0s autopkgtest [17:06:56]: starting date and time: 2024-03-24 17:06:56+0000 0s autopkgtest [17:06:56]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:06:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y3l7pob8/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-2@bos02-arm64-11.secgroup --name adt-noble-arm64-pycoqc-20240324-170656-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/ 116s autopkgtest [17:08:52]: testbed dpkg architecture: arm64 116s autopkgtest [17:08:52]: testbed apt version: 2.7.12 116s autopkgtest [17:08:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 119s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 119s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 119s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 119s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 119s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 119s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 119s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 119s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 120s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 120s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 120s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 130s Fetched 9850 kB in 5s (2028 kB/s) 131s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 139s Calculating upgrade... 140s The following packages will be REMOVED: 140s libssl3 140s The following NEW packages will be installed: 140s libssl3t64 140s The following packages have been kept back: 140s curl 140s The following packages will be upgraded: 140s openssl 140s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 140s Need to get 2777 kB of archives. 140s After this operation, 139 kB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 142s Fetched 2777 kB in 1s (3614 kB/s) 142s (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.) 142s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 142s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 143s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 143s wget depends on libssl3 (>= 3.0.0). 143s u-boot-tools depends on libssl3 (>= 3.0.0). 143s tnftp depends on libssl3 (>= 3.0.0). 143s tcpdump depends on libssl3 (>= 3.0.0). 143s systemd-resolved depends on libssl3 (>= 3.0.0). 143s systemd depends on libssl3 (>= 3.0.0). 143s sudo depends on libssl3 (>= 3.0.0). 143s sbsigntool depends on libssl3 (>= 3.0.0). 143s rsync depends on libssl3 (>= 3.0.0). 143s python3-cryptography depends on libssl3 (>= 3.0.0). 143s openssh-server depends on libssl3 (>= 3.0.10). 143s openssh-client depends on libssl3 (>= 3.0.10). 143s mtd-utils depends on libssl3 (>= 3.0.0). 143s mokutil depends on libssl3 (>= 3.0.0). 143s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 143s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 143s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 143s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 143s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 143s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 143s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 143s libnvme1 depends on libssl3 (>= 3.0.0). 143s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 143s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 143s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 143s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 143s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 143s kmod depends on libssl3 (>= 3.0.0). 143s dhcpcd-base depends on libssl3 (>= 3.0.0). 143s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 143s 143s (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.) 143s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 143s Selecting previously unselected package libssl3t64:arm64. 143s (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 ... 75900 files and directories currently installed.) 143s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 143s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 143s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 143s Setting up openssl (3.0.13-0ubuntu2) ... 143s Processing triggers for man-db (2.12.0-3) ... 145s Processing triggers for libc-bin (2.39-0ubuntu6) ... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 150s sh: Attempting to set up Debian/Ubuntu apt sources automatically 150s sh: Distribution appears to be Ubuntu 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s eatmydata is already the newest version (131-1). 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 157s dbus is already the newest version (1.14.10-4ubuntu1). 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 159s rng-tools-debian is already the newest version (2.4). 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 161s The following packages will be REMOVED: 161s cloud-init* python3-configobj* python3-debconf* 162s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 162s After this operation, 3256 kB disk space will be freed. 163s (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 ... 75913 files and directories currently installed.) 163s Removing cloud-init (24.1.2-0ubuntu1) ... 165s Removing python3-configobj (5.0.8-3) ... 165s Removing python3-debconf (1.5.86) ... 165s Processing triggers for man-db (2.12.0-3) ... 166s (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 ... 75524 files and directories currently installed.) 166s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 169s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 169s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 169s invoke-rc.d: policy-rc.d denied execution of try-restart. 169s Reading package lists... 170s Building dependency tree... 170s Reading state information... 172s linux-generic is already the newest version (6.8.0-11.11+1). 172s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 172s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 172s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 181s Reading package lists... 181s Reading package lists... 182s Building dependency tree... 182s Reading state information... 183s Calculating upgrade... 184s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 184s Reading package lists... 185s Building dependency tree... 185s Reading state information... 187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s autopkgtest [17:10:03]: rebooting testbed after setup commands that affected boot 350s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 360s autopkgtest [17:12:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 363s autopkgtest [17:12:59]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 371s Get:1 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 371s Get:2 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 371s Get:3 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 372s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 372s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 372s gpgv: issuer "tille@debian.org" 372s gpgv: Can't check signature: No public key 372s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 377s autopkgtest [17:13:13]: testing package pycoqc version 2.5.2+dfsg-3 378s autopkgtest [17:13:14]: build not needed 383s autopkgtest [17:13:19]: test run-unit-test: preparing testbed 392s Reading package lists... 393s Building dependency tree... 393s Reading state information... 394s Starting pkgProblemResolver with broken count: 0 394s Starting 2 pkgProblemResolver with broken count: 0 394s Done 395s The following additional packages will be installed: 395s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1 libhdf5-hl-100 395s libhts3 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 395s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 395s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 395s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 395s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 395s Suggested packages: 395s python-fastjsonschema-doc python-h5py-doc python3-pip gcc gfortran 395s python3-dev python3-pytest python-pandas-doc python3-statsmodels 395s python3-matplotlib ipython3 python3-ipykernel python-scipy-doc 395s python-tenacity-doc 395s Recommended packages: 395s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 395s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 395s g++ | c++-compiler python3-pil 396s The following NEW packages will be installed: 396s autopkgtest-satdep libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1 396s libhdf5-hl-100 libhts3 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 396s pycoqc python3-dateutil python3-decorator python3-fastjsonschema 396s python3-h5py python3-h5py-serial python3-jupyter-core python3-nbformat 396s python3-numpy python3-pandas python3-pandas-lib python3-platformdirs 396s python3-plotly python3-pysam python3-scipy python3-tenacity python3-tqdm 396s python3-traitlets 396s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 396s Need to get 47.0 MB/47.0 MB of archives. 396s After this operation, 293 MB of additional disk space will be used. 396s Get:1 /tmp/autopkgtest.hB7u0g/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 396s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 396s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 396s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 396s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 396s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 396s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 397s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 397s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 397s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 397s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 397s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 397s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 397s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 398s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 398s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 398s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 398s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 399s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 399s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fastjsonschema all 2.19.0-1 [19.6 kB] 399s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-platformdirs all 4.2.0-1 [16.1 kB] 399s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] 399s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-core all 5.3.2-1ubuntu1 [25.5 kB] 399s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 399s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tenacity all 8.2.3-2 [14.8 kB] 399s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-plotly all 5.15.0+dfsg1-1 [2222 kB] 399s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 399s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 400s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tqdm all 4.64.1-2 [95.2 kB] 400s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 400s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 pycoqc all 2.5.2+dfsg-3 [36.4 kB] 402s Fetched 47.0 MB in 5s (9966 kB/s) 402s Selecting previously unselected package libaec0:arm64. 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 ... 75469 files and directories currently installed.) 402s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 402s Unpacking libaec0:arm64 (1.1.2-1) ... 402s Selecting previously unselected package libblas3:arm64. 402s Preparing to unpack .../01-libblas3_3.12.0-3_arm64.deb ... 402s Unpacking libblas3:arm64 (3.12.0-3) ... 403s Selecting previously unselected package libdeflate0:arm64. 403s Preparing to unpack .../02-libdeflate0_1.19-1_arm64.deb ... 403s Unpacking libdeflate0:arm64 (1.19-1) ... 403s Selecting previously unselected package libgfortran5:arm64. 403s Preparing to unpack .../03-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 403s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 403s Selecting previously unselected package libsz2:arm64. 403s Preparing to unpack .../04-libsz2_1.1.2-1_arm64.deb ... 403s Unpacking libsz2:arm64 (1.1.2-1) ... 403s Selecting previously unselected package libhdf5-103-1:arm64. 403s Preparing to unpack .../05-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 403s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 403s Selecting previously unselected package libhdf5-hl-100:arm64. 403s Preparing to unpack .../06-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 403s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 403s Selecting previously unselected package libhtscodecs2:arm64. 403s Preparing to unpack .../07-libhtscodecs2_1.6.0-1_arm64.deb ... 403s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 403s Selecting previously unselected package libhts3:arm64. 403s Preparing to unpack .../08-libhts3_1.18+ds-1_arm64.deb ... 403s Unpacking libhts3:arm64 (1.18+ds-1) ... 404s Selecting previously unselected package liblapack3:arm64. 404s Preparing to unpack .../09-liblapack3_3.12.0-3_arm64.deb ... 404s Unpacking liblapack3:arm64 (3.12.0-3) ... 404s Selecting previously unselected package liblbfgsb0:arm64. 404s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 404s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 404s Selecting previously unselected package liblzf1:arm64. 404s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 404s Unpacking liblzf1:arm64 (3.6-4) ... 404s Selecting previously unselected package python3-numpy. 404s Preparing to unpack .../12-python3-numpy_1%3a1.24.2-2_arm64.deb ... 404s Unpacking python3-numpy (1:1.24.2-2) ... 406s Selecting previously unselected package python3-h5py-serial. 406s Preparing to unpack .../13-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ... 406s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 406s Selecting previously unselected package python3-dateutil. 406s Preparing to unpack .../14-python3-dateutil_2.8.2-3_all.deb ... 406s Unpacking python3-dateutil (2.8.2-3) ... 406s Selecting previously unselected package python3-pandas-lib:arm64. 406s Preparing to unpack .../15-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 406s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 407s Selecting previously unselected package python3-pandas. 407s Preparing to unpack .../16-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 407s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 409s Selecting previously unselected package python3-decorator. 409s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ... 409s Unpacking python3-decorator (5.1.1-5) ... 409s Selecting previously unselected package python3-fastjsonschema. 409s Preparing to unpack .../18-python3-fastjsonschema_2.19.0-1_all.deb ... 409s Unpacking python3-fastjsonschema (2.19.0-1) ... 409s Selecting previously unselected package python3-platformdirs. 409s Preparing to unpack .../19-python3-platformdirs_4.2.0-1_all.deb ... 409s Unpacking python3-platformdirs (4.2.0-1) ... 409s Selecting previously unselected package python3-traitlets. 409s Preparing to unpack .../20-python3-traitlets_5.5.0-2_all.deb ... 409s Unpacking python3-traitlets (5.5.0-2) ... 410s Selecting previously unselected package python3-jupyter-core. 410s Preparing to unpack .../21-python3-jupyter-core_5.3.2-1ubuntu1_all.deb ... 410s Unpacking python3-jupyter-core (5.3.2-1ubuntu1) ... 410s Selecting previously unselected package python3-nbformat. 410s Preparing to unpack .../22-python3-nbformat_5.9.1-1_all.deb ... 410s Unpacking python3-nbformat (5.9.1-1) ... 410s Selecting previously unselected package python3-tenacity. 410s Preparing to unpack .../23-python3-tenacity_8.2.3-2_all.deb ... 410s Unpacking python3-tenacity (8.2.3-2) ... 410s Selecting previously unselected package python3-plotly. 410s Preparing to unpack .../24-python3-plotly_5.15.0+dfsg1-1_all.deb ... 410s Unpacking python3-plotly (5.15.0+dfsg1-1) ... 420s Selecting previously unselected package python3-pysam. 420s Preparing to unpack .../25-python3-pysam_0.22.0+ds-1_arm64.deb ... 420s Unpacking python3-pysam (0.22.0+ds-1) ... 422s Selecting previously unselected package python3-scipy. 422s Preparing to unpack .../26-python3-scipy_1.11.4-6_arm64.deb ... 422s Unpacking python3-scipy (1.11.4-6) ... 426s Selecting previously unselected package python3-tqdm. 426s Preparing to unpack .../27-python3-tqdm_4.64.1-2_all.deb ... 426s Unpacking python3-tqdm (4.64.1-2) ... 426s Selecting previously unselected package python3-h5py. 427s Preparing to unpack .../28-python3-h5py_3.10.0-1ubuntu1_all.deb ... 427s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 427s Selecting previously unselected package pycoqc. 427s Preparing to unpack .../29-pycoqc_2.5.2+dfsg-3_all.deb ... 427s Unpacking pycoqc (2.5.2+dfsg-3) ... 427s Selecting previously unselected package autopkgtest-satdep. 427s Preparing to unpack .../30-1-autopkgtest-satdep.deb ... 427s Unpacking autopkgtest-satdep (0) ... 427s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 427s Setting up python3-tenacity (8.2.3-2) ... 427s Setting up python3-tqdm (4.64.1-2) ... 428s Setting up libdeflate0:arm64 (1.19-1) ... 428s Setting up libaec0:arm64 (1.1.2-1) ... 428s Setting up python3-platformdirs (4.2.0-1) ... 429s Setting up python3-decorator (5.1.1-5) ... 429s Setting up libblas3:arm64 (3.12.0-3) ... 429s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 429s Setting up liblzf1:arm64 (3.6-4) ... 429s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 429s Setting up python3-fastjsonschema (2.19.0-1) ... 430s Setting up python3-traitlets (5.5.0-2) ... 431s Setting up python3-dateutil (2.8.2-3) ... 431s Setting up python3-jupyter-core (5.3.2-1ubuntu1) ... 432s Setting up libsz2:arm64 (1.1.2-1) ... 432s Setting up liblapack3:arm64 (3.12.0-3) ... 432s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 432s Setting up libhts3:arm64 (1.18+ds-1) ... 432s Setting up python3-pysam (0.22.0+ds-1) ... 432s Setting up python3-nbformat (5.9.1-1) ... 433s Setting up python3-plotly (5.15.0+dfsg1-1) ... 462s Setting up python3-numpy (1:1.24.2-2) ... 469s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 469s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 469s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 469s Setting up python3-scipy (1.11.4-6) ... 480s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 480s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 481s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 498s Setting up python3-h5py (3.10.0-1ubuntu1) ... 498s Setting up pycoqc (2.5.2+dfsg-3) ... 499s Setting up autopkgtest-satdep (0) ... 499s Processing triggers for man-db (2.12.0-3) ... 500s Processing triggers for libc-bin (2.39-0ubuntu6) ... 508s (Reading database ... 94297 files and directories currently installed.) 508s Removing autopkgtest-satdep (0) ... 509s autopkgtest [17:15:25]: test run-unit-test: [----------------------- 511s Test 1 513s Checking arguments values 513s Check input data files 513s Parse data files 513s Merge data 513s Cleaning data 513s Loading plotting interface 516s PASS 516s 516s Test 2 518s Checking arguments values 518s Check input data files 518s Parse data files 519s Merge data 519s Cleaning data 519s Loading plotting interface 522s PASS 522s 522s Test 3 524s Checking arguments values 524s Check input data files 524s Parse data files 524s Merge data 524s Cleaning data 524s Loading plotting interface 527s PASS 527s 527s Test 4 529s Checking arguments values 529s Check input data files 529s Parse data files 530s Merge data 530s Cleaning data 530s Loading plotting interface 533s PASS 533s 533s Test 5 535s Checking arguments values 535s Check input data files 535s Parse data files 536s Merge data 536s Cleaning data 536s Loading plotting interface 539s PASS 539s 539s Test 6 541s PASS 541s 541s Test 7 543s Checking arguments values 543s Check input data files 543s Parse data files 543s Merge data 543s Cleaning data 543s Loading plotting interface 547s PASS 547s 547s Test 8 549s 0 reads [00:00, ? reads/s] 15 reads [00:00, 147.22 reads/s] 22 reads [00:00, 142.12 reads/s] 549s Total reads: 22 / Average speed: 87.51 reads/s 549s 550s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 550s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 550s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out 550s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 550s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 550s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 550s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 550s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 550s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out 550s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out 550s PASS 550s 550s Test 9 552s Check input data and options 552s Start processing fast5 files 552s 0 reads [00:00, ? reads/s] 22 reads [00:00, 227.85 reads/s] 552s Overall counts valid files: 22 552s 552s fields found mean_qscore_template: 22 552s called_events: 22 552s duration: 22 552s strand_score: 22 552s 552s fields not found 552s Total reads: 22 / Average speed: 109.97 reads/s 552s 553s mean_qscore_template called_events duration strand_score 553s 8.304 1547 23218 -0.0008 553s 8.234 1827 27409 -0.0011 553s 8.119 3181 47720 -0.0004 553s 8.23 2778 51387 -0.0007 553s 7.414 3017 45267 -0.0002 553s 8.544 3740 56107 -0.0003 553s 7.881 1513 24541 -0.0007 553s 9.407 2848 42730 -0.0003 553s 7.805 1438 21583 -0.0006 553s PASS 553s 553s Test 10 555s Check input data and options 555s Start processing fast5 files 555s 0 reads [00:00, ? reads/s] 14 reads [00:00, 138.98 reads/s] 22 reads [00:00, 139.43 reads/s] 555s Overall counts valid files: 22 555s 555s fields found read_id: 22 555s run_id: 22 555s channel: 22 555s start_time: 22 555s sequence_length_template: 22 555s mean_qscore_template: 22 555s calibration_strand_genome_template: 22 555s 555s fields not found barcode_arrangement: 22 555s 555s Total reads: 22 / Average speed: 87.16 reads/s 555s 556s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 556s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 556s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 556s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_36_strand.fast5 556s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 556s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 556s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 556s 2c32553e-62c6-4c7a-bf05-249771364f04 40ebe55356ada6c830fa793745ef4c498d896c73 237 11 1151 8.544 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_237_strand.fast5 556s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 556s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out /tmp/autopkgtest.hB7u0g/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_354_strand.fast5 556s PASS 556s 556s Test 11 558s Import data from sequencing summary file(s) and cleanup 558s Read files and import in a dataframe 558s Check input data files 558s Parse data files 559s Merge data 559s Cleanup missing barcodes values 559s Cleaning up low frequency barcodes 559s Split data per barcode 559s Processing data for Barcode barcode02 559s Processing data for Barcode barcode07 559s Processing data for Barcode barcode08 559s Processing data for Barcode barcode09 560s Processing data for Barcode barcode10 560s Processing data for Barcode barcode11 561s Processing data for Barcode barcode12 561s Processing data for Barcode unclassified 561s Barcode Counts 561s Counts Write 561s barcode02 2 False 561s barcode07 1 False 561s barcode08 30 False 561s barcode09 9945 True 561s barcode10 12644 True 561s barcode11 13594 True 561s barcode12 9813 True 561s unclassified 3971 False 562s PASS 562s 562s Test 12 564s General info 564s package_name: pycoQC 564s package_version: 2.5.2 564s timestamp: 2024-03-24 17:16:20.361187 564s 564s Runtime options 564s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 564s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 564s output_dir: results/ 564s output_unclassified: False 564s min_barcode_percent: 0.1 564s verbose: True 564s quiet: False 564s 564s Import data from sequencing summary file(s) and cleanup 564s Read files and import in a dataframe 564s Check input data files 564s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 564s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 564s Parse data files 564s Parse summary files 564s 3,999 reads found in initial file 564s Parse barcode files 564s Found valid Deepbinner barcode file 564s 3,775 reads with barcodes assigned 564s Merge data 564s Cleanup missing barcodes values 564s Cleaning up low frequency barcodes 564s Split data per barcode 564s Processing data for Barcode 1 564s Processing data for Barcode 2 564s Processing data for Barcode 3 564s Processing data for Barcode 4 564s Processing data for Barcode 5 564s Processing data for Barcode 6 564s Processing data for Barcode 7 564s Processing data for Barcode 8 564s Processing data for Barcode unclassified 564s Barcode Counts 564s Counts Write 564s 1 534 True 564s 2 206 True 564s 3 562 True 564s 4 579 True 564s 5 590 True 564s 6 655 True 564s 7 271 True 564s 8 378 True 564s unclassified 224 False 565s PASS 565s 565s Check if files really exist 565s PASS 565s 565s autopkgtest [17:16:21]: test run-unit-test: -----------------------] 566s autopkgtest [17:16:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 566s run-unit-test PASS 566s autopkgtest [17:16:22]: @@@@@@@@@@@@@@@@@@@@ summary 566s run-unit-test PASS 579s Creating nova instance adt-noble-arm64-pycoqc-20240324-170656-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...