.22.0+ds-1) ... 144s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 144s Setting up python3-all (3.12.1-0ubuntu2) ... 144s Setting up python3.11 (3.11.8-1) ... 145s Setting up python3-numpy (1:1.24.2-2) ... 146s Setting up python3-pybedtools (0.9.1-1) ... 147s Setting up autopkgtest-satdep (0) ... 147s Processing triggers for systemd (255.2-3ubuntu2) ... 147s Processing triggers for man-db (2.12.0-3) ... 147s Processing triggers for libc-bin (2.39-0ubuntu6) ... 150s (Reading database ... 76852 files and directories currently installed.) 150s Removing autopkgtest-satdep (0) ... 151s autopkgtest [03:12:59]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pybedtools; print(pybedtools)" ; done 151s autopkgtest [03:12:59]: test autodep8-python3: [----------------------- 151s Testing with python3.12: 152s 152s autopkgtest [03:13:00]: test autodep8-python3: -----------------------] 153s autopkgtest [03:13:01]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 153s autodep8-python3 PASS (superficial) 153s autopkgtest [03:13:01]: @@@@@@@@@@@@@@@@@@@@ summary 153s autodep8-python3 PASS (superficial) 158s Creating nova instance adt-noble-arm64-python-pybedtools-20240324-025130-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240323.img (UUID 375bc181-4f1c-404a-9515-ae86628c71e3)...