0s autopkgtest [00:01:37]: starting date: 2024-03-18 0s autopkgtest [00:01:37]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [00:01:37]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x8s54_fr/out --timeout-copy=6000 --setup-commands 'ls /etc/apt/sources.list.d/*.list 2>/dev/null || true; 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,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\n" >> /etc/environment' --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-bioc-mofa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- lxd -r lxd-armhf-10.44.124.15 lxd-armhf-10.44.124.15:autopkgtest/ubuntu/noble/armhf 53s autopkgtest [00:02:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 56s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3726 kB] 57s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 57s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 57s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 57s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [574 kB] 57s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 57s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 57s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 57s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3499 kB] 57s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 57s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [33.8 kB] 57s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 69s Fetched 8505 kB in 4s (2069 kB/s) 70s Reading package lists... 85s /etc/apt/sources.list.d/proposed.list 86s tee: /proc/self/fd/2: Permission denied 125s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 125s Hit:2 http://ports.ubuntu.com/ubuntu-ports noble InRelease 125s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 125s Hit:4 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 125s Hit:5 http://ftpmaster.internal/ubuntu noble-security InRelease 125s Hit:6 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 125s Hit:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease 125s Hit:8 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 132s Reading package lists... 132s Reading package lists... 133s Building dependency tree... 133s Reading state information... 135s Calculating upgrade... 137s The following NEW packages will be installed: 137s xdg-user-dirs 137s The following packages have been kept back: 137s curl gir1.2-glib-2.0 openssl 137s The following packages will be upgraded: 137s libglib2.0-data libtirpc-common readline-common 137s 3 upgraded, 1 newly installed, 0 to remove and 3 not upgraded. 137s Need to get 128 kB of archives. 137s After this operation, 143 kB of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 138s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B] 138s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1 [56.4 kB] 138s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB] 141s Fetched 128 kB in 2s (72.8 kB/s) 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 ... 58620 files and directories currently installed.) 141s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 141s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 141s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 141s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 142s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 142s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 142s Selecting previously unselected package xdg-user-dirs. 142s Preparing to unpack .../xdg-user-dirs_0.18-1_armhf.deb ... 142s Unpacking xdg-user-dirs (0.18-1) ... 142s Setting up xdg-user-dirs (0.18-1) ... 142s Setting up libtirpc-common (1.3.4+ds-1.1) ... 142s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 142s Setting up readline-common (8.2-3.1) ... 142s Processing triggers for install-info (7.1-3) ... 144s Processing triggers for man-db (2.12.0-3) ... 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 152s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 154s autopkgtest [00:04:11]: rebooting testbed after setup commands that affected boot 191s autopkgtest [00:04:48]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 194s autopkgtest [00:04:51]: testbed dpkg architecture: armhf 210s autopkgtest [00:05:07]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa 222s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (dsc) [2554 B] 222s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (tar) [915 kB] 222s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (diff) [4216 B] 223s gpgv: Signature made Thu Nov 30 17:10:43 2023 UTC 223s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 223s gpgv: issuer "tille@debian.org" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-12.dsc: no acceptable signature found 223s autopkgtest [00:05:20]: testing package r-bioc-mofa version 1.6.1+dfsg-12 223s autopkgtest [00:05:20]: build not needed 227s autopkgtest [00:05:24]: test autodep8-python3: preparing testbed 243s Reading package lists... 245s Building dependency tree... 245s Reading state information... 246s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 247s Starting 2 pkgProblemResolver with broken count: 0 247s Done 248s Done 249s Starting pkgProblemResolver with broken count: 0 250s Starting 2 pkgProblemResolver with broken count: 0 250s Done 252s The following additional packages will be installed: 252s libaec0 libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3 252s liblbfgsb0 liblzf1 libsz2 python3-all python3-dateutil python3-decorator 252s python3-h5py python3-h5py-serial python3-mofapy python3-numpy python3-pandas 252s python3-pandas-lib python3-scipy 252s Suggested packages: 252s python-h5py-doc r-bioc-mofa gcc gfortran python3-dev python3-pytest 252s python-pandas-doc python3-statsmodels python-scipy-doc 252s Recommended packages: 252s python3-sklearn python3-sklearn-pandas python3-matplotlib python3-bottleneck 252s python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib 252s python3-lxml python3-tables g++ | c++-compiler python3-pil 252s The following NEW packages will be installed: 252s libaec0 libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3 252s liblbfgsb0 liblzf1 libsz2 python3-all python3-dateutil python3-decorator 252s python3-h5py python3-h5py-serial python3-mofapy python3-numpy python3-pandas 252s python3-pandas-lib python3-scipy 252s 0 upgraded, 19 newly installed, 0 to remove and 3 not upgraded. 252s 1 not fully installed or removed. 252s Need to get 39.6 MB of archives. 252s After this operation, 160 MB of additional disk space will be used. 252s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf python3-all armhf 3.12.1-0ubuntu2 [906 B] 252s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3 [123 kB] 253s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libgfortran5 armhf 14-20240303-1ubuntu1 [316 kB] 253s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB] 253s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf python3-numpy armhf 1:1.24.2-2 [4410 kB] 254s Get:6 http://ftpmaster.internal/ubuntu noble/universe armhf libaec0 armhf 1.1.2-1 [20.7 kB] 254s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libsz2 armhf 1.1.2-1 [5262 B] 254s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf libhdf5-103-1 armhf 1.10.10+repack-3ubuntu1 [1336 kB] 254s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf libhdf5-hl-100 armhf 1.10.10+repack-3ubuntu1 [54.6 kB] 254s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf liblzf1 armhf 3.6-4 [6554 B] 255s Get:11 http://ftpmaster.internal/ubuntu noble/universe armhf python3-h5py-serial armhf 3.10.0-1ubuntu1 [1464 kB] 255s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf python3-h5py all 3.10.0-1ubuntu1 [7970 B] 255s Get:13 http://ftpmaster.internal/ubuntu noble/main armhf python3-dateutil all 2.8.2-3 [79.2 kB] 255s Get:14 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pandas-lib armhf 2.1.4+dfsg-4ubuntu2 [8219 kB] 255s Get:15 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 256s Get:16 http://ftpmaster.internal/ubuntu noble/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 256s Get:17 http://ftpmaster.internal/ubuntu noble/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1 [27.1 kB] 256s Get:18 http://ftpmaster.internal/ubuntu noble/universe armhf python3-scipy armhf 1.11.4-6 [18.4 MB] 257s Get:19 http://ftpmaster.internal/ubuntu noble/universe armhf python3-mofapy all 1.6.1+dfsg-12 [34.8 kB] 258s Fetched 39.6 MB in 4s (8938 kB/s) 258s Selecting previously unselected package python3-all. 258s (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 ... 58634 files and directories currently installed.) 258s Preparing to unpack .../00-python3-all_3.12.1-0ubuntu2_armhf.deb ... 258s Unpacking python3-all (3.12.1-0ubuntu2) ... 258s Selecting previously unselected package libblas3:armhf. 258s Preparing to unpack .../01-libblas3_3.12.0-3_armhf.deb ... 258s Unpacking libblas3:armhf (3.12.0-3) ... 258s Selecting previously unselected package libgfortran5:armhf. 258s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_armhf.deb ... 258s Unpacking libgfortran5:armhf (14-20240303-1ubuntu1) ... 259s Selecting previously unselected package liblapack3:armhf. 259s Preparing to unpack .../03-liblapack3_3.12.0-3_armhf.deb ... 259s Unpacking liblapack3:armhf (3.12.0-3) ... 259s Selecting previously unselected package python3-numpy. 259s Preparing to unpack .../04-python3-numpy_1%3a1.24.2-2_armhf.deb ... 259s Unpacking python3-numpy (1:1.24.2-2) ... 260s Selecting previously unselected package libaec0:armhf. 260s Preparing to unpack .../05-libaec0_1.1.2-1_armhf.deb ... 260s Unpacking libaec0:armhf (1.1.2-1) ... 260s Selecting previously unselected package libsz2:armhf. 260s Preparing to unpack .../06-libsz2_1.1.2-1_armhf.deb ... 260s Unpacking libsz2:armhf (1.1.2-1) ... 260s Selecting previously unselected package libhdf5-103-1:armhf. 260s Preparing to unpack .../07-libhdf5-103-1_1.10.10+repack-3ubuntu1_armhf.deb ... 260s Unpacking libhdf5-103-1:armhf (1.10.10+repack-3ubuntu1) ... 261s Selecting previously unselected package libhdf5-hl-100:armhf. 261s Preparing to unpack .../08-libhdf5-hl-100_1.10.10+repack-3ubuntu1_armhf.deb ... 261s Unpacking libhdf5-hl-100:armhf (1.10.10+repack-3ubuntu1) ... 261s Selecting previously unselected package liblzf1:armhf. 261s Preparing to unpack .../09-liblzf1_3.6-4_armhf.deb ... 261s Unpacking liblzf1:armhf (3.6-4) ... 261s Selecting previously unselected package python3-h5py-serial. 261s Preparing to unpack .../10-python3-h5py-serial_3.10.0-1ubuntu1_armhf.deb ... 261s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 261s Selecting previously unselected package python3-h5py. 261s Preparing to unpack .../11-python3-h5py_3.10.0-1ubuntu1_all.deb ... 261s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 261s Selecting previously unselected package python3-dateutil. 261s Preparing to unpack .../12-python3-dateutil_2.8.2-3_all.deb ... 261s Unpacking python3-dateutil (2.8.2-3) ... 261s Selecting previously unselected package python3-pandas-lib:armhf. 261s Preparing to unpack .../13-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_armhf.deb ... 261s Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-4ubuntu2) ... 262s Selecting previously unselected package python3-pandas. 262s Preparing to unpack .../14-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 262s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 264s Selecting previously unselected package python3-decorator. 264s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 264s Unpacking python3-decorator (5.1.1-5) ... 264s Selecting previously unselected package liblbfgsb0:armhf. 264s Preparing to unpack .../16-liblbfgsb0_3.0+dfsg.4-1_armhf.deb ... 264s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1) ... 264s Selecting previously unselected package python3-scipy. 264s Preparing to unpack .../17-python3-scipy_1.11.4-6_armhf.deb ... 264s Unpacking python3-scipy (1.11.4-6) ... 267s Selecting previously unselected package python3-mofapy. 267s Preparing to unpack .../18-python3-mofapy_1.6.1+dfsg-12_all.deb ... 267s Unpacking python3-mofapy (1.6.1+dfsg-12) ... 267s Setting up python3-all (3.12.1-0ubuntu2) ... 267s Setting up libaec0:armhf (1.1.2-1) ... 267s Setting up python3-decorator (5.1.1-5) ... 268s Setting up libblas3:armhf (3.12.0-3) ... 268s 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 268s Setting up liblzf1:armhf (3.6-4) ... 268s Setting up libgfortran5:armhf (14-20240303-1ubuntu1) ... 268s Setting up python3-dateutil (2.8.2-3) ... 268s Setting up libsz2:armhf (1.1.2-1) ... 268s Setting up liblapack3:armhf (3.12.0-3) ... 268s 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 269s Setting up python3-numpy (1:1.24.2-2) ... 277s Setting up libhdf5-103-1:armhf (1.10.10+repack-3ubuntu1) ... 277s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1) ... 277s Setting up libhdf5-hl-100:armhf (1.10.10+repack-3ubuntu1) ... 277s Setting up python3-scipy (1.11.4-6) ... 288s Setting up python3-pandas-lib:armhf (2.1.4+dfsg-4ubuntu2) ... 288s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 289s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 308s Setting up python3-h5py (3.10.0-1ubuntu1) ... 308s Setting up python3-mofapy (1.6.1+dfsg-12) ... 309s /usr/lib/python3/dist-packages/mofapy/core/entry_point.py:41: SyntaxWarning: invalid escape sequence '\/' 309s banner = """ 309s /usr/lib/python3/dist-packages/mofapy/core/nongaussian_nodes.py:144: SyntaxWarning: invalid escape sequence '\p' 309s """ 309s /usr/lib/python3/dist-packages/mofapy/core/utils.py:178: SyntaxWarning: invalid escape sequence '\m' 309s """Diagonal of :math:`\mathrm A\mathrm B^\intercal`. 309s Setting up autopkgtest-satdep (0) ... 309s Processing triggers for man-db (2.12.0-3) ... 310s Processing triggers for libc-bin (2.39-0ubuntu2) ... 329s (Reading database ... 63129 files and directories currently installed.) 329s Removing autopkgtest-satdep (0) ... 341s autopkgtest [00:07:18]: 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 341s autopkgtest [00:07:18]: test autodep8-python3: [----------------------- 345s Testing with python3.12: 345s 345s autopkgtest [00:07:22]: test autodep8-python3: -----------------------] 350s autodep8-python3 PASS (superficial) 350s autopkgtest [00:07:27]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 354s autopkgtest [00:07:31]: @@@@@@@@@@@@@@@@@@@@ summary 354s autodep8-python3 PASS (superficial)