0s autopkgtest [01:03:21]: starting date and time: 2024-11-14 01:03:21+0000 0s autopkgtest [01:03:21]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [01:03:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w_ay27hp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-iow --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-13.secgroup --name adt-plucky-amd64-python-iow-20241114-010321-juju-7f2275-prod-proposed-migration-environment-15-f585707d-3375-4f9e-8d2c-58c04f7862b5 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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,keyserver.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/ 1197s autopkgtest [01:23:18]: testbed dpkg architecture: amd64 1197s autopkgtest [01:23:18]: testbed apt version: 2.9.8 1197s autopkgtest [01:23:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1198s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1198s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1198s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [990 kB] 1199s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.6 kB] 1199s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 1199s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [75.0 kB] 1199s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [133 kB] 1199s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 1199s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [735 kB] 1199s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [282 kB] 1199s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [38.8 kB] 1199s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.3 kB] 1199s Fetched 2497 kB in 1s (2786 kB/s) 1199s Reading package lists... 1201s Reading package lists... 1201s Building dependency tree... 1201s Reading state information... 1202s Calculating upgrade... 1202s The following NEW packages will be installed: 1202s python3.13-gdbm 1202s The following packages will be upgraded: 1202s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libgpgme11t64 1202s libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 libpython3-stdlib 1202s libutempter0 python3 python3-bpfcc python3-gdbm python3-minimal python3-newt 1202s whiptail 1202s 16 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1202s Need to get 4731 kB of archives. 1202s After this operation, 608 kB of additional disk space will be used. 1202s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 1202s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 1202s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 1202s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls30t64 amd64 3.8.8-2ubuntu1 [1085 kB] 1202s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-2ubuntu4 [21.4 kB] 1202s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-2ubuntu4 [55.4 kB] 1202s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-2ubuntu4 [19.0 kB] 1202s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 1202s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 1202s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libbpfcc amd64 0.30.0+ds-1ubuntu5 [680 kB] 1202s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 1202s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 1203s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftrace amd64 0.21.2-2ubuntu2 [1791 kB] 1203s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 1203s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 1203s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-glib-1.0-0 amd64 1.10.0+ds-3 [73.1 kB] 1203s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libutempter0 amd64 1.2.1-4 [9694 B] 1203s Fetched 4731 kB in 1s (5877 kB/s) 1203s (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 ... 75541 files and directories currently installed.) 1203s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 1203s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 1203s Setting up python3-minimal (3.12.7-1) ... 1203s (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 ... 75541 files and directories currently installed.) 1203s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 1203s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1203s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 1203s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1203s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_amd64.deb ... 1203s Unpacking libgnutls30t64:amd64 (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 1203s Setting up libgnutls30t64:amd64 (3.8.8-2ubuntu1) ... 1203s (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 ... 75541 files and directories currently installed.) 1203s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_amd64.deb ... 1204s Unpacking python3-newt:amd64 (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 1204s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_amd64.deb ... 1204s Unpacking libnewt0.52:amd64 (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 1204s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_amd64.deb ... 1204s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 1204s Selecting previously unselected package python3.13-gdbm. 1204s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_amd64.deb ... 1204s Unpacking python3.13-gdbm (3.13.0-2) ... 1204s Preparing to unpack .../04-python3-gdbm_3.12.7-1_amd64.deb ... 1204s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 1204s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_amd64.deb ... 1204s Unpacking libbpfcc:amd64 (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 1204s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 1204s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 1204s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 1204s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 1204s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_amd64.deb ... 1204s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 1204s Preparing to unpack .../09-libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 1204s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 1204s Preparing to unpack .../10-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 1204s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 1204s Preparing to unpack .../11-libjson-glib-1.0-0_1.10.0+ds-3_amd64.deb ... 1204s Unpacking libjson-glib-1.0-0:amd64 (1.10.0+ds-3) over (1.10.0+ds-2) ... 1204s Preparing to unpack .../12-libutempter0_1.2.1-4_amd64.deb ... 1204s Unpacking libutempter0:amd64 (1.2.1-4) over (1.2.1-3build1) ... 1204s Setting up libnewt0.52:amd64 (0.52.24-2ubuntu4) ... 1204s Setting up libutempter0:amd64 (1.2.1-4) ... 1204s Setting up whiptail (0.52.24-2ubuntu4) ... 1204s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 1204s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 1204s Setting up libbpfcc:amd64 (0.30.0+ds-1ubuntu5) ... 1204s Setting up python3.13-gdbm (3.13.0-2) ... 1204s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 1204s Setting up bpftrace (0.21.2-2ubuntu2) ... 1204s Setting up python3 (3.12.7-1) ... 1204s Setting up python3-newt:amd64 (0.52.24-2ubuntu4) ... 1204s Setting up libjson-glib-1.0-0:amd64 (1.10.0+ds-3) ... 1204s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 1205s Setting up python3-gdbm:amd64 (3.12.7-1) ... 1205s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 1205s Processing triggers for man-db (2.12.1-3) ... 1205s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1206s Reading package lists... 1206s Building dependency tree... 1206s Reading state information... 1206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1207s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1207s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1208s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1208s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1208s Reading package lists... 1208s Reading package lists... 1209s Building dependency tree... 1209s Reading state information... 1209s Calculating upgrade... 1209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1209s Reading package lists... 1209s Building dependency tree... 1209s Reading state information... 1209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1212s autopkgtest [01:23:33]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 1212s autopkgtest [01:23:33]: @@@@@@@@@@@@@@@@@@@@ apt-source python-iow 1214s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-iow 1.0.7-1 (dsc) [2353 B] 1214s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-iow 1.0.7-1 (tar) [160 kB] 1214s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-iow 1.0.7-1 (diff) [4720 B] 1214s gpgv: Signature made Sat Aug 31 10:16:19 2024 UTC 1214s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 1214s gpgv: issuer "emollier@debian.org" 1214s gpgv: Can't check signature: No public key 1214s dpkg-source: warning: cannot verify inline signature for ./python-iow_1.0.7-1.dsc: no acceptable signature found 1214s autopkgtest [01:23:35]: testing package python-iow version 1.0.7-1 1215s autopkgtest [01:23:36]: build not needed 1217s autopkgtest [01:23:38]: test run-unit-test: preparing testbed 1218s Reading package lists... 1218s Building dependency tree... 1218s Reading state information... 1218s Starting pkgProblemResolver with broken count: 0 1218s Starting 2 pkgProblemResolver with broken count: 0 1218s Done 1218s The following additional packages will be installed: 1218s libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 libhdf5-hl-100t64 1218s liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib 1218s libssw0 libsz2 python3-all python3-biom-format python3-click 1218s python3-colorama python3-dateutil python3-decorator python3-h5py 1218s python3-h5py-serial python3-hdmedians python3-iow python3-natsort 1218s python3-numpy python3-packaging python3-pandas python3-pandas-lib 1218s python3-patsy python3-scipy python3-six python3-skbio python3-statsmodels 1218s python3-statsmodels-lib python3-tz python3.13 python3.13-minimal 1218s Suggested packages: 1218s python-biom-format-doc python-h5py-doc python-natsort-doc gcc gfortran 1218s python-numpy-doc python3-dev python3-pytest python-pandas-doc 1218s python-patsy-doc python-scipy-doc python-skbio-doc python-statsmodels-doc 1218s python3.13-venv python3.13-doc binfmt-support 1218s Recommended packages: 1218s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 1218s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 1218s python3-numba g++ | c++-compiler python3-pil python3-joblib python3-cvxopt 1218s The following NEW packages will be installed: 1218s autopkgtest-satdep libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 1218s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal 1218s libpython3.13-stdlib libssw0 libsz2 python3-all python3-biom-format 1218s python3-click python3-colorama python3-dateutil python3-decorator 1218s python3-h5py python3-h5py-serial python3-hdmedians python3-iow 1218s python3-natsort python3-numpy python3-packaging python3-pandas 1218s python3-pandas-lib python3-patsy python3-scipy python3-six python3-skbio 1218s python3-statsmodels python3-statsmodels-lib python3-tz python3.13 1218s python3.13-minimal 1218s 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. 1218s Need to get 52.7 MB/52.7 MB of archives. 1218s After this operation, 237 MB of additional disk space will be used. 1218s Get:1 /tmp/autopkgtest.vHJ2vn/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 1219s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 1219s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 1219s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 1219s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 1219s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 1219s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 1219s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 1219s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 1219s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 1219s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 1219s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1219s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 1219s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 1220s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw0 amd64 1.1-15 [22.5 kB] 1220s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 1220s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 1220s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 1220s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 1220s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 1220s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 1220s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 1220s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 1220s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 1220s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 1220s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 1220s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 1220s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1220s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 1221s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1 [141 kB] 1221s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hdmedians amd64 0.14.2-5.1build1 [124 kB] 1221s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 1221s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 1221s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-patsy all 0.5.6-1 [181 kB] 1221s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-statsmodels-lib amd64 0.14.4+dfsg-1 [1783 kB] 1221s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-statsmodels all 0.14.4+dfsg-1 [5010 kB] 1221s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-skbio amd64 0.6.2-3 [1407 kB] 1221s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iow amd64 1.0.7-1 [448 kB] 1221s Fetched 52.7 MB in 3s (20.8 MB/s) 1221s Selecting previously unselected package libpython3.13-minimal:amd64. 1221s (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 ... 75549 files and directories currently installed.) 1221s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 1221s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 1221s Selecting previously unselected package python3.13-minimal. 1221s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 1221s Unpacking python3.13-minimal (3.13.0-2) ... 1221s Selecting previously unselected package libaec0:amd64. 1221s Preparing to unpack .../02-libaec0_1.1.3-1_amd64.deb ... 1221s Unpacking libaec0:amd64 (1.1.3-1) ... 1221s Selecting previously unselected package libblas3:amd64. 1221s Preparing to unpack .../03-libblas3_3.12.0-3build2_amd64.deb ... 1221s Unpacking libblas3:amd64 (3.12.0-3build2) ... 1221s Selecting previously unselected package libgfortran5:amd64. 1221s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 1221s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 1221s Selecting previously unselected package libgomp1:amd64. 1221s Preparing to unpack .../05-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 1221s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 1222s Selecting previously unselected package libsz2:amd64. 1222s Preparing to unpack .../06-libsz2_1.1.3-1_amd64.deb ... 1222s Unpacking libsz2:amd64 (1.1.3-1) ... 1222s Selecting previously unselected package libhdf5-103-1t64:amd64. 1222s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 1222s Unpacking 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python3-tz (2024.1-2) ... 1222s Selecting previously unselected package python3-pandas-lib:amd64. 1222s Preparing to unpack .../24-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 1222s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 1222s Selecting previously unselected package python3-pandas. 1222s Preparing to unpack .../25-python3-pandas_2.2.3+dfsg-5_all.deb ... 1222s Unpacking python3-pandas (2.2.3+dfsg-5) ... 1223s Selecting previously unselected package python3-decorator. 1223s Preparing to unpack .../26-python3-decorator_5.1.1-5_all.deb ... 1223s Unpacking python3-decorator (5.1.1-5) ... 1223s Selecting previously unselected package python3-scipy. 1223s Preparing to unpack .../27-python3-scipy_1.13.1-5_amd64.deb ... 1223s Unpacking python3-scipy (1.13.1-5) ... 1223s Selecting previously unselected package python3-biom-format. 1223s Preparing to unpack .../28-python3-biom-format_2.1.16-1_amd64.deb ... 1223s Unpacking python3-biom-format (2.1.16-1) ... 1223s Selecting previously unselected package python3-hdmedians. 1223s Preparing to unpack .../29-python3-hdmedians_0.14.2-5.1build1_amd64.deb ... 1223s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 1223s Selecting previously unselected package python3-natsort. 1223s Preparing to unpack .../30-python3-natsort_8.0.2-2_all.deb ... 1223s Unpacking python3-natsort (8.0.2-2) ... 1223s Selecting previously unselected package python3-packaging. 1223s Preparing to unpack .../31-python3-packaging_24.1-1_all.deb ... 1223s Unpacking python3-packaging (24.1-1) ... 1223s Selecting previously unselected package python3-patsy. 1223s Preparing to unpack .../32-python3-patsy_0.5.6-1_all.deb ... 1223s Unpacking python3-patsy (0.5.6-1) ... 1223s Selecting previously unselected package python3-statsmodels-lib:amd64. 1223s Preparing to unpack .../33-python3-statsmodels-lib_0.14.4+dfsg-1_amd64.deb ... 1223s Unpacking python3-statsmodels-lib:amd64 (0.14.4+dfsg-1) ... 1224s Selecting previously unselected package python3-statsmodels. 1224s Preparing to unpack .../34-python3-statsmodels_0.14.4+dfsg-1_all.deb ... 1224s Unpacking python3-statsmodels (0.14.4+dfsg-1) ... 1224s Selecting previously unselected package python3-skbio. 1224s Preparing to unpack .../35-python3-skbio_0.6.2-3_amd64.deb ... 1224s Unpacking python3-skbio (0.6.2-3) ... 1224s Selecting previously unselected package python3-iow. 1224s Preparing to unpack .../36-python3-iow_1.0.7-1_amd64.deb ... 1224s Unpacking python3-iow (1.0.7-1) ... 1224s Selecting previously unselected package autopkgtest-satdep. 1224s Preparing to unpack .../37-1-autopkgtest-satdep.deb ... 1224s Unpacking autopkgtest-satdep (0) ... 1224s Setting up python3-colorama (0.4.6-4) ... 1224s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 1224s Setting up python3-click (8.1.7-2) ... 1224s Setting up libaec0:amd64 (1.1.3-1) ... 1224s Setting up python3-tz (2024.1-2) ... 1225s Setting up python3-natsort (8.0.2-2) ... 1225s Setting up python3-six (1.16.0-7) ... 1225s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 1225s Setting up python3-decorator (5.1.1-5) ... 1225s Setting up libblas3:amd64 (3.12.0-3build2) ... 1225s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 1225s Setting up python3-packaging (24.1-1) ... 1225s Setting up liblzf1:amd64 (3.6-4) ... 1225s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 1225s Setting up python3.13-minimal (3.13.0-2) ... 1226s Setting up python3-dateutil (2.9.0-2) ... 1226s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 1226s Setting up libssw0:amd64 (1.1-15) ... 1226s Setting up libsz2:amd64 (1.1.3-1) ... 1226s Setting up liblapack3:amd64 (3.12.0-3build2) ... 1226s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 1226s Setting up python3.13 (3.13.0-2) ... 1227s Setting up python3-all (3.12.7-1) ... 1227s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 1230s Setting up python3-hdmedians (0.14.2-5.1build1) ... 1230s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 1230s Setting up python3-statsmodels-lib:amd64 (0.14.4+dfsg-1) ... 1230s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1230s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 1230s Setting up python3-scipy (1.13.1-5) ... 1235s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 1235s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 1235s Setting up python3-patsy (0.5.6-1) ... 1236s Setting up python3-pandas (2.2.3+dfsg-5) ... 1243s Setting up python3-h5py (3.11.0-5ubuntu1) ... 1243s Setting up python3-statsmodels (0.14.4+dfsg-1) ... 1247s Setting up python3-biom-format (2.1.16-1) ... 1247s Setting up python3-skbio (0.6.2-3) ... 1248s Setting up python3-iow (1.0.7-1) ... 1248s Setting up autopkgtest-satdep (0) ... 1248s Processing triggers for systemd (256.5-2ubuntu4) ... 1248s Processing triggers for man-db (2.12.1-3) ... 1249s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1251s (Reading database ... 83199 files and directories currently installed.) 1251s Removing autopkgtest-satdep (0) ... 1252s autopkgtest [01:24:13]: test run-unit-test: [----------------------- 1252s EEEE 1252s ====================================================================== 1252s ERROR: tests.test_bp (unittest.loader._FailedTest.tests.test_bp) 1252s ---------------------------------------------------------------------- 1252s ImportError: Failed to import test module: tests.test_bp 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1252s from . import multiarray 1252s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1252s from . import overrides 1252s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1252s from numpy.core._multiarray_umath import ( 1252s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1252s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1252s 1252s During handling of the above exception, another exception occurred: 1252s 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1252s from numpy.__config__ import show as show_config 1252s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1252s from numpy.core._multiarray_umath import ( 1252s ...<3 lines>... 1252s ) 1252s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1252s raise ImportError(msg) 1252s ImportError: 1252s 1252s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1252s 1252s Importing the numpy C-extensions failed. This error can happen for 1252s many reasons, often due to issues with your setup or how NumPy was 1252s installed. 1252s 1252s We have compiled some common reasons and troubleshooting tips at: 1252s 1252s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1252s 1252s Please note and check the following: 1252s 1252s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1252s * The NumPy version is: "1.26.4" 1252s 1252s and make sure that they are the versions you expect. 1252s Please carefully study the documentation linked above for further help. 1252s 1252s Original error was: No module named 'numpy.core._multiarray_umath' 1252s 1252s 1252s The above exception was the direct cause of the following exception: 1252s 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 1252s module = self._get_module_from_name(name) 1252s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 1252s __import__(name) 1252s ~~~~~~~~~~^^^^^^ 1252s File "/tmp/autopkgtest.vHJ2vn/autopkgtest_tmp/tests/tests/test_bp.py", line 14, in 1252s import numpy as np 1252s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1252s raise ImportError(msg) from e 1252s ImportError: Error importing numpy: you should not try to import numpy from 1252s its source directory; please exit the numpy source tree, and relaunch 1252s your python interpreter from there. 1252s 1252s 1252s ====================================================================== 1252s ERROR: tests.test_conv (unittest.loader._FailedTest.tests.test_conv) 1252s ---------------------------------------------------------------------- 1252s ImportError: Failed to import test module: tests.test_conv 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 1252s from . import _debian_h5py_serial as _h5py 1252s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 1252s from . import _errors 1252s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 1252s 1252s During handling of the above exception, another exception occurred: 1252s 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 1252s module = self._get_module_from_name(name) 1252s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 1252s __import__(name) 1252s ~~~~~~~~~~^^^^^^ 1252s File "/tmp/autopkgtest.vHJ2vn/autopkgtest_tmp/tests/tests/test_conv.py", line 4, in 1252s import skbio 1252s File "/usr/lib/python3/dist-packages/skbio/__init__.py", line 12, in 1252s import skbio.io # noqa 1252s ^^^^^^^^^^^^^^^ 1252s File "/usr/lib/python3/dist-packages/skbio/io/__init__.py", line 251, in 1252s from .registry import write, read, sniff, create_format, io_registry 1252s File "/usr/lib/python3/dist-packages/skbio/io/registry.py", line 181, in 1252s from .util import _resolve_file, open_file, open_files, _d as _open_kwargs 1252s File "/usr/lib/python3/dist-packages/skbio/io/util.py", line 32, in 1252s from skbio.io._iosources import get_io_sources, get_compression_handler 1252s File "/usr/lib/python3/dist-packages/skbio/io/_iosources.py", line 18, in 1252s from ._fileobject import ( 1252s ...<3 lines>... 1252s ) 1252s File "/usr/lib/python3/dist-packages/skbio/io/_fileobject.py", line 10, in 1252s import h5py 1252s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 1252s from . import _debian_h5py_mpi as _h5py 1252s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 1252s 1252s 1252s ====================================================================== 1252s ERROR: tests.test_insert (unittest.loader._FailedTest.tests.test_insert) 1252s ---------------------------------------------------------------------- 1252s ImportError: Failed to import test module: tests.test_insert 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 1252s module = self._get_module_from_name(name) 1252s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 1252s __import__(name) 1252s ~~~~~~~~~~^^^^^^ 1252s File "/tmp/autopkgtest.vHJ2vn/autopkgtest_tmp/tests/tests/test_insert.py", line 3, in 1252s from bp import parse_jplace, insert_fully_resolved 1252s File "/usr/lib/python3/dist-packages/bp/__init__.py", line 8, in 1252s from ._bp import BP 1252s ModuleNotFoundError: No module named 'bp._bp' 1252s 1252s 1252s ====================================================================== 1252s ERROR: tests.test_io (unittest.loader._FailedTest.tests.test_io) 1252s ---------------------------------------------------------------------- 1252s ImportError: Failed to import test module: tests.test_io 1252s Traceback (most recent call last): 1252s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 1252s module = self._get_module_from_name(name) 1252s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 1252s __import__(name) 1252s ~~~~~~~~~~^^^^^^ 1252s File "/tmp/autopkgtest.vHJ2vn/autopkgtest_tmp/tests/tests/test_io.py", line 2, in 1252s from bp import parse_newick, to_skbio_treenode, write_newick, parse_jplace 1252s File "/usr/lib/python3/dist-packages/bp/__init__.py", line 8, in 1252s from ._bp import BP 1252s ModuleNotFoundError: No module named 'bp._bp' 1252s 1252s 1252s ---------------------------------------------------------------------- 1252s Ran 4 tests in 0.000s 1252s 1252s FAILED (errors=4) 1253s .........................................../usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'e' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'f' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'g' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name None does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'l' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'a' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'b' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'd' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'c' does not have an associated length, so a length of 0.0 will be used. 1253s warn( 1253s ... 1253s ---------------------------------------------------------------------- 1253s Ran 46 tests in 0.172s 1253s 1253s OK 1254s autopkgtest [01:24:15]: test run-unit-test: -----------------------] 1254s autopkgtest [01:24:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1254s run-unit-test PASS 1255s autopkgtest [01:24:16]: @@@@@@@@@@@@@@@@@@@@ summary 1255s run-unit-test PASS 1745s nova [W] Skipping flock for amd64 1745s Creating nova instance adt-plucky-amd64-python-iow-20241114-010321-juju-7f2275-prod-proposed-migration-environment-15-f585707d-3375-4f9e-8d2c-58c04f7862b5 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)... 1745s nova [E] Timed out waiting for cc7ed314-268d-47bc-8ec7-0aca97b23e82 to get deleted. 1745s nova [E] Timed out waiting for cc7ed314-268d-47bc-8ec7-0aca97b23e82 to get deleted. 1745s nova [E] Timed out waiting for cc7ed314-268d-47bc-8ec7-0aca97b23e82 to get deleted.