0s autopkgtest [10:42:21]: starting date and time: 2025-11-01 10:42:21+0000 0s autopkgtest [10:42:21]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [10:42:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ololys54/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-4.secgroup --name adt-resolute-s390x-r-bioc-mofa-20251101-104221-juju-7f2275-prod-proposed-migration-environment-15-257a3c28-ff64-4036-a768-d7b56fc99f8f --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-r-bioc-mofa-20251101-104221-juju-7f2275-prod-proposed-migration-environment-15-257a3c28-ff64-4036-a768-d7b56fc99f8f from image adt/ubuntu-resolute-s390x-server-20251031.img (UUID 0c045c9f-9f12-44be-973b-1d1fecbe207a)... 48s autopkgtest [10:43:09]: testbed dpkg architecture: s390x 48s autopkgtest [10:43:09]: testbed apt version: 3.1.11 48s autopkgtest [10:43:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 48s autopkgtest [10:43:09]: testbed release detected to be: None 49s autopkgtest [10:43:10]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 50s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 50s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 50s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 50s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 50s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2408 kB] 52s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [50.0 kB] 52s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [198 kB] 52s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 52s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1727 kB] 53s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [28.9 kB] 53s Fetched 4647 kB in 4s (1180 kB/s) 54s Reading package lists... 54s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 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 55s Reading package lists... 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages will be upgraded: 56s gcc-15-base libatomic1 libfribidi0 libgcc-s1 libstdc++6 publicsuffix 56s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 1174 kB of archives. 56s After this operation, 14.3 kB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libatomic1 s390x 15.2.0-7ubuntu1 [9488 B] 56s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++6 s390x 15.2.0-7ubuntu1 [907 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-base s390x 15.2.0-7ubuntu1 [58.4 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-s1 s390x 15.2.0-7ubuntu1 [35.7 kB] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libfribidi0 s390x 1.0.16-3 [27.6 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x publicsuffix all 20251016.1743-0.1 [136 kB] 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory 57s Fetched 1174 kB in 1s (900 kB/s) 57s (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 ... 56953 files and directories currently installed.) 57s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_s390x.deb ... 57s Unpacking libatomic1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 57s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_s390x.deb ... 57s Unpacking libstdc++6:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 57s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_s390x.deb ... 57s Unpacking gcc-15-base:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 58s Setting up gcc-15-base:s390x (15.2.0-7ubuntu1) ... 58s (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 ... 56953 files and directories currently installed.) 58s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_s390x.deb ... 58s Unpacking libgcc-s1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 58s Setting up libgcc-s1:s390x (15.2.0-7ubuntu1) ... 58s (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 ... 56953 files and directories currently installed.) 58s Preparing to unpack .../libfribidi0_1.0.16-3_s390x.deb ... 58s Unpacking libfribidi0:s390x (1.0.16-3) over (1.0.16-1) ... 58s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 58s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 58s Setting up libfribidi0:s390x (1.0.16-3) ... 58s Setting up libatomic1:s390x (15.2.0-7ubuntu1) ... 58s Setting up publicsuffix (20251016.1743-0.1) ... 58s Setting up libstdc++6:s390x (15.2.0-7ubuntu1) ... 58s Processing triggers for libc-bin (2.42-0ubuntu3) ... 58s autopkgtest [10:43:19]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [10:43:22]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 61s autopkgtest [10:43:22]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa 64s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-15 (dsc) [2553 B] 64s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-15 (tar) [915 kB] 64s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-15 (diff) [4332 B] 64s gpgv: Signature made Mon Jan 13 14:15:48 2025 UTC 64s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 64s gpgv: issuer "crusoe@debian.org" 64s gpgv: Can't check signature: No public key 64s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-15.dsc: no acceptable signature found 64s autopkgtest [10:43:25]: testing package r-bioc-mofa version 1.6.1+dfsg-15 64s autopkgtest [10:43:25]: build not needed 67s autopkgtest [10:43:28]: test autodep8-python3: preparing testbed 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s The following NEW packages will be installed: 67s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 liblzf1 67s libqhull-r8.0 libsz2 python3-all python3-dateutil python3-decorator 67s python3-h5py python3-h5py-serial python3-mofapy python3-numpy 67s python3-numpy-dev python3-pandas python3-pandas-lib python3-pytz 67s python3-scipy 67s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 42.7 MB of archives. 67s After this operation, 217 MB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 68s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-7ubuntu1 [629 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 70s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 72s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x libaec0 s390x 1.1.4-2 [26.1 kB] 72s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x libsz2 s390x 1.1.4-2 [5628 B] 72s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x libhdf5-310 s390x 1.14.5+repack-3build1 [1477 kB] 74s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3build1 [61.1 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x liblzf1 s390x 3.6-4 [7020 B] 74s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 74s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.7-1 [886 B] 74s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 74s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x python3-decorator all 5.2.1-2 [28.1 kB] 74s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-h5py-serial s390x 3.13.0-1ubuntu1 [1182 kB] 75s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-h5py all 3.13.0-1ubuntu1 [8230 B] 75s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pytz all 2025.2-4 [32.3 kB] 75s Get:18 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-1ubuntu1 [8668 kB] 81s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 83s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-scipy s390x 1.16.3-1 [19.6 MB] 91s Get:21 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mofapy all 1.6.1+dfsg-15 [34.9 kB] 91s Fetched 42.7 MB in 24s (1800 kB/s) 91s Selecting previously unselected package python3-numpy-dev:s390x. 91s (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 ... 56953 files and directories currently installed.) 91s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 91s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 91s Selecting previously unselected package libblas3:s390x. 91s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 91s Unpacking libblas3:s390x (3.12.1-6build1) ... 91s Selecting previously unselected package libgfortran5:s390x. 91s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_s390x.deb ... 91s Unpacking libgfortran5:s390x (15.2.0-7ubuntu1) ... 91s Selecting previously unselected package liblapack3:s390x. 91s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 91s Unpacking liblapack3:s390x (3.12.1-6build1) ... 91s Selecting previously unselected package python3-numpy. 91s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 91s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 91s Selecting previously unselected package libaec0:s390x. 91s Preparing to unpack .../05-libaec0_1.1.4-2_s390x.deb ... 91s Unpacking libaec0:s390x (1.1.4-2) ... 91s Selecting previously unselected package libsz2:s390x. 91s Preparing to unpack .../06-libsz2_1.1.4-2_s390x.deb ... 91s Unpacking libsz2:s390x (1.1.4-2) ... 91s Selecting previously unselected package libhdf5-310:s390x. 91s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3build1_s390x.deb ... 91s Unpacking libhdf5-310:s390x (1.14.5+repack-3build1) ... 91s Selecting previously unselected package libhdf5-hl-310:s390x. 91s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3build1_s390x.deb ... 91s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3build1) ... 91s Selecting previously unselected package liblzf1:s390x. 91s Preparing to unpack .../09-liblzf1_3.6-4_s390x.deb ... 91s Unpacking liblzf1:s390x (3.6-4) ... 91s Selecting previously unselected package libqhull-r8.0:s390x. 91s Preparing to unpack .../10-libqhull-r8.0_2020.2-6build1_s390x.deb ... 91s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 91s Selecting previously unselected package python3-all. 91s Preparing to unpack .../11-python3-all_3.13.7-1_s390x.deb ... 91s Unpacking python3-all (3.13.7-1) ... 91s Selecting previously unselected package python3-dateutil. 91s Preparing to unpack .../12-python3-dateutil_2.9.0-4_all.deb ... 91s Unpacking python3-dateutil (2.9.0-4) ... 91s Selecting previously unselected package python3-decorator. 91s Preparing to unpack .../13-python3-decorator_5.2.1-2_all.deb ... 91s Unpacking python3-decorator (5.2.1-2) ... 91s Selecting previously unselected package python3-h5py-serial. 91s Preparing to unpack .../14-python3-h5py-serial_3.13.0-1ubuntu1_s390x.deb ... 91s Unpacking python3-h5py-serial (3.13.0-1ubuntu1) ... 91s Selecting previously unselected package python3-h5py. 91s Preparing to unpack .../15-python3-h5py_3.13.0-1ubuntu1_all.deb ... 91s Unpacking python3-h5py (3.13.0-1ubuntu1) ... 91s Selecting previously unselected package python3-pytz. 91s Preparing to unpack .../16-python3-pytz_2025.2-4_all.deb ... 91s Unpacking python3-pytz (2025.2-4) ... 92s Selecting previously unselected package python3-pandas-lib:s390x. 92s Preparing to unpack .../17-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_s390x.deb ... 92s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 92s Selecting previously unselected package python3-pandas. 92s Preparing to unpack .../18-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 92s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 92s Selecting previously unselected package python3-scipy. 92s Preparing to unpack .../19-python3-scipy_1.16.3-1_s390x.deb ... 92s Unpacking python3-scipy (1.16.3-1) ... 92s Selecting previously unselected package python3-mofapy. 92s Preparing to unpack .../20-python3-mofapy_1.6.1+dfsg-15_all.deb ... 92s Unpacking python3-mofapy (1.6.1+dfsg-15) ... 92s Setting up libqhull-r8.0:s390x (2020.2-6build1) ... 92s Setting up python3-all (3.13.7-1) ... 92s Setting up python3-pytz (2025.2-4) ... 92s Setting up libaec0:s390x (1.1.4-2) ... 92s Setting up python3-decorator (5.2.1-2) ... 92s Setting up libblas3:s390x (3.12.1-6build1) ... 92s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 92s Setting up liblzf1:s390x (3.6-4) ... 92s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 92s Setting up libgfortran5:s390x (15.2.0-7ubuntu1) ... 92s Setting up python3-dateutil (2.9.0-4) ... 93s Setting up libsz2:s390x (1.1.4-2) ... 93s Setting up liblapack3:s390x (3.12.1-6build1) ... 93s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 93s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 94s Setting up libhdf5-310:s390x (1.14.5+repack-3build1) ... 94s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3build1) ... 94s Setting up python3-scipy (1.16.3-1) ... 97s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 97s Setting up python3-h5py-serial (3.13.0-1ubuntu1) ... 98s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 102s Setting up python3-h5py (3.13.0-1ubuntu1) ... 102s Setting up python3-mofapy (1.6.1+dfsg-15) ... 102s /usr/lib/python3/dist-packages/mofapy/core/entry_point.py:44: SyntaxWarning: invalid escape sequence '\/' 102s ### | \/ |/ _ \| ___/ \ ### 102s /usr/lib/python3/dist-packages/mofapy/core/nongaussian_nodes.py:147: SyntaxWarning: invalid escape sequence '\p' 102s p(y|x) \prop gamma(x) * e^{-gamma(x)} (1) 102s /usr/lib/python3/dist-packages/mofapy/core/utils.py:178: SyntaxWarning: invalid escape sequence '\m' 102s """Diagonal of :math:`\mathrm A\mathrm B^\intercal`. 102s Processing triggers for libc-bin (2.42-0ubuntu3) ... 102s Processing triggers for man-db (2.13.1-1) ... 104s autopkgtest [10:44:05]: 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 104s autopkgtest [10:44:05]: test autodep8-python3: [----------------------- 104s Testing with python3.13: 104s 104s autopkgtest [10:44:05]: test autodep8-python3: -----------------------] 105s autopkgtest [10:44:06]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 105s autodep8-python3 PASS (superficial) 105s autopkgtest [10:44:06]: @@@@@@@@@@@@@@@@@@@@ summary 105s autodep8-python3 PASS (superficial)