0s autopkgtest [01:28:44]: starting date and time: 2024-03-23 01:28:44+0000 0s autopkgtest [01:28:44]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [01:28:44]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2nwk_orz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade xpore --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-13.secgroup --name adt-noble-s390x-xpore-20240323-012843-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 91s autopkgtest [01:30:15]: testbed dpkg architecture: s390x 91s autopkgtest [01:30:15]: testbed apt version: 2.7.12 91s autopkgtest [01:30:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3979 kB] 94s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 94s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 94s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 94s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [665 kB] 94s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 94s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 94s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 94s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4162 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 95s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.5 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 97s Fetched 9545 kB in 4s (2566 kB/s) 97s Reading package lists... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Unknown architecture, assuming PC-style ttyS0 101s sh: Attempting to set up Debian/Ubuntu apt sources automatically 101s sh: Distribution appears to be Ubuntu 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s eatmydata is already the newest version (131-1). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s dbus is already the newest version (1.14.10-4ubuntu1). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s rng-tools-debian is already the newest version (2.4). 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s The following packages will be REMOVED: 103s cloud-init* python3-configobj* python3-debconf* 103s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 103s After this operation, 3256 kB disk space will be freed. 103s (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 ... 52170 files and directories currently installed.) 103s Removing cloud-init (24.1.2-0ubuntu1) ... 104s Removing python3-configobj (5.0.8-3) ... 104s Removing python3-debconf (1.5.86) ... 104s Processing triggers for man-db (2.12.0-3) ... 104s (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 ... 51781 files and directories currently installed.) 104s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 105s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 105s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 105s invoke-rc.d: policy-rc.d denied execution of try-restart. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s linux-generic is already the newest version (6.8.0-11.11+1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 107s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [01:30:32]: rebooting testbed after setup commands that affected boot 132s autopkgtest [01:30:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 135s autopkgtest [01:30:59]: @@@@@@@@@@@@@@@@@@@@ apt-source xpore 144s Get:1 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (dsc) [1727 B] 144s Get:2 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (tar) [84.3 MB] 144s Get:3 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (tar) [169 kB] 144s Get:4 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (diff) [9684 B] 144s gpgv: Signature made Sun Dec 31 22:02:48 2023 UTC 144s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./xpore_2.1-2.dsc: no acceptable signature found 146s autopkgtest [01:31:10]: testing package xpore version 2.1-2 147s autopkgtest [01:31:11]: build not needed 170s autopkgtest [01:31:34]: test run-data-preprocess-test: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 174s The following additional packages will be installed: 174s libaec0 libblas3 libdouble-conversion3 libgfortran5 libhdf5-103-1 174s libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libsz2 pyensembl pylint 174s python3-appdirs python3-astroid python3-datacache python3-dateutil 174s python3-decorator python3-dill python3-gtfparse python3-h5py 174s python3-h5py-serial python3-importlib-metadata python3-isort 174s python3-logilab-common python3-mccabe python3-memoized-property 174s python3-more-itertools python3-mypy-extensions python3-numpy python3-pandas 174s python3-pandas-lib python3-platformdirs python3-scipy python3-serializable 174s python3-simplejson python3-toml python3-tomlkit python3-typechecks 174s python3-ujson python3-zipp xpore 174s Suggested packages: 174s python3-objgraph python-h5py-doc gcc gfortran python3-dev python3-pytest 174s python-pandas-doc python3-statsmodels python-scipy-doc xpore-doc 174s Recommended packages: 174s python3-tk python3-matplotlib python3-bottleneck python3-numexpr python3-odf 174s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 174s g++ | c++-compiler python3-pil 174s The following NEW packages will be installed: 174s autopkgtest-satdep libaec0 libblas3 libdouble-conversion3 libgfortran5 174s libhdf5-103-1 libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libsz2 pyensembl 174s pylint python3-appdirs python3-astroid python3-datacache python3-dateutil 174s python3-decorator python3-dill python3-gtfparse python3-h5py 174s python3-h5py-serial python3-importlib-metadata python3-isort 174s python3-logilab-common python3-mccabe python3-memoized-property 174s python3-more-itertools python3-mypy-extensions python3-numpy python3-pandas 174s python3-pandas-lib python3-platformdirs python3-scipy python3-serializable 174s python3-simplejson python3-toml python3-tomlkit python3-typechecks 174s python3-ujson python3-zipp xpore 174s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 45.5 MB/45.5 MB of archives. 174s After this operation, 226 MB of additional disk space will be used. 174s Get:1 /tmp/autopkgtest.J689U0/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 174s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libaec0 s390x 1.1.2-1 [25.7 kB] 174s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 175s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libdouble-conversion3 s390x 3.3.0-1 [39.6 kB] 175s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 175s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libsz2 s390x 1.1.2-1 [5346 B] 175s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-103-1 s390x 1.10.10+repack-3ubuntu1 [1425 kB] 175s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-hl-100 s390x 1.10.10+repack-3ubuntu1 [57.5 kB] 175s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 175s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1 [28.4 kB] 175s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x liblzf1 s390x 3.6-4 [7020 B] 175s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x python3-astroid all 3.0.2-2 [174 kB] 175s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x python3-toml all 0.10.2-1 [16.5 kB] 175s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x python3-isort all 5.6.4-1 [63.1 kB] 175s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x python3-more-itertools all 10.2.0-1 [52.9 kB] 175s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x python3-zipp all 1.0.0-6 [6090 B] 175s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x python3-importlib-metadata all 4.12.0-1 [17.8 kB] 175s Get:18 http://ftpmaster.internal/ubuntu noble/universe s390x python3-mypy-extensions all 1.0.0-1 [6148 B] 175s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x python3-logilab-common all 1.9.8-2 [280 kB] 176s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x python3-dill all 0.3.8-1 [83.0 kB] 176s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x python3-mccabe all 0.7.0-1 [8678 B] 176s Get:22 http://ftpmaster.internal/ubuntu noble/universe s390x python3-platformdirs all 4.2.0-1 [16.1 kB] 176s Get:23 http://ftpmaster.internal/ubuntu noble/universe s390x python3-tomlkit all 0.12.4-1 [37.5 kB] 176s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x pylint all 3.0.3-1 [337 kB] 176s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x python3-appdirs all 1.4.4-4 [10.9 kB] 176s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x python3-dateutil all 2.8.2-3 [79.2 kB] 176s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 176s Get:28 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pandas-lib s390x 2.1.4+dfsg-4ubuntu2 [8852 kB] 177s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 177s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x python3-typechecks all 0.1.0+ds-3 [4440 B] 177s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x python3-datacache all 1.2.1-2 [12.8 kB] 177s Get:32 http://ftpmaster.internal/ubuntu noble/universe s390x python3-gtfparse all 1.3.0+ds-1 [10.1 kB] 177s Get:33 http://ftpmaster.internal/ubuntu noble/universe s390x python3-memoized-property all 1.0.3-2 [5286 B] 177s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x python3-simplejson s390x 3.19.2-1build1 [63.6 kB] 177s Get:35 http://ftpmaster.internal/ubuntu noble/universe s390x python3-serializable all 0.4.0+ds-1 [8210 B] 177s Get:36 http://ftpmaster.internal/ubuntu noble/universe s390x pyensembl all 2.3.9-2 [36.8 kB] 177s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 177s Get:38 http://ftpmaster.internal/ubuntu noble/universe s390x python3-h5py-serial s390x 3.10.0-1ubuntu1 [1535 kB] 177s Get:39 http://ftpmaster.internal/ubuntu noble/universe s390x python3-h5py all 3.10.0-1ubuntu1 [7970 B] 177s Get:40 http://ftpmaster.internal/ubuntu noble/universe s390x python3-ujson s390x 5.9.0-1 [34.0 kB] 177s Get:41 http://ftpmaster.internal/ubuntu noble/universe s390x python3-scipy s390x 1.11.4-6 [20.1 MB] 179s Get:42 http://ftpmaster.internal/ubuntu noble/universe s390x xpore all 2.1-2 [42.9 kB] 179s Fetched 45.5 MB in 5s (9283 kB/s) 179s Selecting previously unselected package libaec0:s390x. 179s (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 ... 51726 files and directories currently installed.) 179s Preparing to unpack .../00-libaec0_1.1.2-1_s390x.deb ... 179s Unpacking libaec0:s390x (1.1.2-1) ... 179s Selecting previously unselected package libblas3:s390x. 179s Preparing to unpack .../01-libblas3_3.12.0-3_s390x.deb ... 179s Unpacking libblas3:s390x (3.12.0-3) ... 179s Selecting previously unselected package libdouble-conversion3:s390x. 179s Preparing to unpack .../02-libdouble-conversion3_3.3.0-1_s390x.deb ... 179s Unpacking libdouble-conversion3:s390x (3.3.0-1) ... 179s Selecting previously unselected package libgfortran5:s390x. 179s Preparing to unpack .../03-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 179s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 179s Selecting previously unselected package libsz2:s390x. 179s Preparing to unpack .../04-libsz2_1.1.2-1_s390x.deb ... 179s Unpacking libsz2:s390x (1.1.2-1) ... 179s Selecting previously unselected package libhdf5-103-1:s390x. 179s Preparing to unpack .../05-libhdf5-103-1_1.10.10+repack-3ubuntu1_s390x.deb ... 179s Unpacking libhdf5-103-1:s390x (1.10.10+repack-3ubuntu1) ... 179s Selecting previously unselected package libhdf5-hl-100:s390x. 179s Preparing to unpack .../06-libhdf5-hl-100_1.10.10+repack-3ubuntu1_s390x.deb ... 179s Unpacking libhdf5-hl-100:s390x (1.10.10+repack-3ubuntu1) ... 179s Selecting previously unselected package liblapack3:s390x. 179s Preparing to unpack .../07-liblapack3_3.12.0-3_s390x.deb ... 179s Unpacking liblapack3:s390x (3.12.0-3) ... 179s Selecting previously unselected package liblbfgsb0:s390x. 179s Preparing to unpack .../08-liblbfgsb0_3.0+dfsg.4-1_s390x.deb ... 179s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1) ... 179s Selecting previously unselected package liblzf1:s390x. 179s Preparing to unpack .../09-liblzf1_3.6-4_s390x.deb ... 179s Unpacking liblzf1:s390x (3.6-4) ... 179s Selecting previously unselected package python3-astroid. 179s Preparing to unpack .../10-python3-astroid_3.0.2-2_all.deb ... 179s Unpacking python3-astroid (3.0.2-2) ... 179s Selecting previously unselected package python3-toml. 179s Preparing to unpack .../11-python3-toml_0.10.2-1_all.deb ... 179s Unpacking python3-toml (0.10.2-1) ... 179s Selecting previously unselected package python3-isort. 179s Preparing to unpack .../12-python3-isort_5.6.4-1_all.deb ... 179s Unpacking python3-isort (5.6.4-1) ... 179s Selecting previously unselected package python3-more-itertools. 180s Preparing to unpack .../13-python3-more-itertools_10.2.0-1_all.deb ... 180s Unpacking python3-more-itertools (10.2.0-1) ... 180s Selecting previously unselected package python3-zipp. 180s Preparing to unpack .../14-python3-zipp_1.0.0-6_all.deb ... 180s Unpacking python3-zipp (1.0.0-6) ... 180s Selecting previously unselected package python3-importlib-metadata. 180s Preparing to unpack .../15-python3-importlib-metadata_4.12.0-1_all.deb ... 180s Unpacking python3-importlib-metadata (4.12.0-1) ... 180s Selecting previously unselected package python3-mypy-extensions. 180s Preparing to unpack .../16-python3-mypy-extensions_1.0.0-1_all.deb ... 180s Unpacking python3-mypy-extensions (1.0.0-1) ... 180s Selecting previously unselected package python3-logilab-common. 180s Preparing to unpack .../17-python3-logilab-common_1.9.8-2_all.deb ... 180s Unpacking python3-logilab-common (1.9.8-2) ... 180s Selecting previously unselected package python3-dill. 180s Preparing to unpack .../18-python3-dill_0.3.8-1_all.deb ... 180s Unpacking python3-dill (0.3.8-1) ... 180s Selecting previously unselected package python3-mccabe. 180s Preparing to unpack .../19-python3-mccabe_0.7.0-1_all.deb ... 180s Unpacking python3-mccabe (0.7.0-1) ... 180s Selecting previously unselected package python3-platformdirs. 180s Preparing to unpack .../20-python3-platformdirs_4.2.0-1_all.deb ... 180s Unpacking python3-platformdirs (4.2.0-1) ... 180s Selecting previously unselected package python3-tomlkit. 180s Preparing to unpack .../21-python3-tomlkit_0.12.4-1_all.deb ... 180s Unpacking python3-tomlkit (0.12.4-1) ... 180s Selecting previously unselected package pylint. 180s Preparing to unpack .../22-pylint_3.0.3-1_all.deb ... 180s Unpacking pylint (3.0.3-1) ... 180s Selecting previously unselected package python3-appdirs. 180s Preparing to unpack .../23-python3-appdirs_1.4.4-4_all.deb ... 180s Unpacking python3-appdirs (1.4.4-4) ... 180s Selecting previously unselected package python3-dateutil. 180s Preparing to unpack .../24-python3-dateutil_2.8.2-3_all.deb ... 180s Unpacking python3-dateutil (2.8.2-3) ... 180s Selecting previously unselected package python3-numpy. 180s Preparing to unpack .../25-python3-numpy_1%3a1.24.2-2_s390x.deb ... 180s Unpacking python3-numpy (1:1.24.2-2) ... 180s Selecting previously unselected package python3-pandas-lib:s390x. 180s Preparing to unpack .../26-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_s390x.deb ... 180s Unpacking python3-pandas-lib:s390x (2.1.4+dfsg-4ubuntu2) ... 180s Selecting previously unselected package python3-pandas. 180s Preparing to unpack .../27-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 180s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 181s Selecting previously unselected package python3-typechecks. 181s Preparing to unpack .../28-python3-typechecks_0.1.0+ds-3_all.deb ... 181s Unpacking python3-typechecks (0.1.0+ds-3) ... 181s Selecting previously unselected package python3-datacache. 181s Preparing to unpack .../29-python3-datacache_1.2.1-2_all.deb ... 181s Unpacking python3-datacache (1.2.1-2) ... 181s Selecting previously unselected package python3-gtfparse. 181s Preparing to unpack .../30-python3-gtfparse_1.3.0+ds-1_all.deb ... 181s Unpacking python3-gtfparse (1.3.0+ds-1) ... 181s Selecting previously unselected package python3-memoized-property. 181s Preparing to unpack .../31-python3-memoized-property_1.0.3-2_all.deb ... 181s Unpacking python3-memoized-property (1.0.3-2) ... 181s Selecting previously unselected package python3-simplejson. 181s Preparing to unpack .../32-python3-simplejson_3.19.2-1build1_s390x.deb ... 181s Unpacking python3-simplejson (3.19.2-1build1) ... 181s Selecting previously unselected package python3-serializable. 181s Preparing to unpack .../33-python3-serializable_0.4.0+ds-1_all.deb ... 181s Unpacking python3-serializable (0.4.0+ds-1) ... 181s Selecting previously unselected package pyensembl. 181s Preparing to unpack .../34-pyensembl_2.3.9-2_all.deb ... 181s Unpacking pyensembl (2.3.9-2) ... 181s Selecting previously unselected package python3-decorator. 181s Preparing to unpack .../35-python3-decorator_5.1.1-5_all.deb ... 181s Unpacking python3-decorator (5.1.1-5) ... 181s Selecting previously unselected package python3-h5py-serial. 181s Preparing to unpack .../36-python3-h5py-serial_3.10.0-1ubuntu1_s390x.deb ... 181s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 181s Selecting previously unselected package python3-h5py. 181s Preparing to unpack .../37-python3-h5py_3.10.0-1ubuntu1_all.deb ... 181s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 181s Selecting previously unselected package python3-ujson:s390x. 181s Preparing to unpack .../38-python3-ujson_5.9.0-1_s390x.deb ... 181s Unpacking python3-ujson:s390x (5.9.0-1) ... 181s Selecting previously unselected package python3-scipy. 181s Preparing to unpack .../39-python3-scipy_1.11.4-6_s390x.deb ... 181s Unpacking python3-scipy (1.11.4-6) ... 181s Selecting previously 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demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_227_ch_12_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_15769_ch_334_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_8268_ch_299_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_8940_ch_323_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_913_ch_225_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_44620_ch_390_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_759_ch_215_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_21528_ch_34_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_11723_ch_145_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_8879_ch_28_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_362_ch_323_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_6952_ch_151_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_14068_ch_261_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_984_ch_476_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_423_ch_142_strand.fast5 199s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_1857_ch_501_strand.fast5 199s demo/data/HEK293T-WT-rep1/fastq/ 199s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq 200s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index.readdb 200s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index.fai 200s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index 200s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index.gzi 200s demo/data/HEK293T-WT-rep1/nanopolish/ 200s demo/data/HEK293T-WT-rep1/nanopolish/summary.txt 200s demo/data/HEK293T-WT-rep1/nanopolish/eventalign.txt 200s demo/Hek293T_config.yml 202s /usr/lib/python3/dist-packages/xpore/scripts/dataprep.py:72: SettingWithCopyWarning: 202s A value is trying to be set on a copy of a slice from a DataFrame. 202s Try using .loc[row_indexer,col_indexer] = value instead 202s 202s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 202s chunk_split['line_length'] = np.array(lines) 203s /usr/lib/python3/dist-packages/xpore/scripts/dataprep.py:21: PerformanceWarning: indexing past lexsort depth may impact performance. 203s pos_end += eventalign_result.loc[index]['line_length'].sum() 208s Output Directory Generated 208s PASS 208s autopkgtest [01:32:12]: test run-data-preprocess-test: -----------------------] 209s autopkgtest [01:32:13]: test run-data-preprocess-test: - - - - - - - - - - results - - - - - - - - - - 209s run-data-preprocess-test PASS 210s autopkgtest [01:32:14]: @@@@@@@@@@@@@@@@@@@@ summary 210s run-data-preprocess-test PASS 222s Creating nova instance adt-noble-s390x-xpore-20240323-012843-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...