0s autopkgtest [23:18:19]: starting date and time: 2026-02-09 23:18:19+0000 0s autopkgtest [23:18:19]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:18:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7q37sfrj/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-bioc-mofa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-17.secgroup --name adt-resolute-arm64-r-bioc-mofa-20260209-231819-juju-7f2275-prod-proposed-migration-environment-2-e621c145-f003-4656-920f-a89ca7462895 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-r-bioc-mofa-20260209-231819-juju-7f2275-prod-proposed-migration-environment-2-e621c145-f003-4656-920f-a89ca7462895 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 128s autopkgtest [23:20:27]: testbed dpkg architecture: arm64 128s autopkgtest [23:20:27]: testbed apt version: 3.1.15 129s autopkgtest [23:20:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 129s autopkgtest [23:20:28]: testbed release detected to be: None 130s autopkgtest [23:20:29]: updating testbed package index (apt update) 130s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 130s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 130s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 130s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 130s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 134s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 134s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 134s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 134s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 134s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 137s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 137s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 137s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 138s Fetched 3862 kB in 7s (554 kB/s) 139s Reading package lists... 140s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 140s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 140s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 141s Reading package lists... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Calculating upgrade... 141s The following packages will be upgraded: 141s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 141s libip6tc2 libxtables12 wget 142s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Need to get 2534 kB of archives. 142s After this operation, 18.4 kB of additional disk space will be used. 142s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 142s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 142s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 142s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 142s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 145s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 145s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 145s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 145s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 146s dpkg-preconfigure: unable to re-open stdin: No such file or directory 146s Fetched 2534 kB in 4s (620 kB/s) 146s (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 ... 136597 files and directories currently installed.) 146s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 146s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 146s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 146s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 146s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 146s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 146s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 146s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 146s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 146s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 147s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 147s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 147s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 147s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 147s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 147s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 147s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 147s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 147s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 147s Setting up wget (1.25.0-2ubuntu4) ... 147s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 147s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 147s Setting up dracut-install (109-11ubuntu1) ... 147s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 147s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 147s Setting up iptables (1.8.11-2ubuntu3) ... 147s Setting up iproute2 (6.18.0-1ubuntu1) ... 147s Processing triggers for man-db (2.13.1-1build1) ... 148s Processing triggers for install-info (7.2-5) ... 148s Processing triggers for libc-bin (2.42-2ubuntu4) ... 148s autopkgtest [23:20:47]: upgrading testbed (apt dist-upgrade and autopurge) 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Solving dependencies... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s autopkgtest [23:20:51]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 153s autopkgtest [23:20:52]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa 157s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-16 (dsc) [2562 B] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-16 (tar) [915 kB] 157s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-16 (diff) [5008 B] 157s gpgv: Signature made Wed Sep 24 20:55:53 2025 UTC 157s gpgv: using RSA key 67CB311005C4EDBE32175308DEE50D0D567EA266 157s gpgv: issuer "rebecca_palmer@zoho.com" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-16.dsc: no acceptable signature found 157s autopkgtest [23:20:56]: testing package r-bioc-mofa version 1.6.1+dfsg-16 157s autopkgtest [23:20:56]: build not needed 158s autopkgtest [23:20:57]: test autodep8-python3: preparing testbed 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s Solving dependencies... 159s The following NEW packages will be installed: 159s libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 liblzf1 159s libqhull-r8.0 libsz2 python3-all python3-decorator python3-h5py 159s python3-h5py-serial python3-mofapy python3-numpy python3-numpy-dev 159s python3-pandas python3-pandas-lib python3-pytz python3-scipy python3.14 159s python3.14-minimal 159s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 41.1 MB of archives. 159s After this operation, 228 MB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 159s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 159s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 159s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 162s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 170s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 174s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.5-1 [17.0 kB] 174s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.6+repack-2 [1287 kB] 176s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.6+repack-2 [59.1 kB] 176s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblzf1 arm64 3.6-4build1 [7330 B] 176s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-8 [191 kB] 176s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 177s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.9-3 [890 B] 177s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 177s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py-serial arm64 3.15.1-4 [1483 kB] 180s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-h5py all 3.15.1-4 [11.3 kB] 180s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 180s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 192s Get:19 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 197s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.16.3-4 [17.5 MB] 229s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mofapy all 1.6.1+dfsg-16 [34.9 kB] 230s Fetched 41.1 MB in 1min 11s (581 kB/s) 230s Selecting previously unselected package python3-numpy-dev:arm64. 230s (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 ... 136600 files and directories currently installed.) 230s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 230s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 230s Selecting previously unselected package libblas3:arm64. 230s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 230s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 230s Selecting previously unselected package libgfortran5:arm64. 230s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 230s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 230s Selecting previously unselected package liblapack3:arm64. 230s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 230s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 230s Selecting previously unselected package python3-numpy. 230s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 230s Unpacking python3-numpy (1:2.3.5+ds-3) ... 230s Selecting previously unselected package python3.14-minimal. 230s Preparing to unpack .../05-python3.14-minimal_3.14.2-1_arm64.deb ... 230s Unpacking python3.14-minimal (3.14.2-1) ... 230s Selecting previously unselected package libsz2:arm64. 230s Preparing to unpack .../06-libsz2_1.1.5-1_arm64.deb ... 230s Unpacking libsz2:arm64 (1.1.5-1) ... 230s Selecting previously unselected package libhdf5-310:arm64. 230s Preparing to unpack .../07-libhdf5-310_1.14.6+repack-2_arm64.deb ... 230s Unpacking libhdf5-310:arm64 (1.14.6+repack-2) ... 230s Selecting previously unselected package libhdf5-hl-310:arm64. 230s Preparing to unpack .../08-libhdf5-hl-310_1.14.6+repack-2_arm64.deb ... 230s Unpacking libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 230s Selecting previously unselected package liblzf1:arm64. 230s Preparing to unpack .../09-liblzf1_3.6-4build1_arm64.deb ... 230s Unpacking liblzf1:arm64 (3.6-4build1) ... 230s Selecting previously unselected package libqhull-r8.0:arm64. 230s Preparing to unpack .../10-libqhull-r8.0_2020.2-8_arm64.deb ... 230s Unpacking libqhull-r8.0:arm64 (2020.2-8) ... 230s Selecting previously unselected package python3.14. 230s Preparing to unpack .../11-python3.14_3.14.2-1_arm64.deb ... 230s Unpacking python3.14 (3.14.2-1) ... 230s Selecting previously unselected package python3-all. 231s Preparing to unpack .../12-python3-all_3.13.9-3_arm64.deb ... 231s Unpacking python3-all (3.13.9-3) ... 231s Selecting previously unselected package python3-decorator. 231s Preparing to unpack .../13-python3-decorator_5.2.1-2_all.deb ... 231s Unpacking python3-decorator (5.2.1-2) ... 231s Selecting previously unselected package python3-h5py-serial. 231s Preparing to unpack .../14-python3-h5py-serial_3.15.1-4_arm64.deb ... 231s Unpacking python3-h5py-serial (3.15.1-4) ... 231s Selecting previously unselected package python3-h5py. 231s Preparing to unpack .../15-python3-h5py_3.15.1-4_all.deb ... 231s Unpacking python3-h5py (3.15.1-4) ... 231s Selecting previously unselected package python3-pytz. 231s Preparing to unpack .../16-python3-pytz_2025.2-5_all.deb ... 231s Unpacking python3-pytz (2025.2-5) ... 231s Selecting previously unselected package python3-pandas-lib:arm64. 231s Preparing to unpack .../17-python3-pandas-lib_2.3.3+dfsg-3_arm64.deb ... 231s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 231s Selecting previously unselected package python3-pandas. 231s Preparing to unpack .../18-python3-pandas_2.3.3+dfsg-3_all.deb ... 231s Unpacking python3-pandas (2.3.3+dfsg-3) ... 231s Selecting previously unselected package python3-scipy. 231s Preparing to unpack .../19-python3-scipy_1.16.3-4_arm64.deb ... 231s Unpacking python3-scipy (1.16.3-4) ... 231s Selecting previously unselected package python3-mofapy. 232s Preparing to unpack .../20-python3-mofapy_1.6.1+dfsg-16_all.deb ... 232s Unpacking python3-mofapy (1.6.1+dfsg-16) ... 232s Setting up libqhull-r8.0:arm64 (2020.2-8) ... 232s Setting up python3-pytz (2025.2-5) ... 232s Setting up python3-decorator (5.2.1-2) ... 232s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 232s 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 232s Setting up liblzf1:arm64 (3.6-4build1) ... 232s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 232s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 232s Setting up python3.14-minimal (3.14.2-1) ... 233s Setting up libsz2:arm64 (1.1.5-1) ... 233s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 233s 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 233s Setting up python3-numpy (1:2.3.5+ds-3) ... 236s Setting up libhdf5-310:arm64 (1.14.6+repack-2) ... 236s Setting up python3.14 (3.14.2-1) ... 237s Setting up libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 237s Setting up python3-scipy (1.16.3-4) ... 244s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 244s Setting up python3-h5py-serial (3.15.1-4) ... 245s Setting up python3-all (3.13.9-3) ... 245s Setting up python3-pandas (2.3.3+dfsg-3) ... 253s Setting up python3-h5py (3.15.1-4) ... 254s Setting up python3-mofapy (1.6.1+dfsg-16) ... 254s Processing triggers for libc-bin (2.42-2ubuntu4) ... 254s Processing triggers for systemd (259-1ubuntu3) ... 254s Processing triggers for man-db (2.13.1-1build1) ... 255s autopkgtest [23:22:34]: 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 255s autopkgtest [23:22:34]: test autodep8-python3: [----------------------- 255s Testing with python3.14: 255s 255s Testing with python3.13: 255s 256s autopkgtest [23:22:35]: test autodep8-python3: -----------------------] 256s autopkgtest [23:22:35]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 256s autodep8-python3 PASS (superficial) 256s autopkgtest [23:22:35]: @@@@@@@@@@@@@@@@@@@@ summary 256s autodep8-python3 PASS (superficial)