0s autopkgtest [19:58:03]: starting date and time: 2024-03-14 19:58:03+0000 0s autopkgtest [19:58:03]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:58:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bforpgt8/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 pycoqc --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@bos01-ppc64el-16.secgroup --name adt-noble-ppc64el-pycoqc-20240314-195803-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://us.ports.ubuntu.com/ubuntu-ports/ 102s autopkgtest [19:59:45]: testbed dpkg architecture: ppc64el 102s autopkgtest [19:59:45]: testbed apt version: 2.7.12 102s autopkgtest [19:59:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 103s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3020 kB] 104s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [48.4 kB] 104s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [454 kB] 104s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 104s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [607 kB] 104s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 104s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 104s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 104s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3317 kB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [42.8 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 107s Fetched 7625 kB in 2s (3831 kB/s) 107s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Calculating upgrade... 111s The following packages will be REMOVED: 111s libssl3 111s The following NEW packages will be installed: 111s libssl3t64 111s The following packages will be upgraded: 111s dosfstools openssl 111s 2 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 111s Need to get 3297 kB of archives. 111s After this operation, 3072 B disk space will be freed. 111s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu1 [1028 kB] 112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu1 [2168 kB] 112s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el dosfstools ppc64el 4.2-1.1 [101 kB] 113s Fetched 3297 kB in 2s (2113 kB/s) 113s (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 ... 70096 files and directories currently installed.) 113s Preparing to unpack .../openssl_3.0.13-0ubuntu1_ppc64el.deb ... 113s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 113s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 113s wget depends on libssl3 (>= 3.0.0). 113s tnftp depends on libssl3 (>= 3.0.0). 113s tcpdump depends on libssl3 (>= 3.0.0). 113s systemd-resolved depends on libssl3 (>= 3.0.0). 113s systemd depends on libssl3 (>= 3.0.0). 113s sudo depends on libssl3 (>= 3.0.0). 113s rsync depends on libssl3 (>= 3.0.0). 113s python3-cryptography depends on libssl3 (>= 3.0.0). 113s openssh-server depends on libssl3 (>= 3.0.10). 113s openssh-client depends on libssl3 (>= 3.0.10). 113s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 113s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 113s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 113s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 113s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 113s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 113s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 113s libnvme1 depends on libssl3 (>= 3.0.0). 113s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 113s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 113s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 113s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 113s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 113s kmod depends on libssl3 (>= 3.0.0). 113s dhcpcd-base depends on libssl3 (>= 3.0.0). 113s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 113s 113s (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 ... 70096 files and directories currently installed.) 113s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 113s Selecting previously unselected package libssl3t64:ppc64el. 113s (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 ... 70085 files and directories currently installed.) 113s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_ppc64el.deb ... 113s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 113s Preparing to unpack .../dosfstools_4.2-1.1_ppc64el.deb ... 113s Unpacking dosfstools (4.2-1.1) over (4.2-1build3) ... 113s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 113s Setting up dosfstools (4.2-1.1) ... 113s Setting up openssl (3.0.13-0ubuntu1) ... 113s Processing triggers for man-db (2.12.0-3) ... 114s Processing triggers for libc-bin (2.39-0ubuntu2) ... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 115s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 116s Reading package lists... 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s autopkgtest [20:00:04]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 121s autopkgtest [20:00:04]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 127s Get:1 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 127s Get:2 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 127s Get:3 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 127s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 127s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 127s gpgv: issuer "tille@debian.org" 127s gpgv: Can't check signature: No public key 127s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 129s autopkgtest [20:00:12]: testing package pycoqc version 2.5.2+dfsg-3 130s autopkgtest [20:00:13]: build not needed 161s autopkgtest [20:00:44]: test run-unit-test: preparing testbed 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 163s The following additional packages will be installed: 163s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 163s libhts3 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 163s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 163s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 163s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 163s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 163s Suggested packages: 163s python-fastjsonschema-doc python-h5py-doc python3-pip gcc gfortran 163s python3-dev python3-pytest python-pandas-doc python3-statsmodels 163s python3-matplotlib ipython3 python3-ipykernel python-scipy-doc 163s python-tenacity-doc 163s Recommended packages: 163s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 163s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 163s g++ | c++-compiler python3-pil 163s The following NEW packages will be installed: 163s autopkgtest-satdep libaec0 libblas3 libdeflate0 libgfortran5 163s libhdf5-103-1t64 libhdf5-hl-100t64 libhts3 libhtscodecs2 liblapack3 163s liblbfgsb0 liblzf1 libsz2 pycoqc python3-dateutil python3-decorator 163s python3-fastjsonschema python3-h5py python3-h5py-serial python3-jupyter-core 163s python3-nbformat python3-numpy python3-pandas python3-pandas-lib 163s python3-platformdirs python3-plotly python3-pysam python3-scipy 163s python3-tenacity python3-tqdm python3-traitlets 163s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 53.4 MB/53.4 MB of archives. 163s After this operation, 347 MB of additional disk space will be used. 163s Get:1 /tmp/autopkgtest.O3Zd9R/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 163s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 163s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 163s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 164s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 164s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 164s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-3.1ubuntu2 [1395 kB] 165s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-3.1ubuntu2 [70.9 kB] 165s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 165s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 166s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 167s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 167s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 167s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 171s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu2 [955 kB] 171s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 171s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 176s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 178s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 178s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-fastjsonschema all 2.19.0-1 [19.6 kB] 178s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-platformdirs all 4.2.0-1 [16.1 kB] 178s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-traitlets all 5.5.0-2 [85.0 kB] 178s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-jupyter-core all 5.3.2-1ubuntu1 [25.5 kB] 178s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-nbformat all 5.9.1-1 [41.2 kB] 178s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tenacity all 8.2.3-2 [14.8 kB] 178s Get:26 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-plotly all 5.15.0+dfsg1-1 [2222 kB] 179s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 181s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 192s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-tqdm all 4.64.1-2 [95.2 kB] 192s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py all 3.10.0-1ubuntu2 [7980 B] 192s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el pycoqc all 2.5.2+dfsg-3 [36.4 kB] 193s Fetched 53.4 MB in 30s (1786 kB/s) 193s Selecting previously unselected package libaec0:ppc64el. 193s (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 ... 70097 files and directories currently installed.) 193s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ... 193s Unpacking libaec0:ppc64el (1.1.2-1) ... 193s Selecting previously unselected package libblas3:ppc64el. 193s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 193s Unpacking libblas3:ppc64el (3.12.0-3) ... 193s Selecting previously unselected package libdeflate0:ppc64el. 193s Preparing to unpack .../02-libdeflate0_1.19-1_ppc64el.deb ... 193s Unpacking libdeflate0:ppc64el (1.19-1) ... 193s Selecting previously unselected package libgfortran5:ppc64el. 193s Preparing to unpack .../03-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 193s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 193s Selecting previously unselected package libsz2:ppc64el. 193s Preparing to unpack .../04-libsz2_1.1.2-1_ppc64el.deb ... 193s Unpacking libsz2:ppc64el (1.1.2-1) ... 193s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 193s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ... 193s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 193s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 193s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ... 193s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 193s Selecting previously unselected package libhtscodecs2:ppc64el. 193s Preparing to unpack .../07-libhtscodecs2_1.6.0-1_ppc64el.deb ... 193s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 193s Selecting previously unselected package libhts3:ppc64el. 193s Preparing to unpack .../08-libhts3_1.18+ds-1_ppc64el.deb ... 193s Unpacking libhts3:ppc64el (1.18+ds-1) ... 193s Selecting previously unselected package liblapack3:ppc64el. 193s Preparing to unpack .../09-liblapack3_3.12.0-3_ppc64el.deb ... 194s Unpacking liblapack3:ppc64el (3.12.0-3) ... 194s Selecting previously unselected package liblbfgsb0:ppc64el. 194s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 194s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 194s Selecting previously unselected package liblzf1:ppc64el. 194s Preparing to unpack .../11-liblzf1_3.6-4_ppc64el.deb ... 194s Unpacking liblzf1:ppc64el (3.6-4) ... 194s Selecting previously unselected package python3-numpy. 194s Preparing to unpack .../12-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 194s Unpacking python3-numpy (1:1.24.2-2) ... 194s Selecting previously unselected package python3-h5py-serial. 194s Preparing to unpack .../13-python3-h5py-serial_3.10.0-1ubuntu2_ppc64el.deb ... 194s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 194s Selecting previously unselected package python3-dateutil. 194s Preparing to unpack .../14-python3-dateutil_2.8.2-3_all.deb ... 194s Unpacking python3-dateutil (2.8.2-3) ... 194s Selecting previously unselected package python3-pandas-lib:ppc64el. 194s Preparing to unpack .../15-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 194s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 194s Selecting previously unselected package python3-pandas. 194s Preparing to unpack .../16-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 194s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 195s Selecting previously unselected package python3-decorator. 195s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ... 195s Unpacking python3-decorator (5.1.1-5) ... 195s Selecting previously unselected package python3-fastjsonschema. 195s Preparing to unpack .../18-python3-fastjsonschema_2.19.0-1_all.deb ... 195s Unpacking python3-fastjsonschema (2.19.0-1) ... 195s Selecting previously unselected package python3-platformdirs. 195s Preparing to unpack .../19-python3-platformdirs_4.2.0-1_all.deb ... 195s Unpacking python3-platformdirs (4.2.0-1) ... 195s Selecting previously unselected package python3-traitlets. 195s Preparing to unpack .../20-python3-traitlets_5.5.0-2_all.deb ... 195s Unpacking python3-traitlets (5.5.0-2) ... 195s Selecting previously unselected package python3-jupyter-core. 195s Preparing to unpack .../21-python3-jupyter-core_5.3.2-1ubuntu1_all.deb ... 195s Unpacking python3-jupyter-core (5.3.2-1ubuntu1) ... 195s Selecting previously unselected package python3-nbformat. 195s Preparing to unpack .../22-python3-nbformat_5.9.1-1_all.deb ... 195s Unpacking python3-nbformat (5.9.1-1) ... 195s Selecting previously unselected package python3-tenacity. 195s Preparing to unpack .../23-python3-tenacity_8.2.3-2_all.deb ... 195s Unpacking python3-tenacity (8.2.3-2) ... 195s Selecting previously unselected package python3-plotly. 195s Preparing to unpack .../24-python3-plotly_5.15.0+dfsg1-1_all.deb ... 195s Unpacking python3-plotly (5.15.0+dfsg1-1) ... 197s Selecting previously unselected package python3-pysam. 197s Preparing to unpack .../25-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 197s Unpacking python3-pysam (0.22.0+ds-1) ... 197s Selecting previously unselected package python3-scipy. 197s Preparing to unpack .../26-python3-scipy_1.11.4-6_ppc64el.deb ... 197s Unpacking python3-scipy (1.11.4-6) ... 198s Selecting previously unselected package python3-tqdm. 199s Preparing to unpack .../27-python3-tqdm_4.64.1-2_all.deb ... 199s Unpacking python3-tqdm (4.64.1-2) ... 199s Selecting previously unselected package python3-h5py. 199s Preparing to unpack .../28-python3-h5py_3.10.0-1ubuntu2_all.deb ... 199s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 199s Selecting previously unselected package pycoqc. 199s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-3_all.deb ... 199s Unpacking pycoqc (2.5.2+dfsg-3) ... 199s Selecting previously unselected package autopkgtest-satdep. 199s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 199s Unpacking autopkgtest-satdep (0) ... 199s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 199s Setting up python3-tenacity (8.2.3-2) ... 199s Setting up python3-tqdm (4.64.1-2) ... 199s Setting up libdeflate0:ppc64el (1.19-1) ... 199s Setting up libaec0:ppc64el (1.1.2-1) ... 199s Setting up python3-platformdirs (4.2.0-1) ... 199s Setting up python3-decorator (5.1.1-5) ... 199s Setting up libblas3:ppc64el (3.12.0-3) ... 199s 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 199s Setting up liblzf1:ppc64el (3.6-4) ... 199s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 199s Setting up python3-fastjsonschema (2.19.0-1) ... 199s Setting up python3-traitlets (5.5.0-2) ... 199s Setting up python3-dateutil (2.8.2-3) ... 199s Setting up python3-jupyter-core (5.3.2-1ubuntu1) ... 200s Setting up libsz2:ppc64el (1.1.2-1) ... 200s Setting up liblapack3:ppc64el (3.12.0-3) ... 200s 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 200s Setting up libhts3:ppc64el (1.18+ds-1) ... 200s Setting up python3-pysam (0.22.0+ds-1) ... 200s Setting up python3-nbformat (5.9.1-1) ... 200s Setting up python3-plotly (5.15.0+dfsg1-1) ... 209s Setting up python3-numpy (1:1.24.2-2) ... 211s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 211s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 211s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 211s Setting up python3-scipy (1.11.4-6) ... 215s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 215s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 215s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 220s Setting up python3-h5py (3.10.0-1ubuntu2) ... 220s Setting up pycoqc (2.5.2+dfsg-3) ... 220s Setting up autopkgtest-satdep (0) ... 220s Processing triggers for man-db (2.12.0-3) ... 221s Processing triggers for libc-bin (2.39-0ubuntu2) ... 224s (Reading database ... 88903 files and directories currently installed.) 224s Removing autopkgtest-satdep (0) ... 225s autopkgtest [20:01:48]: test run-unit-test: [----------------------- 225s Test 1 226s Checking arguments values 226s Check input data files 226s Parse data files 226s Merge data 226s Cleaning data 226s Loading plotting interface 227s PASS 227s 227s Test 2 228s Checking arguments values 228s Check input data files 228s Parse data files 228s Merge data 228s Cleaning data 228s Loading plotting interface 229s PASS 229s 229s Test 3 229s Checking arguments values 229s Check input data files 229s Parse data files 229s Merge data 229s Cleaning data 229s Loading plotting interface 230s PASS 230s 230s Test 4 230s Checking arguments values 230s Check input data files 230s Parse data files 231s Merge data 231s Cleaning data 231s Loading plotting interface 232s PASS 232s 232s Test 5 232s Checking arguments values 232s Check input data files 232s Parse data files 232s Merge data 232s Cleaning data 232s Loading plotting interface 233s PASS 233s 233s Test 6 234s PASS 234s 234s Test 7 234s Checking arguments values 234s Check input data files 234s Parse data files 234s Merge data 234s Cleaning data 234s Loading plotting interface 235s PASS 235s 235s Test 8 236s 0 reads [00:00, ? reads/s] 22 reads [00:00, 524.17 reads/s] 236s Total reads: 22 / Average speed: 384.32 reads/s 236s 236s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 236s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 236s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 236s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 236s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out 236s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out 236s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 236s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 236s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 236s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 236s PASS 236s 236s Test 9 236s Check input data and options 236s Start processing fast5 files 236s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1142.14 reads/s] 236s Overall counts valid files: 22 236s 236s fields found mean_qscore_template: 22 236s called_events: 22 236s duration: 22 236s strand_score: 22 236s 236s fields not found 236s Total reads: 22 / Average speed: 566.99 reads/s 236s 236s mean_qscore_template called_events duration strand_score 236s 7.881 1513 24541 -0.0007 236s 8.56 5838 87570 -0.0003 236s 8.544 3740 56107 -0.0003 236s 7.608 1615 24233 -0.0007 236s 8.304 1547 23218 -0.0008 236s 8.119 3181 47720 -0.0004 236s 8.23 2778 51387 -0.0007 236s 8.693 2383 35752 -0.0005 236s 7.805 1438 21583 -0.0006 236s PASS 236s 236s Test 10 237s Check input data and options 237s Start processing fast5 files 237s 0 reads [00:00, ? reads/s] 22 reads [00:00, 588.31 reads/s] 237s Overall counts valid files: 22 237s 237s fields found read_id: 22 237s run_id: 22 237s channel: 22 237s start_time: 22 237s sequence_length_template: 22 237s mean_qscore_template: 22 237s calibration_strand_genome_template: 22 237s 237s fields not found barcode_arrangement: 22 237s 237s Total reads: 22 / Average speed: 386.94 reads/s 237s 237s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 237s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 237s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_237_strand.fast5 237s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 237s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 237s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_301_strand.fast5 237s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 237s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 237s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 237s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.O3Zd9R/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 237s PASS 237s 237s Test 11 238s Import data from sequencing summary file(s) and cleanup 238s Read files and import in a dataframe 238s Check input data files 238s Parse data files 238s Merge data 238s Cleanup missing barcodes values 238s Cleaning up low frequency barcodes 238s Split data per barcode 238s Processing data for Barcode barcode02 238s Processing data for Barcode barcode07 238s Processing data for Barcode barcode08 238s Processing data for Barcode barcode09 238s Processing data for Barcode barcode10 238s Processing data for Barcode barcode11 239s Processing data for Barcode barcode12 240s Processing data for Barcode unclassified 240s Barcode Counts 240s PASS 240s 240s Test 12 240s PASS 240s 240s Check if files really exist 240s PASS 240s 240s Counts Write 240s barcode02 2 False 240s barcode07 1 False 240s barcode08 30 False 240s barcode09 9945 True 240s barcode10 12644 True 240s barcode11 13594 True 240s barcode12 9813 True 240s unclassified 3971 False 240s General info 240s package_name: pycoQC 240s package_version: 2.5.2 240s timestamp: 2024-03-14 20:02:02.935901 240s 240s Runtime options 240s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 240s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 240s output_dir: results/ 240s output_unclassified: False 240s min_barcode_percent: 0.1 240s verbose: True 240s quiet: False 240s 240s Import data from sequencing summary file(s) and cleanup 240s Read files and import in a dataframe 240s Check input data files 240s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 240s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 240s Parse data files 240s Parse summary files 240s 3,999 reads found in initial file 240s Parse barcode files 240s Found valid Deepbinner barcode file 240s 3,775 reads with barcodes assigned 240s Merge data 240s Cleanup missing barcodes values 240s Cleaning up low frequency barcodes 240s Split data per barcode 240s Processing data for Barcode 1 240s Processing data for Barcode 2 240s Processing data for Barcode 3 240s Processing data for Barcode 4 240s Processing data for Barcode 5 240s Processing data for Barcode 6 240s Processing data for Barcode 7 240s Processing data for Barcode 8 240s Processing data for Barcode unclassified 240s Barcode Counts 240s Counts Write 240s 1 534 True 240s 2 206 True 240s 3 562 True 240s 4 579 True 240s 5 590 True 240s 6 655 True 240s 7 271 True 240s 8 378 True 240s unclassified 224 False 240s autopkgtest [20:02:03]: test run-unit-test: -----------------------] 240s run-unit-test PASS 240s autopkgtest [20:02:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 241s autopkgtest [20:02:04]: @@@@@@@@@@@@@@@@@@@@ summary 241s run-unit-test PASS 263s Creating nova instance adt-noble-ppc64el-pycoqc-20240314-195803-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240314.img (UUID 438daa89-732e-4eab-98ca-4d7eade8166d)...