0s autopkgtest [20:00:57]: starting date and time: 2024-03-14 20:00:57+0000
  0s autopkgtest [20:00:57]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [20:00:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.t3edp4tc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:hdf5,src:openmpi,src:openssl,src:pmix --apt-upgrade r-bioc-mofa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 openssl/3.0.13-0ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-5.secgroup --name adt-noble-ppc64el-r-bioc-mofa-20240314-200057-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
212s autopkgtest [20:04:29]: testbed dpkg architecture: ppc64el
212s autopkgtest [20:04:29]: testbed apt version: 2.7.12
212s autopkgtest [20:04:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup
213s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
213s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [48.4 kB]
213s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B]
213s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3020 kB]
214s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [454 kB]
214s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [607 kB]
214s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
214s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
214s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
214s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3317 kB]
214s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
214s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [42.8 kB]
214s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
217s Fetched 7625 kB in 2s (3502 kB/s)
218s Reading package lists...
220s Reading package lists...
221s Building dependency tree...
221s Reading state information...
221s Calculating upgrade...
221s The following packages will be REMOVED:
221s   libssl3
221s The following NEW packages will be installed:
221s   libssl3t64
221s The following packages will be upgraded:
221s   openssl
221s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded.
221s Need to get 3195 kB of archives.
221s After this operation, 6144 B of additional disk space will be used.
221s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu1 [1028 kB]
221s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu1 [2168 kB]
222s Fetched 3195 kB in 1s (4210 kB/s)
222s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 70095 files and directories currently installed.)
222s Preparing to unpack .../openssl_3.0.13-0ubuntu1_ppc64el.deb ...
222s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
222s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
222s  wget depends on libssl3 (>= 3.0.0).
222s  tnftp depends on libssl3 (>= 3.0.0).
222s  tcpdump depends on libssl3 (>= 3.0.0).
222s  systemd-resolved depends on libssl3 (>= 3.0.0).
222s  systemd depends on libssl3 (>= 3.0.0).
222s  sudo depends on libssl3 (>= 3.0.0).
222s  rsync depends on libssl3 (>= 3.0.0).
222s  python3-cryptography depends on libssl3 (>= 3.0.0).
222s  openssh-server depends on libssl3 (>= 3.0.10).
222s  openssh-client depends on libssl3 (>= 3.0.10).
222s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
222s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
222s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
222s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
222s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
222s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
222s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
222s  libnvme1 depends on libssl3 (>= 3.0.0).
222s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
222s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
222s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
222s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
222s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
222s  kmod depends on libssl3 (>= 3.0.0).
222s  dhcpcd-base depends on libssl3 (>= 3.0.0).
222s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
222s 
222s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70095 files and directories currently installed.)
222s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
222s Selecting previously unselected package libssl3t64:ppc64el.
222s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 70084 files and directories currently installed.)
222s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_ppc64el.deb ...
222s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu1) ...
222s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu1) ...
222s Setting up openssl (3.0.13-0ubuntu1) ...
222s Processing triggers for man-db (2.12.0-3) ...
223s Processing triggers for libc-bin (2.39-0ubuntu2) ...
223s Reading package lists...
223s Building dependency tree...
223s Reading state information...
224s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
224s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
224s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
224s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
224s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
226s Reading package lists...
226s Reading package lists...
226s Building dependency tree...
226s Reading state information...
226s Calculating upgrade...
226s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
226s Reading package lists...
226s Building dependency tree...
226s Reading state information...
227s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
229s autopkgtest [20:04:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
230s autopkgtest [20:04:47]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa
232s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (dsc) [2554 B]
232s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (tar) [915 kB]
232s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (diff) [4216 B]
232s gpgv: Signature made Thu Nov 30 17:10:43 2023 UTC
232s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
232s gpgv:                issuer "tille@debian.org"
232s gpgv: Can't check signature: No public key
232s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-12.dsc: no acceptable signature found
232s autopkgtest [20:04:49]: testing package r-bioc-mofa version 1.6.1+dfsg-12
233s autopkgtest [20:04:50]: build not needed
233s autopkgtest [20:04:50]: test autodep8-python3: preparing testbed
234s Reading package lists...
235s Building dependency tree...
235s Reading state information...
235s Starting pkgProblemResolver with broken count: 0
235s Starting 2 pkgProblemResolver with broken count: 0
235s Done
235s The following additional packages will be installed:
235s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3
235s   liblbfgsb0 liblzf1 libsz2 python3-all python3-dateutil python3-decorator
235s   python3-h5py python3-h5py-serial python3-mofapy python3-numpy python3-pandas
235s   python3-pandas-lib python3-scipy
235s Suggested packages:
235s   python-h5py-doc r-bioc-mofa gcc gfortran python3-dev python3-pytest
235s   python-pandas-doc python3-statsmodels python-scipy-doc
235s Recommended packages:
235s   python3-sklearn python3-sklearn-pandas python3-matplotlib python3-bottleneck
235s   python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib
235s   python3-lxml python3-tables g++ | c++-compiler python3-pil
235s The following NEW packages will be installed:
235s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
235s   libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libsz2 python3-all
235s   python3-dateutil python3-decorator python3-h5py python3-h5py-serial
235s   python3-mofapy python3-numpy python3-pandas python3-pandas-lib python3-scipy
235s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
235s Need to get 45.1 MB/45.1 MB of archives.
235s After this operation, 255 MB of additional disk space will be used.
235s Get:1 /tmp/autopkgtest.hnqwsU/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B]
235s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB]
236s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB]
236s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB]
236s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B]
236s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-3.1ubuntu2 [1395 kB]
237s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-3.1ubuntu2 [70.9 kB]
237s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB]
238s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB]
238s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B]
238s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B]
238s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB]
238s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB]
238s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB]
240s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu2 [955 kB]
241s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py all 3.10.0-1ubuntu2 [7980 B]
241s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB]
245s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB]
246s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB]
253s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-mofapy all 1.6.1+dfsg-12 [34.8 kB]
254s Fetched 45.1 MB in 18s (2492 kB/s)
254s Selecting previously unselected package libaec0:ppc64el.
254s (Reading database ... 
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(Reading database ... 70097 files and directories currently installed.)
254s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ...
254s Unpacking libaec0:ppc64el (1.1.2-1) ...
254s Selecting previously unselected package libblas3:ppc64el.
254s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ...
254s Unpacking libblas3:ppc64el (3.12.0-3) ...
254s Selecting previously unselected package libgfortran5:ppc64el.
254s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ...
254s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
254s Selecting previously unselected package libsz2:ppc64el.
254s Preparing to unpack .../03-libsz2_1.1.2-1_ppc64el.deb ...
254s Unpacking libsz2:ppc64el (1.1.2-1) ...
254s Selecting previously unselected package libhdf5-103-1t64:ppc64el.
254s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ...
254s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ...
254s Selecting previously unselected package libhdf5-hl-100t64:ppc64el.
254s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ...
254s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ...
254s Selecting previously unselected package liblapack3:ppc64el.
254s Preparing to unpack .../06-liblapack3_3.12.0-3_ppc64el.deb ...
254s Unpacking liblapack3:ppc64el (3.12.0-3) ...
254s Selecting previously unselected package liblbfgsb0:ppc64el.
254s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ...
254s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ...
254s Selecting previously unselected package liblzf1:ppc64el.
254s Preparing to unpack .../08-liblzf1_3.6-4_ppc64el.deb ...
254s Unpacking liblzf1:ppc64el (3.6-4) ...
254s Selecting previously unselected package python3-all.
254s Preparing to unpack .../09-python3-all_3.12.1-0ubuntu2_ppc64el.deb ...
254s Unpacking python3-all (3.12.1-0ubuntu2) ...
254s Selecting previously unselected package python3-dateutil.
254s Preparing to unpack .../10-python3-dateutil_2.8.2-3_all.deb ...
254s Unpacking python3-dateutil (2.8.2-3) ...
254s Selecting previously unselected package python3-decorator.
254s Preparing to unpack .../11-python3-decorator_5.1.1-5_all.deb ...
254s Unpacking python3-decorator (5.1.1-5) ...
254s Selecting previously unselected package python3-numpy.
254s Preparing to unpack .../12-python3-numpy_1%3a1.24.2-2_ppc64el.deb ...
254s Unpacking python3-numpy (1:1.24.2-2) ...
254s Selecting previously unselected package python3-h5py-serial.
254s Preparing to unpack .../13-python3-h5py-serial_3.10.0-1ubuntu2_ppc64el.deb ...
254s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ...
254s Selecting previously unselected package python3-h5py.
254s Preparing to unpack .../14-python3-h5py_3.10.0-1ubuntu2_all.deb ...
254s Unpacking python3-h5py (3.10.0-1ubuntu2) ...
254s Selecting previously unselected package python3-pandas-lib:ppc64el.
254s Preparing to unpack .../15-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ...
254s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ...
255s Selecting previously unselected package python3-pandas.
255s Preparing to unpack .../16-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ...
255s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ...
255s Selecting previously unselected package python3-scipy.
255s Preparing to unpack .../17-python3-scipy_1.11.4-6_ppc64el.deb ...
255s Unpacking python3-scipy (1.11.4-6) ...
256s Selecting previously unselected package python3-mofapy.
256s Preparing to unpack .../18-python3-mofapy_1.6.1+dfsg-12_all.deb ...
256s Unpacking python3-mofapy (1.6.1+dfsg-12) ...
256s Selecting previously unselected package autopkgtest-satdep.
256s Preparing to unpack .../19-1-autopkgtest-satdep.deb ...
256s Unpacking autopkgtest-satdep (0) ...
256s Setting up python3-all (3.12.1-0ubuntu2) ...
256s Setting up libaec0:ppc64el (1.1.2-1) ...
256s Setting up python3-decorator (5.1.1-5) ...
256s Setting up libblas3:ppc64el (3.12.0-3) ...
256s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
256s Setting up liblzf1:ppc64el (3.6-4) ...
256s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
256s Setting up python3-dateutil (2.8.2-3) ...
256s Setting up libsz2:ppc64el (1.1.2-1) ...
256s Setting up liblapack3:ppc64el (3.12.0-3) ...
256s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
256s Setting up python3-numpy (1:1.24.2-2) ...
259s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ...
259s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ...
259s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ...
259s Setting up python3-scipy (1.11.4-6) ...
262s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ...
262s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ...
262s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ...
268s Setting up python3-h5py (3.10.0-1ubuntu2) ...
268s Setting up python3-mofapy (1.6.1+dfsg-12) ...
268s /usr/lib/python3/dist-packages/mofapy/core/entry_point.py:41: SyntaxWarning: invalid escape sequence '\/'
268s   banner = """
268s /usr/lib/python3/dist-packages/mofapy/core/nongaussian_nodes.py:144: SyntaxWarning: invalid escape sequence '\p'
268s   """
268s /usr/lib/python3/dist-packages/mofapy/core/utils.py:178: SyntaxWarning: invalid escape sequence '\m'
268s   """Diagonal of :math:`\mathrm A\mathrm B^\intercal`.
268s Setting up autopkgtest-satdep (0) ...
268s Processing triggers for man-db (2.12.0-3) ...
268s Processing triggers for libc-bin (2.39-0ubuntu2) ...
271s (Reading database ... 74570 files and directories currently installed.)
271s Removing autopkgtest-satdep (0) ...
272s autopkgtest [20:05:29]: 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
272s autopkgtest [20:05:29]: test autodep8-python3: [-----------------------
272s Testing with python3.12:
272s <module 'mofapy' from '/usr/lib/python3/dist-packages/mofapy/__init__.py'>
272s autopkgtest [20:05:29]: test autodep8-python3: -----------------------]
273s autopkgtest [20:05:30]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
273s autodep8-python3     PASS (superficial)
273s autopkgtest [20:05:30]: @@@@@@@@@@@@@@@@@@@@ summary
273s autodep8-python3     PASS (superficial)
300s Creating nova instance adt-noble-ppc64el-r-bioc-mofa-20240314-200057-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240314.img (UUID a031584c-aec8-4412-bff6-4238354f4d17)...