0s autopkgtest [09:13:48]: starting date and time: 2024-03-24 09:13:48+0000 0s autopkgtest [09:13:48]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [09:13:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.efd6_8f3/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-2@bos02-arm64-7.secgroup --name adt-noble-arm64-xpore-20240324-091348-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 168s autopkgtest [09:16:36]: testbed dpkg architecture: arm64 168s autopkgtest [09:16:36]: testbed apt version: 2.7.12 168s autopkgtest [09:16:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 169s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 170s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 171s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 171s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 171s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3991 kB] 171s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [706 kB] 171s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 171s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 171s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 171s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 172s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 172s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 172s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 183s Fetched 9850 kB in 6s (1712 kB/s) 184s Reading package lists... 190s Reading package lists... 191s Building dependency tree... 191s Reading state information... 193s Calculating upgrade... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s Reading package lists... 197s Building dependency tree... 197s Reading state information... 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s sh: Attempting to set up Debian/Ubuntu apt sources automatically 201s sh: Distribution appears to be Ubuntu 205s Reading package lists... 206s Building dependency tree... 206s Reading state information... 208s eatmydata is already the newest version (131-1). 208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 211s dbus is already the newest version (1.14.10-4ubuntu1). 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s Reading package lists... 212s Building dependency tree... 212s Reading state information... 214s rng-tools-debian is already the newest version (2.4). 214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 214s Reading package lists... 215s Building dependency tree... 215s Reading state information... 217s The following packages will be REMOVED: 217s cloud-init* python3-configobj* python3-debconf* 218s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 218s After this operation, 3256 kB disk space will be freed. 219s (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 ... 75911 files and directories currently installed.) 219s Removing cloud-init (24.1.2-0ubuntu1) ... 222s Removing python3-configobj (5.0.8-3) ... 222s Removing python3-debconf (1.5.86) ... 222s Processing triggers for man-db (2.12.0-3) ... 224s (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 ... 75522 files and directories currently installed.) 224s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 227s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 227s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 227s invoke-rc.d: policy-rc.d denied execution of try-restart. 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 230s linux-generic is already the newest version (6.8.0-11.11+1). 230s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 231s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 231s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 231s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 242s Reading package lists... 242s Reading package lists... 243s Building dependency tree... 243s Reading state information... 244s Calculating upgrade... 246s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 246s Reading package lists... 246s Building dependency tree... 246s Reading state information... 249s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 249s autopkgtest [09:17:57]: rebooting testbed after setup commands that affected boot 413s autopkgtest [09:20:41]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 417s autopkgtest [09:20:45]: @@@@@@@@@@@@@@@@@@@@ apt-source xpore 425s Get:1 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (dsc) [1727 B] 425s Get:2 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (tar) [84.3 MB] 425s Get:3 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (tar) [169 kB] 425s Get:4 http://ftpmaster.internal/ubuntu noble/universe xpore 2.1-2 (diff) [9684 B] 426s gpgv: Signature made Sun Dec 31 22:02:48 2023 UTC 426s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 426s gpgv: Can't check signature: No public key 426s dpkg-source: warning: cannot verify inline signature for ./xpore_2.1-2.dsc: no acceptable signature found 430s autopkgtest [09:20:58]: testing package xpore version 2.1-2 430s autopkgtest [09:20:58]: build not needed 434s autopkgtest [09:21:02]: test run-data-preprocess-test: preparing testbed 439s Reading package lists... 440s Building dependency tree... 440s Reading state information... 440s Starting pkgProblemResolver with broken count: 0 441s Starting 2 pkgProblemResolver with broken count: 0 441s Done 442s The following additional packages will be installed: 442s libaec0 libblas3 libdouble-conversion3 libgfortran5 libhdf5-103-1 442s libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libsz2 pyensembl pylint 442s python3-appdirs python3-astroid python3-datacache python3-dateutil 442s python3-decorator python3-dill python3-gtfparse python3-h5py 442s python3-h5py-serial python3-importlib-metadata python3-isort 442s python3-logilab-common python3-mccabe python3-memoized-property 442s python3-more-itertools python3-mypy-extensions python3-numpy python3-pandas 442s python3-pandas-lib python3-platformdirs python3-scipy python3-serializable 442s python3-simplejson python3-toml python3-tomlkit python3-typechecks 443s python3-ujson python3-zipp xpore 443s Suggested packages: 443s python3-objgraph python-h5py-doc gcc gfortran python3-dev python3-pytest 443s python-pandas-doc python3-statsmodels python-scipy-doc xpore-doc 443s Recommended packages: 443s python3-tk python3-matplotlib python3-bottleneck python3-numexpr python3-odf 443s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 443s g++ | c++-compiler python3-pil 443s The following NEW packages will be installed: 443s autopkgtest-satdep libaec0 libblas3 libdouble-conversion3 libgfortran5 443s libhdf5-103-1 libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libsz2 pyensembl 443s pylint python3-appdirs python3-astroid python3-datacache python3-dateutil 443s python3-decorator python3-dill python3-gtfparse python3-h5py 443s python3-h5py-serial python3-importlib-metadata python3-isort 443s python3-logilab-common python3-mccabe python3-memoized-property 443s python3-more-itertools python3-mypy-extensions python3-numpy python3-pandas 443s python3-pandas-lib python3-platformdirs python3-scipy python3-serializable 443s python3-simplejson python3-toml python3-tomlkit python3-typechecks 443s python3-ujson python3-zipp xpore 443s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 443s Need to get 40.9 MB/40.9 MB of archives. 443s After this operation, 216 MB of additional disk space will be used. 443s Get:1 /tmp/autopkgtest.MtVEwd/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 443s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 443s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 443s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libdouble-conversion3 arm64 3.3.0-1 [37.2 kB] 443s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 443s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 443s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 444s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 444s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 444s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 444s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 444s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-astroid all 3.0.2-2 [174 kB] 444s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 444s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-isort all 5.6.4-1 [63.1 kB] 444s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 444s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3-zipp all 1.0.0-6 [6090 B] 444s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] 444s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mypy-extensions all 1.0.0-1 [6148 B] 444s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-logilab-common all 1.9.8-2 [280 kB] 444s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-dill all 0.3.8-1 [83.0 kB] 444s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mccabe all 0.7.0-1 [8678 B] 444s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-platformdirs all 4.2.0-1 [16.1 kB] 444s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tomlkit all 0.12.4-1 [37.5 kB] 444s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 pylint all 3.0.3-1 [337 kB] 444s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 444s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 444s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 444s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 444s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 444s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-typechecks all 0.1.0+ds-3 [4440 B] 444s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-datacache all 1.2.1-2 [12.8 kB] 444s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-gtfparse all 1.3.0+ds-1 [10.1 kB] 445s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-memoized-property all 1.0.3-2 [5286 B] 445s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 python3-simplejson arm64 3.19.2-1build1 [61.4 kB] 445s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-serializable all 0.4.0+ds-1 [8210 B] 445s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 pyensembl all 2.3.9-2 [36.8 kB] 445s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 445s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 445s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 445s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ujson arm64 5.9.0-1 [32.7 kB] 445s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 445s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 xpore all 2.1-2 [42.9 kB] 447s Fetched 40.9 MB in 3s (16.0 MB/s) 447s Selecting previously unselected package libaec0:arm64. 447s (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 ... 75467 files and directories currently installed.) 447s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 447s Unpacking libaec0:arm64 (1.1.2-1) ... 447s Selecting previously unselected package libblas3:arm64. 447s Preparing to unpack .../01-libblas3_3.12.0-3_arm64.deb ... 447s Unpacking libblas3:arm64 (3.12.0-3) ... 447s Selecting previously unselected package libdouble-conversion3:arm64. 447s Preparing to unpack .../02-libdouble-conversion3_3.3.0-1_arm64.deb ... 447s Unpacking libdouble-conversion3:arm64 (3.3.0-1) ... 447s Selecting previously unselected package libgfortran5:arm64. 447s Preparing to unpack .../03-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 447s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 448s Selecting previously unselected package libsz2:arm64. 448s Preparing to unpack .../04-libsz2_1.1.2-1_arm64.deb ... 448s Unpacking libsz2:arm64 (1.1.2-1) ... 448s Selecting previously unselected package libhdf5-103-1:arm64. 448s Preparing to unpack .../05-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 448s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 448s Selecting previously unselected package libhdf5-hl-100:arm64. 448s Preparing to unpack .../06-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 448s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 448s Selecting previously unselected package liblapack3:arm64. 448s Preparing to unpack .../07-liblapack3_3.12.0-3_arm64.deb ... 448s Unpacking liblapack3:arm64 (3.12.0-3) ... 448s Selecting previously unselected package liblbfgsb0:arm64. 448s Preparing to unpack .../08-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 448s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 448s Selecting previously unselected package liblzf1:arm64. 448s Preparing to unpack .../09-liblzf1_3.6-4_arm64.deb ... 448s Unpacking liblzf1:arm64 (3.6-4) ... 448s Selecting previously unselected package python3-astroid. 448s Preparing to unpack .../10-python3-astroid_3.0.2-2_all.deb ... 448s Unpacking python3-astroid (3.0.2-2) ... 449s Selecting previously unselected package python3-toml. 449s Preparing to unpack .../11-python3-toml_0.10.2-1_all.deb ... 449s Unpacking python3-toml (0.10.2-1) ... 449s Selecting previously unselected package python3-isort. 449s Preparing to unpack .../12-python3-isort_5.6.4-1_all.deb ... 449s Unpacking python3-isort (5.6.4-1) ... 449s Selecting previously unselected package python3-more-itertools. 449s Preparing to unpack .../13-python3-more-itertools_10.2.0-1_all.deb ... 449s Unpacking python3-more-itertools (10.2.0-1) ... 449s Selecting previously unselected package python3-zipp. 449s Preparing to unpack .../14-python3-zipp_1.0.0-6_all.deb ... 449s Unpacking python3-zipp (1.0.0-6) ... 449s Selecting previously unselected package python3-importlib-metadata. 449s Preparing to unpack .../15-python3-importlib-metadata_4.12.0-1_all.deb ... 449s Unpacking python3-importlib-metadata (4.12.0-1) ... 449s Selecting previously unselected package python3-mypy-extensions. 449s Preparing to unpack .../16-python3-mypy-extensions_1.0.0-1_all.deb ... 449s Unpacking python3-mypy-extensions (1.0.0-1) ... 449s Selecting previously unselected package python3-logilab-common. 449s Preparing to unpack .../17-python3-logilab-common_1.9.8-2_all.deb ... 449s Unpacking python3-logilab-common (1.9.8-2) ... 450s Selecting previously unselected package python3-dill. 450s Preparing to unpack .../18-python3-dill_0.3.8-1_all.deb ... 450s Unpacking python3-dill (0.3.8-1) ... 450s Selecting previously unselected package python3-mccabe. 450s Preparing to unpack .../19-python3-mccabe_0.7.0-1_all.deb ... 450s Unpacking python3-mccabe (0.7.0-1) ... 450s Selecting previously unselected package python3-platformdirs. 450s Preparing to unpack .../20-python3-platformdirs_4.2.0-1_all.deb ... 450s Unpacking python3-platformdirs (4.2.0-1) ... 450s Selecting previously unselected package python3-tomlkit. 450s Preparing to unpack .../21-python3-tomlkit_0.12.4-1_all.deb ... 450s Unpacking python3-tomlkit (0.12.4-1) ... 450s Selecting previously unselected package pylint. 450s Preparing to unpack .../22-pylint_3.0.3-1_all.deb ... 450s Unpacking pylint (3.0.3-1) ... 450s Selecting previously unselected package python3-appdirs. 450s Preparing to unpack .../23-python3-appdirs_1.4.4-4_all.deb ... 450s Unpacking python3-appdirs (1.4.4-4) ... 450s Selecting previously unselected package python3-dateutil. 450s Preparing to unpack .../24-python3-dateutil_2.8.2-3_all.deb ... 450s Unpacking python3-dateutil (2.8.2-3) ... 451s Selecting previously unselected package python3-numpy. 451s Preparing to unpack .../25-python3-numpy_1%3a1.24.2-2_arm64.deb ... 451s Unpacking python3-numpy (1:1.24.2-2) ... 452s Selecting previously unselected package python3-pandas-lib:arm64. 452s Preparing to unpack .../26-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 452s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 453s Selecting previously unselected package python3-pandas. 453s Preparing to unpack .../27-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 453s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 455s Selecting previously unselected package python3-typechecks. 455s Preparing to unpack .../28-python3-typechecks_0.1.0+ds-3_all.deb ... 455s Unpacking python3-typechecks (0.1.0+ds-3) ... 455s Selecting previously unselected package python3-datacache. 455s Preparing to unpack .../29-python3-datacache_1.2.1-2_all.deb ... 455s Unpacking python3-datacache (1.2.1-2) ... 456s Selecting previously unselected package python3-gtfparse. 456s Preparing to unpack .../30-python3-gtfparse_1.3.0+ds-1_all.deb ... 456s Unpacking python3-gtfparse (1.3.0+ds-1) ... 456s Selecting previously unselected package python3-memoized-property. 456s Preparing to unpack .../31-python3-memoized-property_1.0.3-2_all.deb ... 456s Unpacking python3-memoized-property (1.0.3-2) ... 456s Selecting previously unselected package python3-simplejson. 456s Preparing to unpack .../32-python3-simplejson_3.19.2-1build1_arm64.deb ... 456s Unpacking python3-simplejson (3.19.2-1build1) ... 456s Selecting previously unselected package python3-serializable. 456s Preparing to unpack .../33-python3-serializable_0.4.0+ds-1_all.deb ... 456s Unpacking python3-serializable (0.4.0+ds-1) ... 456s Selecting previously unselected package pyensembl. 456s Preparing to unpack .../34-pyensembl_2.3.9-2_all.deb ... 456s Unpacking pyensembl (2.3.9-2) ... 456s Selecting previously unselected package python3-decorator. 456s Preparing to unpack .../35-python3-decorator_5.1.1-5_all.deb ... 456s Unpacking python3-decorator (5.1.1-5) ... 456s Selecting previously unselected package python3-h5py-serial. 456s Preparing to unpack .../36-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ... 456s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 457s Selecting previously unselected package python3-h5py. 457s Preparing to unpack .../37-python3-h5py_3.10.0-1ubuntu1_all.deb ... 457s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 457s Selecting previously unselected package python3-ujson:arm64. 457s Preparing to unpack .../38-python3-ujson_5.9.0-1_arm64.deb ... 457s Unpacking python3-ujson:arm64 (5.9.0-1) ... 457s Selecting previously unselected package python3-scipy. 457s Preparing to unpack .../39-python3-scipy_1.11.4-6_arm64.deb ... 457s Unpacking python3-scipy (1.11.4-6) ... 462s Selecting previously 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demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_14068_ch_261_strand.fast5 546s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_984_ch_476_strand.fast5 546s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_423_ch_142_strand.fast5 546s demo/data/HEK293T-WT-rep1/fast5/GISPC936_20181120_FAK27249_MN18749_sequencing_run_SHO_20112018_EmptyE2_9_36177_read_1857_ch_501_strand.fast5 546s demo/data/HEK293T-WT-rep1/fastq/ 546s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq 546s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index.readdb 546s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index.fai 546s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index 546s demo/data/HEK293T-WT-rep1/fastq/basecalled.fastq.index.gzi 546s demo/data/HEK293T-WT-rep1/nanopolish/ 546s demo/data/HEK293T-WT-rep1/nanopolish/summary.txt 546s demo/data/HEK293T-WT-rep1/nanopolish/eventalign.txt 548s demo/Hek293T_config.yml 559s /usr/lib/python3/dist-packages/xpore/scripts/dataprep.py:72: SettingWithCopyWarning: 559s A value is trying to be set on a copy of a slice from a DataFrame. 559s Try using .loc[row_indexer,col_indexer] = value instead 559s 559s See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy 559s chunk_split['line_length'] = np.array(lines) 561s /usr/lib/python3/dist-packages/xpore/scripts/dataprep.py:21: PerformanceWarning: indexing past lexsort depth may impact performance. 561s pos_end += eventalign_result.loc[index]['line_length'].sum() 590s Output Directory Generated 590s PASS 591s autopkgtest [09:23:39]: test run-data-preprocess-test: -----------------------] 591s autopkgtest [09:23:39]: test run-data-preprocess-test: - - - - - - - - - - results - - - - - - - - - - 591s run-data-preprocess-test PASS 592s autopkgtest [09:23:40]: @@@@@@@@@@@@@@@@@@@@ summary 592s run-data-preprocess-test PASS 611s Creating nova instance adt-noble-arm64-xpore-20240324-091348-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...