0s autopkgtest [12:33:33]: starting date and time: 2025-11-01 12:33:33+0000 0s autopkgtest [12:33:33]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:33:33]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.em1c0l0s/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scipy --apt-upgrade r-bioc-mofa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scipy/1.16.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-14.secgroup --name adt-resolute-arm64-r-bioc-mofa-20251101-123333-juju-7f2275-prod-proposed-migration-environment-15-ce65e042-ffed-4353-8e9d-1b374700dbc7 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-r-bioc-mofa-20251101-123333-juju-7f2275-prod-proposed-migration-environment-15-ce65e042-ffed-4353-8e9d-1b374700dbc7 from image adt/ubuntu-resolute-arm64-server-20251101.img (UUID 895f8d05-65a0-4cf8-81a2-1a04d79b538c)... 53s autopkgtest [12:34:26]: testbed dpkg architecture: arm64 54s autopkgtest [12:34:27]: testbed apt version: 3.1.11 54s autopkgtest [12:34:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [12:34:27]: testbed release detected to be: None 55s autopkgtest [12:34:28]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [49.4 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2242 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 57s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [206 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [4948 B] 57s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [107 kB] 57s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B] 57s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1619 kB] 57s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [48.3 kB] 57s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [34.8 kB] 57s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [1700 B] 58s Fetched 4550 kB in 2s (2241 kB/s) 59s Reading package lists... 59s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 61s Reading package lists... 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 61s The following packages will be upgraded: 61s gcc-15-base libatomic1 libgcc-s1 libstdc++6 publicsuffix 62s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 1027 kB of archives. 62s After this operation, 14.3 kB of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libatomic1 arm64 15.2.0-7ubuntu1 [11.2 kB] 62s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++6 arm64 15.2.0-7ubuntu1 [760 kB] 62s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-base arm64 15.2.0-7ubuntu1 [58.4 kB] 62s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-s1 arm64 15.2.0-7ubuntu1 [61.1 kB] 62s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 publicsuffix all 20251016.1743-0.1 [136 kB] 63s dpkg-preconfigure: unable to re-open stdin: No such file or directory 63s Fetched 1027 kB in 1s (1486 kB/s) 63s (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 ... 83460 files and directories currently installed.) 63s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_arm64.deb ... 63s Unpacking libatomic1:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 63s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_arm64.deb ... 63s Unpacking libstdc++6:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 63s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_arm64.deb ... 63s Unpacking gcc-15-base:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 63s Setting up gcc-15-base:arm64 (15.2.0-7ubuntu1) ... 63s (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 ... 83460 files and directories currently installed.) 63s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_arm64.deb ... 63s Unpacking libgcc-s1:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 63s Setting up libgcc-s1:arm64 (15.2.0-7ubuntu1) ... 63s (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 ... 83460 files and directories currently installed.) 63s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 63s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 64s Setting up libatomic1:arm64 (15.2.0-7ubuntu1) ... 64s Setting up publicsuffix (20251016.1743-0.1) ... 64s Setting up libstdc++6:arm64 (15.2.0-7ubuntu1) ... 64s Processing triggers for libc-bin (2.42-0ubuntu3) ... 64s autopkgtest [12:34:37]: upgrading testbed (apt dist-upgrade and autopurge) 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Calculating upgrade... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Solving dependencies... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [12:34:41]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 69s autopkgtest [12:34:42]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa 71s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-15 (dsc) [2553 B] 71s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-15 (tar) [915 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-15 (diff) [4332 B] 71s gpgv: Signature made Mon Jan 13 14:15:48 2025 UTC 71s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 71s gpgv: issuer "crusoe@debian.org" 71s gpgv: Can't check signature: No public key 71s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-15.dsc: no acceptable signature found 71s autopkgtest [12:34:44]: testing package r-bioc-mofa version 1.6.1+dfsg-15 72s autopkgtest [12:34:45]: build not needed 72s autopkgtest [12:34:45]: test autodep8-python3: preparing testbed 72s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Solving dependencies... 73s The following NEW packages will be installed: 73s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 liblzf1 73s libqhull-r8.0 libsz2 python3-all python3-dateutil python3-decorator 73s python3-h5py python3-h5py-serial python3-mofapy python3-numpy 73s python3-numpy-dev python3-pandas python3-pandas-lib python3-pytz 73s python3-scipy 73s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 73s Need to get 37.4 MB of archives. 73s After this operation, 207 MB of additional disk space will be used. 73s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 74s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 74s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-7ubuntu1 [450 kB] 74s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 75s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 75s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 libaec0 arm64 1.1.4-2 [22.2 kB] 75s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.4-2 [5258 B] 75s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.5+repack-3build1 [1331 kB] 75s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3build1 [59.8 kB] 75s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 75s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 75s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.7-1 [884 B] 75s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 75s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 75s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py-serial arm64 3.13.0-1ubuntu1 [1123 kB] 76s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py all 3.13.0-1ubuntu1 [8230 B] 76s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-4 [32.3 kB] 76s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-1ubuntu1 [6979 kB] 76s Get:19 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 76s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-scipy arm64 1.16.3-1 [17.4 MB] 77s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mofapy all 1.6.1+dfsg-15 [34.9 kB] 77s Fetched 37.4 MB in 4s (9854 kB/s) 77s Selecting previously unselected package python3-numpy-dev:arm64. 77s (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 ... 83460 files and directories currently installed.) 77s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 77s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 77s Selecting previously unselected package libblas3:arm64. 77s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 77s Unpacking libblas3:arm64 (3.12.1-6build1) ... 77s Selecting previously unselected package libgfortran5:arm64. 78s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_arm64.deb ... 78s Unpacking libgfortran5:arm64 (15.2.0-7ubuntu1) ... 78s Selecting previously unselected package liblapack3:arm64. 78s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 78s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 78s Selecting previously unselected package python3-numpy. 78s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 78s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 78s Selecting previously unselected package libaec0:arm64. 78s Preparing to unpack .../05-libaec0_1.1.4-2_arm64.deb ... 78s Unpacking libaec0:arm64 (1.1.4-2) ... 78s Selecting previously unselected package libsz2:arm64. 78s Preparing to unpack .../06-libsz2_1.1.4-2_arm64.deb ... 78s Unpacking libsz2:arm64 (1.1.4-2) ... 78s Selecting previously unselected package libhdf5-310:arm64. 78s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3build1_arm64.deb ... 78s Unpacking libhdf5-310:arm64 (1.14.5+repack-3build1) ... 78s Selecting previously unselected package libhdf5-hl-310:arm64. 78s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3build1_arm64.deb ... 78s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3build1) ... 78s Selecting previously unselected package liblzf1:arm64. 78s Preparing to unpack .../09-liblzf1_3.6-4_arm64.deb ... 78s Unpacking liblzf1:arm64 (3.6-4) ... 78s Selecting previously unselected package libqhull-r8.0:arm64. 78s Preparing to unpack .../10-libqhull-r8.0_2020.2-6build1_arm64.deb ... 78s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 78s Selecting previously unselected package python3-all. 78s Preparing to unpack .../11-python3-all_3.13.7-1_arm64.deb ... 78s Unpacking python3-all (3.13.7-1) ... 78s Selecting previously unselected package python3-dateutil. 78s Preparing to unpack .../12-python3-dateutil_2.9.0-4_all.deb ... 78s Unpacking python3-dateutil (2.9.0-4) ... 78s Selecting previously unselected package python3-decorator. 78s Preparing to unpack .../13-python3-decorator_5.2.1-2_all.deb ... 78s Unpacking python3-decorator (5.2.1-2) ... 78s Selecting previously unselected package python3-h5py-serial. 78s Preparing to unpack .../14-python3-h5py-serial_3.13.0-1ubuntu1_arm64.deb ... 78s Unpacking python3-h5py-serial (3.13.0-1ubuntu1) ... 78s Selecting previously unselected package python3-h5py. 78s Preparing to unpack .../15-python3-h5py_3.13.0-1ubuntu1_all.deb ... 78s Unpacking python3-h5py (3.13.0-1ubuntu1) ... 78s Selecting previously unselected package python3-pytz. 78s Preparing to unpack .../16-python3-pytz_2025.2-4_all.deb ... 78s Unpacking python3-pytz (2025.2-4) ... 78s Selecting previously unselected package python3-pandas-lib:arm64. 78s Preparing to unpack .../17-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_arm64.deb ... 78s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 78s Selecting previously unselected package python3-pandas. 78s Preparing to unpack .../18-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 78s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 79s Selecting previously unselected package python3-scipy. 79s Preparing to unpack .../19-python3-scipy_1.16.3-1_arm64.deb ... 79s Unpacking python3-scipy (1.16.3-1) ... 79s Selecting previously unselected package python3-mofapy. 79s Preparing to unpack .../20-python3-mofapy_1.6.1+dfsg-15_all.deb ... 79s Unpacking python3-mofapy (1.6.1+dfsg-15) ... 79s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 79s Setting up python3-all (3.13.7-1) ... 79s Setting up python3-pytz (2025.2-4) ... 79s Setting up libaec0:arm64 (1.1.4-2) ... 79s Setting up python3-decorator (5.2.1-2) ... 79s Setting up libblas3:arm64 (3.12.1-6build1) ... 79s 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 79s Setting up liblzf1:arm64 (3.6-4) ... 79s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 79s Setting up libgfortran5:arm64 (15.2.0-7ubuntu1) ... 79s Setting up python3-dateutil (2.9.0-4) ... 80s Setting up libsz2:arm64 (1.1.4-2) ... 80s Setting up liblapack3:arm64 (3.12.1-6build1) ... 80s 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 80s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 81s Setting up libhdf5-310:arm64 (1.14.5+repack-3build1) ... 81s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3build1) ... 81s Setting up python3-scipy (1.16.3-1) ... 85s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 85s Setting up python3-h5py-serial (3.13.0-1ubuntu1) ... 85s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 90s Setting up python3-h5py (3.13.0-1ubuntu1) ... 90s Setting up python3-mofapy (1.6.1+dfsg-15) ... 90s /usr/lib/python3/dist-packages/mofapy/core/entry_point.py:44: SyntaxWarning: invalid escape sequence '\/' 90s ### | \/ |/ _ \| ___/ \ ### 90s /usr/lib/python3/dist-packages/mofapy/core/nongaussian_nodes.py:147: SyntaxWarning: invalid escape sequence '\p' 90s p(y|x) \prop gamma(x) * e^{-gamma(x)} (1) 90s /usr/lib/python3/dist-packages/mofapy/core/utils.py:178: SyntaxWarning: invalid escape sequence '\m' 90s """Diagonal of :math:`\mathrm A\mathrm B^\intercal`. 90s Processing triggers for libc-bin (2.42-0ubuntu3) ... 90s Processing triggers for man-db (2.13.1-1) ... 92s autopkgtest [12:35:05]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import mofapy; print(mofapy)" ; done 92s autopkgtest [12:35:05]: test autodep8-python3: [----------------------- 92s Testing with python3.13: 92s 92s autopkgtest [12:35:05]: test autodep8-python3: -----------------------] 93s autopkgtest [12:35:06]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 93s autodep8-python3 PASS (superficial) 93s autopkgtest [12:35:06]: @@@@@@@@@@@@@@@@@@@@ summary 93s autodep8-python3 PASS (superficial)