0s autopkgtest [15:25:00]: starting date and time: 2024-03-23 15:25:00+0000 0s autopkgtest [15:25:00]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:25:00]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sqviirrs/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:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade pycoqc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-4.secgroup --name adt-noble-ppc64el-pycoqc-20240323-152459-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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/ 390s autopkgtest [15:31:30]: testbed dpkg architecture: ppc64el 390s autopkgtest [15:31:30]: testbed apt version: 2.7.12 390s autopkgtest [15:31:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 391s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 391s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 393s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 393s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 393s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 393s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 393s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 393s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 393s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 393s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 394s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 394s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 394s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 397s Fetched 9623 kB in 3s (2785 kB/s) 397s Reading package lists... 400s Reading package lists... 400s Building dependency tree... 400s Reading state information... 400s Calculating upgrade... 400s The following packages will be REMOVED: 400s libssl3 400s The following NEW packages will be installed: 400s libssl3t64 400s The following packages have been kept back: 400s curl 400s The following packages will be upgraded: 400s openssl 400s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 400s Need to get 3151 kB of archives. 400s After this operation, 73.7 kB of additional disk space will be used. 400s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 401s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 401s Fetched 3151 kB in 1s (4474 kB/s) 401s (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 ... 70156 files and directories currently installed.) 401s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 401s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 401s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 401s wget depends on libssl3 (>= 3.0.0). 401s tnftp depends on libssl3 (>= 3.0.0). 401s tcpdump depends on libssl3 (>= 3.0.0). 401s systemd-resolved depends on libssl3 (>= 3.0.0). 401s systemd depends on libssl3 (>= 3.0.0). 401s sudo depends on libssl3 (>= 3.0.0). 401s rsync depends on libssl3 (>= 3.0.0). 401s python3-cryptography depends on libssl3 (>= 3.0.0). 401s openssh-server depends on libssl3 (>= 3.0.10). 401s openssh-client depends on libssl3 (>= 3.0.10). 401s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 401s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 401s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 401s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 401s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 401s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 401s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 401s libnvme1 depends on libssl3 (>= 3.0.0). 401s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 401s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 401s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 401s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 401s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 401s kmod depends on libssl3 (>= 3.0.0). 401s dhcpcd-base depends on libssl3 (>= 3.0.0). 401s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 401s 402s (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 ... 70156 files and directories currently installed.) 402s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 402s Selecting previously unselected package libssl3t64:ppc64el. 402s (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 ... 70145 files and directories currently installed.) 402s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 402s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 402s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 402s Setting up openssl (3.0.13-0ubuntu2) ... 402s Processing triggers for man-db (2.12.0-3) ... 402s Processing triggers for libc-bin (2.39-0ubuntu6) ... 402s Reading package lists... 403s Building dependency tree... 403s Reading state information... 403s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 404s sh: Attempting to set up Debian/Ubuntu apt sources automatically 404s sh: Distribution appears to be Ubuntu 404s Reading package lists... 405s Building dependency tree... 405s Reading state information... 405s eatmydata is already the newest version (131-1). 405s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 405s Reading package lists... 405s Building dependency tree... 405s Reading state information... 405s dbus is already the newest version (1.14.10-4ubuntu1). 405s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 405s Reading package lists... 405s Building dependency tree... 405s Reading state information... 406s rng-tools-debian is already the newest version (2.4). 406s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 406s Reading package lists... 406s Building dependency tree... 406s Reading state information... 406s The following packages will be REMOVED: 406s cloud-init* python3-configobj* python3-debconf* 406s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 406s After this operation, 3256 kB disk space will be freed. 406s (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 ... 70158 files and directories currently installed.) 406s Removing cloud-init (24.1.2-0ubuntu1) ... 407s Removing python3-configobj (5.0.8-3) ... 407s Removing python3-debconf (1.5.86) ... 407s Processing triggers for man-db (2.12.0-3) ... 407s (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 ... 69769 files and directories currently installed.) 407s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 408s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 408s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 408s invoke-rc.d: policy-rc.d denied execution of try-restart. 408s Reading package lists... 408s Building dependency tree... 408s Reading state information... 408s linux-generic is already the newest version (6.8.0-11.11+1). 408s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 409s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 409s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 409s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 412s Reading package lists... 412s Reading package lists... 412s Building dependency tree... 412s Reading state information... 412s Calculating upgrade... 412s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 412s Reading package lists... 412s Building dependency tree... 412s Reading state information... 413s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 413s autopkgtest [15:31:53]: rebooting testbed after setup commands that affected boot 457s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 464s autopkgtest [15:32:44]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 467s autopkgtest [15:32:47]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 470s Get:1 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 470s Get:2 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 470s Get:3 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 470s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 470s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 470s gpgv: issuer "tille@debian.org" 470s gpgv: Can't check signature: No public key 470s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 473s autopkgtest [15:32:53]: testing package pycoqc version 2.5.2+dfsg-3 473s autopkgtest [15:32:53]: build not needed 522s autopkgtest [15:33:42]: test run-unit-test: preparing testbed 526s Reading package lists... 526s Building dependency tree... 526s Reading state information... 526s Starting pkgProblemResolver with broken count: 0 526s Starting 2 pkgProblemResolver with broken count: 0 526s Done 527s The following additional packages will be installed: 527s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1 libhdf5-hl-100 527s libhts3 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 527s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 527s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 527s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 527s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 527s Suggested packages: 527s python-fastjsonschema-doc python-h5py-doc python3-pip gcc gfortran 527s python3-dev python3-pytest python-pandas-doc python3-statsmodels 527s python3-matplotlib ipython3 python3-ipykernel python-scipy-doc 527s python-tenacity-doc 527s Recommended packages: 527s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 527s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 527s g++ | c++-compiler python3-pil 527s The following NEW packages will be installed: 527s autopkgtest-satdep libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1 527s libhdf5-hl-100 libhts3 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 527s pycoqc python3-dateutil python3-decorator python3-fastjsonschema 527s python3-h5py python3-h5py-serial python3-jupyter-core python3-nbformat 527s python3-numpy python3-pandas python3-pandas-lib python3-platformdirs 527s python3-plotly python3-pysam python3-scipy python3-tenacity python3-tqdm 527s python3-traitlets 527s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 527s Need to get 54.1 MB/54.1 MB of archives. 527s After this operation, 352 MB of additional disk space will be used. 527s Get:1 /tmp/autopkgtest.nxc1lp/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 527s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 527s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 527s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 527s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 528s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 528s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 528s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 528s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 528s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 528s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 529s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 529s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 529s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 530s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu1 [1635 kB] 530s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 530s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 530s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 531s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 531s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-fastjsonschema all 2.19.0-1 [19.6 kB] 531s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-platformdirs all 4.2.0-1 [16.1 kB] 531s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-traitlets all 5.5.0-2 [85.0 kB] 531s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-jupyter-core all 5.3.2-1ubuntu1 [25.5 kB] 531s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-nbformat all 5.9.1-1 [41.2 kB] 531s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tenacity all 8.2.3-2 [14.8 kB] 531s Get:26 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-plotly all 5.15.0+dfsg1-1 [2222 kB] 531s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 531s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 532s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-tqdm all 4.64.1-2 [95.2 kB] 532s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py all 3.10.0-1ubuntu1 [7970 B] 532s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el pycoqc all 2.5.2+dfsg-3 [36.4 kB] 532s Fetched 54.1 MB in 5s (10.8 MB/s) 532s Selecting previously unselected package libaec0:ppc64el. 532s (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 ... 69714 files and directories currently installed.) 532s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ... 532s Unpacking libaec0:ppc64el (1.1.2-1) ... 532s Selecting previously unselected package libblas3:ppc64el. 532s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 532s Unpacking libblas3:ppc64el (3.12.0-3) ... 532s Selecting previously unselected package libdeflate0:ppc64el. 532s Preparing to unpack .../02-libdeflate0_1.19-1_ppc64el.deb ... 532s Unpacking libdeflate0:ppc64el (1.19-1) ... 532s Selecting previously unselected package libgfortran5:ppc64el. 532s Preparing to unpack .../03-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 532s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 532s Selecting previously unselected package libsz2:ppc64el. 532s Preparing to unpack .../04-libsz2_1.1.2-1_ppc64el.deb ... 532s Unpacking libsz2:ppc64el (1.1.2-1) ... 532s Selecting previously unselected package libhdf5-103-1:ppc64el. 532s Preparing to unpack .../05-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 532s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 532s Selecting previously unselected package libhdf5-hl-100:ppc64el. 532s Preparing to unpack .../06-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 532s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 532s Selecting previously unselected package libhtscodecs2:ppc64el. 532s Preparing to unpack .../07-libhtscodecs2_1.6.0-1_ppc64el.deb ... 532s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 532s Selecting previously unselected package libhts3:ppc64el. 532s Preparing to unpack .../08-libhts3_1.18+ds-1_ppc64el.deb ... 532s Unpacking libhts3:ppc64el (1.18+ds-1) ... 532s Selecting previously unselected package liblapack3:ppc64el. 532s Preparing to unpack .../09-liblapack3_3.12.0-3_ppc64el.deb ... 532s Unpacking liblapack3:ppc64el (3.12.0-3) ... 532s Selecting previously unselected package liblbfgsb0:ppc64el. 532s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 532s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 532s Selecting previously unselected package liblzf1:ppc64el. 532s Preparing to unpack .../11-liblzf1_3.6-4_ppc64el.deb ... 532s Unpacking liblzf1:ppc64el (3.6-4) ... 533s Selecting previously unselected package python3-numpy. 533s Preparing to unpack .../12-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 533s Unpacking python3-numpy (1:1.24.2-2) ... 533s Selecting previously unselected package python3-h5py-serial. 533s Preparing to unpack .../13-python3-h5py-serial_3.10.0-1ubuntu1_ppc64el.deb ... 533s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 533s Selecting previously unselected package python3-dateutil. 533s Preparing to unpack .../14-python3-dateutil_2.8.2-3_all.deb ... 533s Unpacking python3-dateutil (2.8.2-3) ... 533s Selecting previously unselected package python3-pandas-lib:ppc64el. 533s Preparing to unpack .../15-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 533s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 533s Selecting previously unselected package python3-pandas. 533s Preparing to unpack .../16-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 533s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 534s Selecting previously unselected package python3-decorator. 534s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ... 534s Unpacking python3-decorator (5.1.1-5) ... 534s Selecting previously unselected package python3-fastjsonschema. 534s Preparing to unpack .../18-python3-fastjsonschema_2.19.0-1_all.deb ... 534s Unpacking python3-fastjsonschema (2.19.0-1) ... 534s Selecting previously unselected package python3-platformdirs. 534s Preparing to unpack .../19-python3-platformdirs_4.2.0-1_all.deb ... 534s Unpacking python3-platformdirs (4.2.0-1) ... 534s Selecting previously unselected package python3-traitlets. 534s Preparing to unpack .../20-python3-traitlets_5.5.0-2_all.deb ... 534s Unpacking python3-traitlets (5.5.0-2) ... 534s Selecting previously unselected package python3-jupyter-core. 534s Preparing to unpack .../21-python3-jupyter-core_5.3.2-1ubuntu1_all.deb ... 534s Unpacking python3-jupyter-core (5.3.2-1ubuntu1) ... 534s Selecting previously unselected package python3-nbformat. 534s Preparing to unpack .../22-python3-nbformat_5.9.1-1_all.deb ... 534s Unpacking python3-nbformat (5.9.1-1) ... 534s Selecting previously unselected package python3-tenacity. 534s Preparing to unpack .../23-python3-tenacity_8.2.3-2_all.deb ... 534s Unpacking python3-tenacity (8.2.3-2) ... 534s Selecting previously unselected package python3-plotly. 534s Preparing to unpack .../24-python3-plotly_5.15.0+dfsg1-1_all.deb ... 534s Unpacking python3-plotly (5.15.0+dfsg1-1) ... 537s Selecting previously unselected package python3-pysam. 537s Preparing to unpack .../25-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 537s Unpacking python3-pysam (0.22.0+ds-1) ... 537s Selecting previously unselected package python3-scipy. 537s Preparing to unpack .../26-python3-scipy_1.11.4-6_ppc64el.deb ... 537s Unpacking python3-scipy (1.11.4-6) ... 538s Selecting previously unselected package python3-tqdm. 538s Preparing to unpack .../27-python3-tqdm_4.64.1-2_all.deb ... 538s Unpacking python3-tqdm (4.64.1-2) ... 538s Selecting previously unselected package python3-h5py. 538s Preparing to unpack .../28-python3-h5py_3.10.0-1ubuntu1_all.deb ... 538s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 538s Selecting previously unselected package pycoqc. 538s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-3_all.deb ... 538s Unpacking pycoqc (2.5.2+dfsg-3) ... 538s Selecting previously unselected package autopkgtest-satdep. 538s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 538s Unpacking autopkgtest-satdep (0) ... 538s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 538s Setting up python3-tenacity (8.2.3-2) ... 538s Setting up python3-tqdm (4.64.1-2) ... 538s Setting up libdeflate0:ppc64el (1.19-1) ... 538s Setting up libaec0:ppc64el (1.1.2-1) ... 538s Setting up python3-platformdirs (4.2.0-1) ... 538s Setting up python3-decorator (5.1.1-5) ... 538s Setting up libblas3:ppc64el (3.12.0-3) ... 538s 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 538s Setting up liblzf1:ppc64el (3.6-4) ... 538s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 538s Setting up python3-fastjsonschema (2.19.0-1) ... 538s Setting up python3-traitlets (5.5.0-2) ... 539s Setting up python3-dateutil (2.8.2-3) ... 539s Setting up python3-jupyter-core (5.3.2-1ubuntu1) ... 539s Setting up libsz2:ppc64el (1.1.2-1) ... 539s Setting up liblapack3:ppc64el (3.12.0-3) ... 539s 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 539s Setting up libhts3:ppc64el (1.18+ds-1) ... 539s Setting up python3-pysam (0.22.0+ds-1) ... 539s Setting up python3-nbformat (5.9.1-1) ... 539s Setting up python3-plotly (5.15.0+dfsg1-1) ... 550s Setting up python3-numpy (1:1.24.2-2) ... 552s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 552s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 552s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 552s Setting up python3-scipy (1.11.4-6) ... 556s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 556s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 557s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 562s Setting up python3-h5py (3.10.0-1ubuntu1) ... 562s Setting up pycoqc (2.5.2+dfsg-3) ... 563s Setting up autopkgtest-satdep (0) ... 563s Processing triggers for man-db (2.12.0-3) ... 563s Processing triggers for libc-bin (2.39-0ubuntu6) ... 566s (Reading database ... 88542 files and directories currently installed.) 566s Removing autopkgtest-satdep (0) ... 568s autopkgtest [15:34:27]: test run-unit-test: [----------------------- 568s Test 1 569s Checking arguments values 569s Check input data files 569s Parse data files 569s Merge data 569s Cleaning data 569s Loading plotting interface 570s PASS 570s 570s Test 2 570s Checking arguments values 570s Check input data files 570s Parse data files 570s Merge data 570s Cleaning data 571s Loading plotting interface 571s PASS 571s 571s Test 3 572s Checking arguments values 572s Check input data files 572s Parse data files 572s Merge data 572s Cleaning data 572s Loading plotting interface 573s PASS 573s 573s Test 4 573s Checking arguments values 573s Check input data files 573s Parse data files 574s Merge data 574s Cleaning data 574s Loading plotting interface 575s PASS 575s 575s Test 5 575s Checking arguments values 575s Check input data files 575s Parse data files 575s Merge data 575s Cleaning data 575s Loading plotting interface 576s PASS 576s 576s Test 6 577s PASS 577s 577s Test 7 577s Checking arguments values 577s Check input data files 577s Parse data files 577s Merge data 577s Cleaning data 577s Loading plotting interface 578s PASS 578s 578s Test 8 579s 0 reads [00:00, ? reads/s] 22 reads [00:00, 499.35 reads/s] 579s Total reads: 22 / Average speed: 363.1 reads/s 579s 579s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 579s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 579s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out 579s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out 579s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 579s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 579s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 579s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 579s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 579s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 579s PASS 579s 579s Test 9 580s Check input data and options 580s Start processing fast5 files 580s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1318.96 reads/s] 580s Overall counts valid files: 22 580s 580s fields found mean_qscore_template: 22 580s called_events: 22 580s duration: 22 580s strand_score: 22 580s 580s fields not found 580s Total reads: 22 / Average speed: 552.49 reads/s 580s 580s mean_qscore_template called_events duration strand_score 580s 8.56 5838 87570 -0.0003 580s 8.544 3740 56107 -0.0003 580s 7.608 1615 24233 -0.0007 580s 8.304 1547 23218 -0.0008 580s 7.881 1513 24541 -0.0007 580s 7.414 3017 45267 -0.0002 580s 8.23 2778 51387 -0.0007 580s 8.741 3117 46767 -0.0006 580s 9.407 2848 42730 -0.0003 580s PASS 580s 580s Test 10 580s Check input data and options 580s Start processing fast5 files 580s 0 reads [00:00, ? reads/s] 22 reads [00:00, 529.09 reads/s] 580s Overall counts valid files: 22 580s 580s fields found read_id: 22 580s run_id: 22 580s channel: 22 580s start_time: 22 580s sequence_length_template: 22 580s mean_qscore_template: 22 580s calibration_strand_genome_template: 22 580s 580s fields not found barcode_arrangement: 22 580s 580s Total reads: 22 / Average speed: 388.37 reads/s 580s 580s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 580s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 580s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_237_strand.fast5 580s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_301_strand.fast5 580s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 580s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 580s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 580s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 580s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_290_strand.fast5 580s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.nxc1lp/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 580s PASS 580s 580s Test 11 581s Import data from sequencing summary file(s) and cleanup 581s Read files and import in a dataframe 581s Check input data files 581s Parse data files 582s Merge data 582s Cleanup missing barcodes values 582s Cleaning up low frequency barcodes 582s Split data per barcode 582s Processing data for Barcode barcode02 582s Processing data for Barcode barcode07 582s Processing data for Barcode barcode08 582s Processing data for Barcode barcode09 582s Processing data for Barcode barcode10 582s Processing data for Barcode barcode11 582s Processing data for Barcode barcode12 582s Processing data for Barcode unclassified 582s Barcode Counts 582s Counts Write 582s barcode02 2 False 582s barcode07 1 False 582s barcode08 30 False 582s barcode09 9945 True 582s barcode10 12644 True 582s barcode11 13594 True 582s barcode12 9813 True 582s unclassified 3971 False 582s PASS 582s 582s Test 12 583s General info 583s package_name: pycoQC 583s package_version: 2.5.2 583s timestamp: 2024-03-23 15:34:43.445361 583s 583s Runtime options 583s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 583s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 583s output_dir: results/ 583s output_unclassified: False 583s min_barcode_percent: 0.1 583s verbose: True 583s quiet: False 583s 583s Import data from sequencing summary file(s) and cleanup 583s Read files and import in a dataframe 583s Check input data files 583s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 583s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 583s Parse data files 583s Parse summary files 583s 3,999 reads found in initial file 583s Parse barcode files 583s Found valid Deepbinner barcode file 583s 3,775 reads with barcodes assigned 583s Merge data 583s Cleanup missing barcodes values 583s Cleaning up low frequency barcodes 583s Split data per barcode 583s Processing data for Barcode 1 583s Processing data for Barcode 2 583s Processing data for Barcode 3 583s Processing data for Barcode 4 583s Processing data for Barcode 5 583s Processing data for Barcode 6 583s Processing data for Barcode 7 583s Processing data for Barcode 8 583s Processing data for Barcode unclassified 583s Barcode Counts 583s Counts Write 583s 1 534 True 583s 2 206 True 583s 3 562 True 583s 4 579 True 583s 5 590 True 583s 6 655 True 583s 7 271 True 583s 8 378 True 583s unclassified 224 False 583s PASS 583s 583s Check if files really exist 583s PASS 583s 583s autopkgtest [15:34:43]: test run-unit-test: -----------------------] 584s autopkgtest [15:34:44]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 584s run-unit-test PASS 584s autopkgtest [15:34:44]: @@@@@@@@@@@@@@@@@@@@ summary 584s run-unit-test PASS 616s Creating nova instance adt-noble-ppc64el-pycoqc-20240323-152459-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...