0s autopkgtest [23:09:14]: starting date and time: 2026-02-09 23:09:14+0000 0s autopkgtest [23:09:14]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [23:09:14]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7jjmfq6j/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/resolute/armhf 25s autopkgtest [23:09:39]: testbed dpkg architecture: armhf 27s autopkgtest [23:09:41]: testbed apt version: 3.1.15 30s autopkgtest [23:09:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 32s autopkgtest [23:09:46]: testbed release detected to be: None 40s autopkgtest [23:09:54]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 42s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 43s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 43s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 43s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 43s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 45s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 45s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 46s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 48s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 48s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 50s Get:12 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 50s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 82s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 84s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 107s Fetched 43.5 MB in 1min 5s (669 kB/s) 108s Reading package lists... 114s autopkgtest [23:11:08]: upgrading testbed (apt dist-upgrade and autopurge) 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 117s The following packages will be upgraded: 117s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 117s libip6tc2 libxtables12 wget 117s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Need to get 2407 kB of archives. 117s After this operation, 152 kB of additional disk space will be used. 117s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 118s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 118s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 118s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 118s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 120s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 120s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 121s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 121s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 121s Preconfiguring packages ... 122s Fetched 2407 kB in 4s (636 kB/s) 122s (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 ... 68683 files and directories currently installed.) 122s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 122s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 122s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 122s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 122s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 122s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 123s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 123s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 123s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 123s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 123s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 123s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 123s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 123s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 123s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 123s Setting up wget (1.25.0-2ubuntu4) ... 123s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 123s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 123s Setting up dracut-install (109-11ubuntu1) ... 123s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 123s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 123s Setting up iptables (1.8.11-2ubuntu3) ... 123s Setting up iproute2 (6.18.0-1ubuntu1) ... 123s Processing triggers for man-db (2.13.1-1build1) ... 124s Processing triggers for install-info (7.2-5) ... 124s Processing triggers for libc-bin (2.42-2ubuntu4) ... 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Solving dependencies... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [23:11:25]: rebooting testbed after setup commands that affected boot 172s autopkgtest [23:12:06]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 199s autopkgtest [23:12:33]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa 215s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-16 (dsc) [2562 B] 215s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-16 (tar) [915 kB] 215s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mofa 1.6.1+dfsg-16 (diff) [5008 B] 215s gpgv: Signature made Wed Sep 24 20:55:53 2025 UTC 215s gpgv: using RSA key 67CB311005C4EDBE32175308DEE50D0D567EA266 215s gpgv: issuer "rebecca_palmer@zoho.com" 215s gpgv: Can't check signature: No public key 215s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-16.dsc: no acceptable signature found 215s autopkgtest [23:12:49]: testing package r-bioc-mofa version 1.6.1+dfsg-16 218s autopkgtest [23:12:52]: build not needed 221s autopkgtest [23:12:55]: test autodep8-python3: preparing testbed 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 223s Solving dependencies... 224s The following NEW packages will be installed: 224s libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 liblzf1 224s libpython3.14-minimal libpython3.14-stdlib libqhull-r8.0 libsz2 python3-all 224s python3-decorator python3-h5py python3-h5py-serial python3-mofapy 224s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 224s python3-pytz python3-scipy python3.14 python3.14-minimal 224s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 224s Need to get 45.2 MB of archives. 224s After this operation, 208 MB of additional disk space will be used. 224s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 224s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 225s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 225s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 228s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 233s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 234s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 236s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf libsz2 armhf 1.1.5-1 [16.3 kB] 236s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-310 armhf 1.14.6+repack-2 [1423 kB] 239s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-hl-310 armhf 1.14.6+repack-2 [58.9 kB] 239s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf liblzf1 armhf 3.6-4build1 [6592 B] 239s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 241s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-8 [175 kB] 241s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 242s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf python3-all armhf 3.13.9-3 [890 B] 242s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 242s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py-serial armhf 3.15.1-4 [1562 kB] 244s Get:18 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py all 3.15.1-4 [11.3 kB] 244s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytz all 2025.2-5 [32.4 kB] 244s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas-lib armhf 2.3.3+dfsg-3 [7022 kB] 252s Get:21 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas all 2.3.3+dfsg-3 [2948 kB] 255s Get:22 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-scipy armhf 1.16.3-4 [18.3 MB] 281s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mofapy all 1.6.1+dfsg-16 [34.9 kB] 281s Fetched 45.2 MB in 57s (793 kB/s) 281s Selecting previously unselected package python3-numpy-dev:armhf. 281s (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 ... 68686 files and directories currently installed.) 281s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_armhf.deb ... 281s Unpacking python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 281s Selecting previously unselected package libblas3:armhf. 281s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_armhf.deb ... 281s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 282s Selecting previously unselected package libgfortran5:armhf. 282s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 282s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 282s Selecting previously unselected package liblapack3:armhf. 282s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 282s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 282s Selecting previously unselected package python3-numpy. 282s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 282s Unpacking python3-numpy (1:2.3.5+ds-3) ... 282s Selecting previously unselected package libpython3.14-minimal:armhf. 282s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_armhf.deb ... 282s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 282s Selecting previously unselected package python3.14-minimal. 282s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_armhf.deb ... 282s Unpacking python3.14-minimal (3.14.2-1) ... 282s Selecting previously unselected package libsz2:armhf. 282s Preparing to unpack .../07-libsz2_1.1.5-1_armhf.deb ... 282s Unpacking libsz2:armhf (1.1.5-1) ... 282s Selecting previously unselected package libhdf5-310:armhf. 282s Preparing to unpack .../08-libhdf5-310_1.14.6+repack-2_armhf.deb ... 282s Unpacking libhdf5-310:armhf (1.14.6+repack-2) ... 282s Selecting previously unselected package libhdf5-hl-310:armhf. 282s Preparing to unpack .../09-libhdf5-hl-310_1.14.6+repack-2_armhf.deb ... 282s Unpacking libhdf5-hl-310:armhf (1.14.6+repack-2) ... 282s Selecting previously unselected package liblzf1:armhf. 282s Preparing to unpack .../10-liblzf1_3.6-4build1_armhf.deb ... 282s Unpacking liblzf1:armhf (3.6-4build1) ... 282s Selecting previously unselected package libpython3.14-stdlib:armhf. 282s Preparing to unpack .../11-libpython3.14-stdlib_3.14.2-1_armhf.deb ... 282s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 282s Selecting previously unselected package libqhull-r8.0:armhf. 282s Preparing to unpack .../12-libqhull-r8.0_2020.2-8_armhf.deb ... 282s Unpacking libqhull-r8.0:armhf (2020.2-8) ... 282s Selecting previously unselected package python3.14. 282s Preparing to unpack .../13-python3.14_3.14.2-1_armhf.deb ... 282s Unpacking python3.14 (3.14.2-1) ... 282s Selecting previously unselected package python3-all. 282s Preparing to unpack .../14-python3-all_3.13.9-3_armhf.deb ... 282s Unpacking python3-all (3.13.9-3) ... 283s Selecting previously unselected package python3-decorator. 283s Preparing to unpack .../15-python3-decorator_5.2.1-2_all.deb ... 283s Unpacking python3-decorator (5.2.1-2) ... 283s Selecting previously unselected package python3-h5py-serial. 283s Preparing to unpack .../16-python3-h5py-serial_3.15.1-4_armhf.deb ... 283s Unpacking python3-h5py-serial (3.15.1-4) ... 283s Selecting previously unselected package python3-h5py. 283s Preparing to unpack .../17-python3-h5py_3.15.1-4_all.deb ... 283s Unpacking python3-h5py (3.15.1-4) ... 283s Selecting previously unselected package python3-pytz. 283s Preparing to unpack .../18-python3-pytz_2025.2-5_all.deb ... 283s Unpacking python3-pytz (2025.2-5) ... 283s Selecting previously unselected package python3-pandas-lib:armhf. 283s Preparing to unpack .../19-python3-pandas-lib_2.3.3+dfsg-3_armhf.deb ... 283s Unpacking python3-pandas-lib:armhf (2.3.3+dfsg-3) ... 283s Selecting previously unselected package python3-pandas. 283s Preparing to unpack .../20-python3-pandas_2.3.3+dfsg-3_all.deb ... 283s Unpacking python3-pandas (2.3.3+dfsg-3) ... 283s Selecting previously unselected package python3-scipy. 283s Preparing to unpack .../21-python3-scipy_1.16.3-4_armhf.deb ... 283s Unpacking python3-scipy (1.16.3-4) ... 284s Selecting previously unselected package python3-mofapy. 284s Preparing to unpack .../22-python3-mofapy_1.6.1+dfsg-16_all.deb ... 284s Unpacking python3-mofapy (1.6.1+dfsg-16) ... 284s Setting up libpython3.14-minimal:armhf (3.14.2-1) ... 284s Setting up libqhull-r8.0:armhf (2020.2-8) ... 284s Setting up python3-pytz (2025.2-5) ... 284s Setting up python3-decorator (5.2.1-2) ... 285s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 285s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 285s Setting up liblzf1:armhf (3.6-4build1) ... 285s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 285s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 285s Setting up python3.14-minimal (3.14.2-1) ... 286s Setting up libsz2:armhf (1.1.5-1) ... 286s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 286s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 286s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 286s Setting up python3-numpy (1:2.3.5+ds-3) ... 290s Setting up libhdf5-310:armhf (1.14.6+repack-2) ... 290s Setting up python3.14 (3.14.2-1) ... 292s Setting up libhdf5-hl-310:armhf (1.14.6+repack-2) ... 292s Setting up python3-scipy (1.16.3-4) ... 301s Setting up python3-pandas-lib:armhf (2.3.3+dfsg-3) ... 301s Setting up python3-h5py-serial (3.15.1-4) ... 301s Setting up python3-all (3.13.9-3) ... 301s Setting up python3-pandas (2.3.3+dfsg-3) ... 313s Setting up python3-h5py (3.15.1-4) ... 313s Setting up python3-mofapy (1.6.1+dfsg-16) ... 313s Processing triggers for libc-bin (2.42-2ubuntu4) ... 313s Processing triggers for systemd (259-1ubuntu3) ... 313s Processing triggers for man-db (2.13.1-1build1) ... 321s autopkgtest [23:14:35]: 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 321s autopkgtest [23:14:35]: test autodep8-python3: [----------------------- 323s Testing with python3.14: 323s 323s Testing with python3.13: 323s 324s autopkgtest [23:14:38]: test autodep8-python3: -----------------------] 328s autodep8-python3 PASS (superficial) 328s autopkgtest [23:14:42]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 332s autopkgtest [23:14:46]: @@@@@@@@@@@@@@@@@@@@ summary 332s autodep8-python3 PASS (superficial)