0s autopkgtest [23:25:27]: starting date and time: 2024-03-24 23:25:27+0000 0s autopkgtest [23:25:27]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [23:25:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7bw0t0rl/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade pyensembl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.2-0ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-3.secgroup --name adt-noble-i386-pyensembl-20240324-232527-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-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/ 923s autopkgtest [23:40:50]: testbed dpkg architecture: amd64 923s autopkgtest [23:40:50]: testbed apt version: 2.7.12 923s autopkgtest [23:40:50]: test architecture: i386 923s autopkgtest [23:40:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 923s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 923s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 923s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 923s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 923s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.5 kB] 923s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [490 kB] 923s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [727 kB] 923s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 923s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 923s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 923s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 923s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4420 kB] 923s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1300 kB] 923s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 923s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [29.9 kB] 923s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [98.2 kB] 923s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 927s Fetched 11.8 MB in 1s (8179 kB/s) 927s Reading package lists... 928s Reading package lists... 928s Building dependency tree... 928s Reading state information... 929s Calculating upgrade... 929s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 929s Reading package lists... 929s Building dependency tree... 929s Reading state information... 929s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 930s sh: Attempting to set up Debian/Ubuntu apt sources automatically 930s sh: Distribution appears to be Ubuntu 930s Reading package lists... 931s Building dependency tree... 931s Reading state information... 931s eatmydata is already the newest version (131-1). 931s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 931s Reading package lists... 931s Building dependency tree... 931s Reading state information... 931s dbus is already the newest version (1.14.10-4ubuntu1). 931s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 931s Reading package lists... 932s Building dependency tree... 932s Reading state information... 932s rng-tools-debian is already the newest version (2.4). 932s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 932s Reading package lists... 932s Building dependency tree... 932s Reading state information... 932s The following packages will be REMOVED: 932s cloud-init* python3-configobj* python3-debconf* 933s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 933s After this operation, 3256 kB disk space will be freed. 933s (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 ... 71864 files and directories currently installed.) 933s Removing cloud-init (24.1.2-0ubuntu1) ... 933s Removing python3-configobj (5.0.8-3) ... 933s Removing python3-debconf (1.5.86) ... 933s Processing triggers for man-db (2.12.0-3) ... 934s (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 ... 71475 files and directories currently installed.) 934s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 934s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 934s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 934s invoke-rc.d: policy-rc.d denied execution of try-restart. 935s Reading package lists... 935s Building dependency tree... 935s Reading state information... 935s linux-generic is already the newest version (6.8.0-11.11+1). 935s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 935s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 935s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 935s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 937s Reading package lists... 937s Reading package lists... 938s Building dependency tree... 938s Reading state information... 938s Calculating upgrade... 938s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 938s Reading package lists... 938s Building dependency tree... 938s Reading state information... 938s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 938s autopkgtest [23:41:05]: rebooting testbed after setup commands that affected boot 970s autopkgtest [23:41:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 970s autopkgtest [23:41:37]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 971s Get:1 http://ftpmaster.internal/ubuntu noble/universe pyensembl 2.3.9-2 (dsc) [2442 B] 971s Get:2 http://ftpmaster.internal/ubuntu noble/universe pyensembl 2.3.9-2 (tar) [60.2 kB] 971s Get:3 http://ftpmaster.internal/ubuntu noble/universe pyensembl 2.3.9-2 (diff) [5284 B] 971s gpgv: Signature made Wed Feb 28 21:08:10 2024 UTC 971s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 971s gpgv: issuer "emollier@debian.org" 971s gpgv: Can't check signature: No public key 971s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.9-2.dsc: no acceptable signature found 971s autopkgtest [23:41:38]: testing package pyensembl version 2.3.9-2 971s autopkgtest [23:41:38]: build not needed 972s autopkgtest [23:41:39]: test run-unit-test: preparing testbed 974s Note, using file '/tmp/autopkgtest.JO8XuK/1-autopkgtest-satdep.dsc' to get the build dependencies 974s Reading package lists... 974s Building dependency tree... 974s Reading state information... 974s Starting pkgProblemResolver with broken count: 0 974s Starting 2 pkgProblemResolver with broken count: 0 974s Done 975s The following NEW packages will be installed: 975s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++ 975s g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 975s gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libblas3 975s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgfortran5 975s libgomp1 libhwasan0 libisl23 libitm1 liblapack3 liblsan0 libmpc3 975s libquadmath0 libstdc++-13-dev libtsan2 libubsan1 linux-libc-dev pyensembl 975s pylint python3-all python3-appdirs python3-astroid python3-datacache 975s python3-dateutil python3-dill python3-gtfparse python3-importlib-metadata 975s python3-iniconfig python3-isort python3-logilab-common python3-mccabe 975s python3-memoized-property python3-more-itertools python3-mypy-extensions 975s python3-nose python3-numpy python3-packaging python3-pandas 975s python3-pandas-lib python3-platformdirs python3-pluggy python3-pytest 975s python3-serializable python3-simplejson python3-toml python3-tomlkit 975s python3-typechecks python3-zipp python3-zombie-imp rpcsvc-proto 975s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 975s Need to get 90.3 MB of archives. 975s After this operation, 377 MB of additional disk space will be used. 975s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] 975s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 975s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 975s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 975s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] 975s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 975s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 975s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 975s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 975s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 975s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 975s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 975s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 975s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 975s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 975s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 975s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 975s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 975s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 975s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 975s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 975s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 975s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 975s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 975s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 975s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 975s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 975s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 975s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 975s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 975s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 975s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 975s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 975s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 975s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 975s Get:36 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-astroid all 3.0.2-2 [174 kB] 975s Get:37 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 975s Get:38 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-isort all 5.6.4-1 [63.1 kB] 975s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 python3-more-itertools all 10.2.0-1 [52.9 kB] 975s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 python3-zipp all 1.0.0-6 [6090 B] 975s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] 975s Get:42 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-mypy-extensions all 1.0.0-1 [6148 B] 975s Get:43 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-logilab-common all 1.9.8-2 [280 kB] 975s Get:44 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-dill all 0.3.8-1 [83.0 kB] 975s Get:45 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-mccabe all 0.7.0-1 [8678 B] 975s Get:46 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-platformdirs all 4.2.0-1 [16.1 kB] 975s Get:47 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-tomlkit all 0.12.4-1 [37.5 kB] 975s Get:48 http://ftpmaster.internal/ubuntu noble/universe amd64 pylint all 3.0.3-1 [337 kB] 975s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 975s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 python3-dateutil all 2.8.2-3 [79.2 kB] 975s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 python3-numpy amd64 1:1.24.2-2 [7141 kB] 975s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-4ubuntu2 [8348 kB] 975s Get:53 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 975s Get:54 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-typechecks all 0.1.0+ds-3 [4440 B] 975s Get:55 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-datacache all 1.2.1-2 [12.8 kB] 975s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-gtfparse all 1.3.0+ds-1 [10.1 kB] 975s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-memoized-property all 1.0.3-2 [5286 B] 975s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 python3-simplejson amd64 3.19.2-1build1 [62.8 kB] 975s Get:59 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-serializable all 0.4.0+ds-1 [8210 B] 975s Get:60 http://ftpmaster.internal/ubuntu noble/universe amd64 pyensembl all 2.3.9-2 [36.8 kB] 975s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 python3-all amd64 3.12.1-0ubuntu2 [906 B] 975s Get:62 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 975s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-zombie-imp all 0.0.2-2 [11.9 kB] 975s Get:64 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-nose all 1.3.7-12 [117 kB] 975s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 python3-packaging all 23.2-1 [40.6 kB] 975s Get:66 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pluggy all 1.4.0-1 [20.4 kB] 975s Get:67 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 976s Fetched 90.3 MB in 1s (117 MB/s) 976s Selecting previously unselected package libc-dev-bin. 976s (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 ... 71420 files and directories currently installed.) 976s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu6_amd64.deb ... 976s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 976s Selecting previously unselected package linux-libc-dev:amd64. 976s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_amd64.deb ... 976s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 976s Selecting previously unselected package libcrypt-dev:amd64. 976s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 976s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 976s Selecting previously unselected package rpcsvc-proto. 976s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 976s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 976s Selecting previously unselected package libc6-dev:amd64. 976s Preparing to unpack .../04-libc6-dev_2.39-0ubuntu6_amd64.deb ... 976s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ... 976s Selecting previously unselected package libisl23:amd64. 976s Preparing to unpack .../05-libisl23_0.26-3_amd64.deb ... 976s Unpacking libisl23:amd64 (0.26-3) ... 976s Selecting previously unselected package libmpc3:amd64. 976s Preparing to unpack .../06-libmpc3_1.3.1-1_amd64.deb ... 976s Unpacking libmpc3:amd64 (1.3.1-1) ... 976s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 976s Preparing to unpack .../07-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 976s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 977s Selecting previously unselected package cpp-13. 977s Preparing to unpack .../08-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 977s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 977s Selecting previously unselected package cpp-x86-64-linux-gnu. 977s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 977s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 977s Selecting previously unselected package cpp. 977s Preparing to unpack .../10-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 977s Unpacking cpp (4:13.2.0-7ubuntu1) ... 977s Selecting previously unselected package libcc1-0:amd64. 977s Preparing to unpack .../11-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libgomp1:amd64. 977s Preparing to unpack .../12-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libitm1:amd64. 977s Preparing to unpack .../13-libitm1_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libatomic1:amd64. 977s Preparing to unpack .../14-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libasan8:amd64. 977s Preparing to unpack .../15-libasan8_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package liblsan0:amd64. 977s Preparing to unpack .../16-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libtsan2:amd64. 977s Preparing to unpack .../17-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libubsan1:amd64. 977s Preparing to unpack .../18-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libhwasan0:amd64. 977s Preparing to unpack .../19-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libquadmath0:amd64. 977s Preparing to unpack .../20-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 977s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 977s Selecting previously unselected package libgcc-13-dev:amd64. 977s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 977s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 977s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 977s Preparing to unpack .../22-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 977s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 978s Selecting previously unselected package gcc-13. 978s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 978s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 978s Selecting previously unselected package gcc-x86-64-linux-gnu. 978s Preparing to unpack .../24-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 978s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 978s Selecting previously unselected package gcc. 978s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 978s Unpacking gcc (4:13.2.0-7ubuntu1) ... 978s Selecting previously unselected package libstdc++-13-dev:amd64. 978s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 978s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 978s Selecting previously unselected package g++-13-x86-64-linux-gnu. 978s Preparing to unpack .../27-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 978s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 978s Selecting previously unselected package g++-13. 978s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_amd64.deb ... 978s Unpacking g++-13 (13.2.0-17ubuntu2) ... 978s Selecting previously unselected package g++-x86-64-linux-gnu. 978s Preparing to unpack .../29-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 978s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 978s Selecting previously unselected package g++. 978s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 978s Unpacking g++ (4:13.2.0-7ubuntu1) ... 978s Selecting previously unselected package build-essential. 978s Preparing to unpack .../31-build-essential_12.10ubuntu1_amd64.deb ... 978s Unpacking build-essential (12.10ubuntu1) ... 978s Selecting previously unselected package libblas3:amd64. 978s Preparing to unpack .../32-libblas3_3.12.0-3_amd64.deb ... 978s Unpacking libblas3:amd64 (3.12.0-3) ... 978s Selecting previously unselected package libgfortran5:amd64. 978s Preparing to unpack .../33-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 978s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 978s Selecting previously unselected package liblapack3:amd64. 978s Preparing to unpack .../34-liblapack3_3.12.0-3_amd64.deb ... 978s Unpacking liblapack3:amd64 (3.12.0-3) ... 978s Selecting previously unselected package python3-astroid. 978s Preparing to unpack .../35-python3-astroid_3.0.2-2_all.deb ... 978s Unpacking python3-astroid (3.0.2-2) ... 978s Selecting previously unselected package python3-toml. 978s Preparing to unpack .../36-python3-toml_0.10.2-1_all.deb ... 978s Unpacking python3-toml (0.10.2-1) ... 978s Selecting previously unselected package python3-isort. 978s Preparing to unpack .../37-python3-isort_5.6.4-1_all.deb ... 978s Unpacking python3-isort (5.6.4-1) ... 978s Selecting previously unselected package python3-more-itertools. 978s Preparing to unpack .../38-python3-more-itertools_10.2.0-1_all.deb ... 978s Unpacking python3-more-itertools (10.2.0-1) ... 978s Selecting previously unselected package python3-zipp. 978s Preparing to unpack .../39-python3-zipp_1.0.0-6_all.deb ... 978s Unpacking python3-zipp (1.0.0-6) ... 978s Selecting previously unselected package python3-importlib-metadata. 978s Preparing to unpack .../40-python3-importlib-metadata_4.12.0-1_all.deb ... 978s Unpacking python3-importlib-metadata (4.12.0-1) ... 978s Selecting previously unselected package python3-mypy-extensions. 978s Preparing to unpack .../41-python3-mypy-extensions_1.0.0-1_all.deb ... 978s Unpacking python3-mypy-extensions (1.0.0-1) ... 978s Selecting previously unselected package python3-logilab-common. 978s Preparing to unpack .../42-python3-logilab-common_1.9.8-2_all.deb ... 978s Unpacking python3-logilab-common (1.9.8-2) ... 978s Selecting previously unselected package python3-dill. 978s Preparing to unpack .../43-python3-dill_0.3.8-1_all.deb ... 978s Unpacking python3-dill (0.3.8-1) ... 978s Selecting previously unselected package python3-mccabe. 979s Preparing to unpack .../44-python3-mccabe_0.7.0-1_all.deb ... 979s Unpacking python3-mccabe (0.7.0-1) ... 979s Selecting previously unselected package python3-platformdirs. 979s Preparing to unpack .../45-python3-platformdirs_4.2.0-1_all.deb ... 979s Unpacking python3-platformdirs (4.2.0-1) ... 979s Selecting previously unselected package python3-tomlkit. 979s Preparing to unpack .../46-python3-tomlkit_0.12.4-1_all.deb ... 979s Unpacking python3-tomlkit (0.12.4-1) ... 979s Selecting previously unselected package pylint. 979s Preparing to unpack .../47-pylint_3.0.3-1_all.deb ... 979s Unpacking pylint (3.0.3-1) ... 979s Selecting previously unselected package python3-appdirs. 979s Preparing to unpack .../48-python3-appdirs_1.4.4-4_all.deb ... 979s Unpacking python3-appdirs (1.4.4-4) ... 979s Selecting previously unselected package python3-dateutil. 979s Preparing to unpack .../49-python3-dateutil_2.8.2-3_all.deb ... 979s Unpacking python3-dateutil (2.8.2-3) ... 979s Selecting previously unselected package python3-numpy. 979s Preparing to unpack .../50-python3-numpy_1%3a1.24.2-2_amd64.deb ... 979s Unpacking python3-numpy (1:1.24.2-2) ... 979s Selecting previously unselected package python3-pandas-lib:amd64. 979s Preparing to unpack .../51-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_amd64.deb ... 979s Unpacking python3-pandas-lib:amd64 (2.1.4+dfsg-4ubuntu2) ... 979s Selecting previously unselected package python3-pandas. 979s Preparing to unpack .../52-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 979s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 979s Selecting previously unselected package python3-typechecks. 979s Preparing to unpack .../53-python3-typechecks_0.1.0+ds-3_all.deb ... 979s Unpacking python3-typechecks (0.1.0+ds-3) ... 979s Selecting previously unselected package python3-datacache. 979s Preparing to unpack .../54-python3-datacache_1.2.1-2_all.deb ... 979s Unpacking python3-datacache (1.2.1-2) ... 980s Selecting previously unselected package python3-gtfparse. 980s Preparing to unpack .../55-python3-gtfparse_1.3.0+ds-1_all.deb ... 980s Unpacking python3-gtfparse (1.3.0+ds-1) ... 980s Selecting previously unselected package python3-memoized-property. 980s Preparing to unpack .../56-python3-memoized-property_1.0.3-2_all.deb ... 980s Unpacking python3-memoized-property (1.0.3-2) ... 980s Selecting previously unselected package python3-simplejson. 980s Preparing to unpack .../57-python3-simplejson_3.19.2-1build1_amd64.deb ... 980s Unpacking python3-simplejson (3.19.2-1build1) ... 980s Selecting previously unselected package python3-serializable. 980s Preparing to unpack .../58-python3-serializable_0.4.0+ds-1_all.deb ... 980s Unpacking python3-serializable (0.4.0+ds-1) ... 980s Selecting previously unselected package pyensembl. 980s Preparing to unpack .../59-pyensembl_2.3.9-2_all.deb ... 980s Unpacking pyensembl (2.3.9-2) ... 980s Selecting previously unselected package python3-all. 980s Preparing to unpack .../60-python3-all_3.12.1-0ubuntu2_amd64.deb ... 980s Unpacking python3-all (3.12.1-0ubuntu2) ... 980s Selecting previously unselected package python3-iniconfig. 980s Preparing to unpack .../61-python3-iniconfig_1.1.1-2_all.deb ... 980s Unpacking python3-iniconfig (1.1.1-2) ... 980s Selecting previously unselected package python3-zombie-imp. 980s Preparing to unpack .../62-python3-zombie-imp_0.0.2-2_all.deb ... 980s Unpacking python3-zombie-imp (0.0.2-2) ... 980s Selecting previously unselected package python3-nose. 980s Preparing to unpack .../63-python3-nose_1.3.7-12_all.deb ... 980s Unpacking python3-nose (1.3.7-12) ... 980s Selecting previously unselected package python3-packaging. 980s Preparing to unpack .../64-python3-packaging_23.2-1_all.deb ... 980s Unpacking python3-packaging (23.2-1) ... 980s Selecting previously unselected package python3-pluggy. 980s Preparing to unpack .../65-python3-pluggy_1.4.0-1_all.deb ... 980s Unpacking python3-pluggy (1.4.0-1) ... 980s Selecting previously unselected package python3-pytest. 980s Preparing to unpack .../66-python3-pytest_7.4.4-1_all.deb ... 980s Unpacking python3-pytest (7.4.4-1) ... 980s Setting up python3-more-itertools (10.2.0-1) ... 980s Setting up python3-iniconfig (1.1.1-2) ... 980s Setting up python3-zombie-imp (0.0.2-2) ... 980s Setting up python3-typechecks (0.1.0+ds-3) ... 980s Setting up python3-memoized-property (1.0.3-2) ... 980s Setting up python3-mypy-extensions (1.0.0-1) ... 980s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 980s Setting up python3-all (3.12.1-0ubuntu2) ... 980s Setting up python3-zipp (1.0.0-6) ... 980s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 980s Setting up python3-nose (1.3.7-12) ... 981s /usr/lib/python3/dist-packages/nose/config.py:142: SyntaxWarning: invalid escape sequence '\.' 981s """nose configuration. 981s /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:686: SyntaxWarning: invalid escape sequence '\S' 981s _INDENT_RE = re.compile('^([ ]*)(?=\S)', re.MULTILINE) 981s /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:1021: SyntaxWarning: invalid escape sequence '\s' 981s pat = re.compile('(^|.*:)\s*\w*("|\')') 981s /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:1430: SyntaxWarning: invalid escape sequence '\s' 981s want = re.sub('(?m)^%s\s*?$' % re.escape(BLANKLINE_MARKER), 981s /usr/lib/python3/dist-packages/nose/ext/dtcompat.py:1434: SyntaxWarning: invalid escape sequence '\s' 981s got = re.sub('(?m)^\s*?$', '', got) 981s /usr/lib/python3/dist-packages/nose/inspector.py:110: SyntaxWarning: invalid escape sequence '\ ' 981s """Find lines in home that are inspectable. 981s Setting up python3-platformdirs (4.2.0-1) ... 981s Setting up python3-simplejson (3.19.2-1build1) ... 981s Setting up libblas3:amd64 (3.12.0-3) ... 981s 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 981s Setting up python3-packaging (23.2-1) ... 981s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 981s Setting up python3-dill (0.3.8-1) ... 981s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 981s Setting up libmpc3:amd64 (1.3.1-1) ... 981s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 981s Setting up python3-toml (0.10.2-1) ... 981s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 981s Setting up python3-isort (5.6.4-1) ... 981s Setting up python3-pluggy (1.4.0-1) ... 982s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 982s Setting up python3-astroid (3.0.2-2) ... 982s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 982s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 982s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 982s Setting up python3-dateutil (2.8.2-3) ... 982s Setting up python3-mccabe (0.7.0-1) ... 982s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 982s Setting up libisl23:amd64 (0.26-3) ... 982s Setting up libc-dev-bin (2.39-0ubuntu6) ... 982s Setting up python3-tomlkit (0.12.4-1) ... 982s Setting up python3-appdirs (1.4.4-4) ... 982s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 982s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 982s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 982s Setting up liblapack3:amd64 (3.12.0-3) ... 982s 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 982s Setting up python3-importlib-metadata (4.12.0-1) ... 982s Setting up python3-logilab-common (1.9.8-2) ... 982s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 982s Setting up python3-pytest (7.4.4-1) ... 983s Setting up python3-serializable (0.4.0+ds-1) ... 983s Setting up python3-numpy (1:1.24.2-2) ... 984s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 984s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... 984s Setting up pylint (3.0.3-1) ... 985s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 985s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 985s Setting up cpp-13 (13.2.0-17ubuntu2) ... 985s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 985s Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-4ubuntu2) ... 985s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 988s Setting up gcc-13 (13.2.0-17ubuntu2) ... 988s Setting up cpp (4:13.2.0-7ubuntu1) ... 988s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 988s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 988s Setting up python3-datacache (1.2.1-2) ... 988s /usr/lib/python3/dist-packages/datacache/common.py:48: SyntaxWarning: invalid escape sequence '\?' 988s filename = re.sub("/|\\|;|:|\?|=", "_", filename) 988s Setting up python3-gtfparse (1.3.0+ds-1) ... 988s Setting up gcc (4:13.2.0-7ubuntu1) ... 988s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 988s Setting up pyensembl (2.3.9-2) ... 989s Setting up g++-13 (13.2.0-17ubuntu2) ... 989s Setting up g++ (4:13.2.0-7ubuntu1) ... 989s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 989s Setting up build-essential (12.10ubuntu1) ... 989s Processing triggers for man-db (2.12.0-3) ... 989s Processing triggers for libc-bin (2.39-0ubuntu6) ... 990s Reading package lists... 991s Building dependency tree... 991s Reading state information... 991s Starting pkgProblemResolver with broken count: 0 991s Starting 2 pkgProblemResolver with broken count: 0 991s Done 992s The following NEW packages will be installed: 992s autopkgtest: WARNING: package pyensembl:i386 is not installed though it should be 992s autopkgtest-satdep 992s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 992s Need to get 0 B/696 B of archives. 992s After this operation, 0 B of additional disk space will be used. 992s Get:1 /tmp/autopkgtest.JO8XuK/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 992s Selecting previously unselected package autopkgtest-satdep. 992s (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 ... 78205 files and directories currently installed.) 992s Preparing to unpack .../2-autopkgtest-satdep.deb ... 992s Unpacking autopkgtest-satdep (0) ... 992s Setting up autopkgtest-satdep (0) ... 993s (Reading database ... 78205 files and directories currently installed.) 993s Removing autopkgtest-satdep (0) ... 993s autopkgtest [23:42:00]: test run-unit-test: [----------------------- 994s ============================= test session starts ============================== 994s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 994s rootdir: /tmp/autopkgtest.JO8XuK/autopkgtest_tmp 994s collected 15 items 994s 994s tests/test_ensembl_object_properties.py . [ 6%] 994s tests/test_locus.py ...... [ 46%] 994s tests/test_release_versions.py ....... [ 93%] 994s tests/test_shell.py . [100%] 994s 994s =============================== warnings summary =============================== 994s ../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 994s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 994s EPOCH = datetime.datetime.utcfromtimestamp(0) 994s 994s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 994s /usr/lib/python3/dist-packages/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 994s import pkg_resources 994s 994s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871 994s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 994s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 994s declare_namespace(pkg) 994s 994s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:65 994s /usr/lib/python3/dist-packages/pyensembl/shell.py:65: DeprecationWarning: Nesting argument groups is deprecated. 994s release_group = root_group.add_argument_group() 994s 994s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:87 994s /usr/lib/python3/dist-packages/pyensembl/shell.py:87: DeprecationWarning: Nesting argument groups is deprecated. 994s path_group = root_group.add_argument_group() 994s 994s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 994s ======================== 15 passed, 5 warnings in 0.66s ======================== 994s autopkgtest [23:42:01]: test run-unit-test: -----------------------] 995s autopkgtest [23:42:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 995s run-unit-test PASS 995s autopkgtest [23:42:02]: test pybuild-autopkgtest: preparing testbed 996s Note, using file '/tmp/autopkgtest.JO8XuK/3-autopkgtest-satdep.dsc' to get the build dependencies 996s Reading package lists... 996s Building dependency tree... 997s Reading state information... 997s Starting pkgProblemResolver with broken count: 0 997s Starting 2 pkgProblemResolver with broken count: 0 997s Done 997s The following NEW packages will be installed: 997s autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf 997s dh-python dh-strip-nondeterminism dwz gettext intltool-debian 997s libarchive-zip-perl libdebhelper-perl libdw1 997s libfile-stripnondeterminism-perl libsub-override-perl libtool m4 po-debconf 997s pybuild-plugin-autopkgtest 997s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 997s Need to get 4523 kB of archives. 997s After this operation, 13.3 MB of additional disk space will be used. 997s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] 997s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] 997s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] 997s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 997s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14ubuntu1 [422 kB] 997s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 997s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] 997s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] 997s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 997s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] 997s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 997s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] 997s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1 amd64 0.190-1 [260 kB] 997s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] 997s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 dwz amd64 0.15-1 [112 kB] 997s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14ubuntu1 [864 kB] 997s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 997s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 997s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 debhelper all 13.14.1ubuntu1 [869 kB] 997s Get:20 http://ftpmaster.internal/ubuntu noble/universe amd64 dh-python all 6.20231223ubuntu2 [111 kB] 997s Get:21 http://ftpmaster.internal/ubuntu noble/universe amd64 pybuild-plugin-autopkgtest all 6.20231223ubuntu2 [1760 B] 997s Fetched 4523 kB in 0s (42.9 MB/s) 997s Selecting previously unselected package m4. 998s (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 ... 78205 files and directories currently installed.) 998s Preparing to unpack .../00-m4_1.4.19-4_amd64.deb ... 998s Unpacking m4 (1.4.19-4) ... 998s Selecting previously unselected package autoconf. 998s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 998s Unpacking autoconf (2.71-3) ... 998s Selecting previously unselected package autotools-dev. 998s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 998s Unpacking autotools-dev (20220109.1) ... 998s Selecting previously unselected package automake. 998s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 998s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 998s Selecting previously unselected package autopoint. 998s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 998s Unpacking autopoint (0.21-14ubuntu1) ... 998s Selecting previously unselected package libdebhelper-perl. 998s Preparing to unpack .../05-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 998s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 998s Selecting previously unselected package libtool. 998s Preparing to unpack .../06-libtool_2.4.7-7_all.deb ... 998s Unpacking libtool (2.4.7-7) ... 998s Selecting previously unselected package dh-autoreconf. 998s Preparing to unpack .../07-dh-autoreconf_20_all.deb ... 998s Unpacking dh-autoreconf (20) ... 998s Selecting previously unselected package libarchive-zip-perl. 998s Preparing to unpack .../08-libarchive-zip-perl_1.68-1_all.deb ... 998s Unpacking libarchive-zip-perl (1.68-1) ... 998s Selecting previously unselected package libsub-override-perl. 998s Preparing to unpack .../09-libsub-override-perl_0.10-1_all.deb ... 998s Unpacking libsub-override-perl (0.10-1) ... 998s Selecting previously unselected package libfile-stripnondeterminism-perl. 998s Preparing to unpack .../10-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 998s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 998s Selecting previously unselected package dh-strip-nondeterminism. 998s Preparing to unpack .../11-dh-strip-nondeterminism_1.13.1-1_all.deb ... 998s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 998s Selecting previously unselected package libdw1:amd64. 998s Preparing to unpack .../12-libdw1_0.190-1_amd64.deb ... 998s Unpacking libdw1:amd64 (0.190-1) ... 998s Selecting previously unselected package debugedit. 998s Preparing to unpack .../13-debugedit_1%3a5.0-5_amd64.deb ... 998s Unpacking debugedit (1:5.0-5) ... 998s Selecting previously unselected package dwz. 998s Preparing to unpack .../14-dwz_0.15-1_amd64.deb ... 998s Unpacking dwz (0.15-1) ... 998s Selecting previously unselected package gettext. 998s Preparing to unpack .../15-gettext_0.21-14ubuntu1_amd64.deb ... 998s Unpacking gettext (0.21-14ubuntu1) ... 998s Selecting previously unselected package intltool-debian. 998s Preparing to unpack .../16-intltool-debian_0.35.0+20060710.6_all.deb ... 998s Unpacking intltool-debian (0.35.0+20060710.6) ... 998s Selecting previously unselected package po-debconf. 998s Preparing to unpack .../17-po-debconf_1.0.21+nmu1_all.deb ... 998s Unpacking po-debconf (1.0.21+nmu1) ... 998s Selecting previously unselected package debhelper. 998s Preparing to unpack .../18-debhelper_13.14.1ubuntu1_all.deb ... 998s Unpacking debhelper (13.14.1ubuntu1) ... 998s Selecting previously unselected package dh-python. 998s Preparing to unpack .../19-dh-python_6.20231223ubuntu2_all.deb ... 998s Unpacking dh-python (6.20231223ubuntu2) ... 998s Selecting previously unselected package pybuild-plugin-autopkgtest. 998s Preparing to unpack .../20-pybuild-plugin-autopkgtest_6.20231223ubuntu2_all.deb ... 998s Unpacking pybuild-plugin-autopkgtest (6.20231223ubuntu2) ... 998s Setting up dh-python (6.20231223ubuntu2) ... 998s Setting up libdw1:amd64 (0.190-1) ... 998s Setting up gettext (0.21-14ubuntu1) ... 998s Setting up libarchive-zip-perl (1.68-1) ... 998s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 998s Setting up m4 (1.4.19-4) ... 998s Setting up intltool-debian (0.35.0+20060710.6) ... 998s Setting up autotools-dev (20220109.1) ... 998s Setting up autopoint (0.21-14ubuntu1) ... 998s Setting up autoconf (2.71-3) ... 998s Setting up dwz (0.15-1) ... 998s Setting up debugedit (1:5.0-5) ... 998s Setting up libsub-override-perl (0.10-1) ... 998s Setting up automake (1:1.16.5-1.3ubuntu1) ... 998s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 998s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 998s Setting up libtool (2.4.7-7) ... 998s Setting up po-debconf (1.0.21+nmu1) ... 998s Setting up dh-autoreconf (20) ... 998s Setting up dh-strip-nondeterminism (1.13.1-1) ... 998s Setting up debhelper (13.14.1ubuntu1) ... 998s Setting up pybuild-plugin-autopkgtest (6.20231223ubuntu2) ... 998s Processing triggers for install-info (7.1-3) ... 998s Processing triggers for libc-bin (2.39-0ubuntu6) ... 998s Processing triggers for man-db (2.12.0-3) ... 1001s Reading package lists... 1001s Building dependency tree... 1001s Reading state information... 1001s Starting pkgProblemResolver with broken count: 0 1001s Starting 2 pkgProblemResolver with broken count: 0 1001s Done 1001s The following NEW packages will be installed: 1001s autopkgtest-satdep 1001s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1001s Need to get 0 B/696 B of archives. 1001s After this operation, 0 B of additional disk space will be used. 1001s Get:1 /tmp/autopkgtest.JO8XuK/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 1002s Selecting previously unselected package autopkgtest-satdep. 1002s (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 ... 79361 files and directories currently installed.) 1002s Preparing to unpack .../4-autopkgtest-satdep.deb ... 1002s Unpacking autopkgtest-satdep (0) ... 1002s Setting up autopkgtest-satdep (0) ... 1003s (Reading database ... 79361 files and directories currently installed.) 1003s Removing autopkgtest-satdep (0) ... 1003s autopkgtest [23:42:10]: test pybuild-autopkgtest: pybuild-autopkgtest 1003s autopkgtest [23:42:10]: test pybuild-autopkgtest: [----------------------- 1003s pybuild-autopkgtest 1003s I: pybuild base:305: cd /tmp/autopkgtest.JO8XuK/autopkgtest_tmp/build; python3.12 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' 1004s ============================= test session starts ============================== 1004s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.12 1004s cachedir: .pytest_cache 1004s rootdir: /tmp/autopkgtest.JO8XuK/autopkgtest_tmp/build 1004s collecting ... collected 125 items / 1 error / 97 deselected / 28 selected 1004s 1004s ==================================== ERRORS ==================================== 1004s ____________________ ERROR collecting tests/test_contigs.py ____________________ 1004s ImportError while importing test module '/tmp/autopkgtest.JO8XuK/autopkgtest_tmp/build/tests/test_contigs.py'. 1004s Hint: make sure your test modules/packages have valid Python names. 1004s Traceback: 1004s /usr/lib/python3.12/importlib/__init__.py:90: in import_module 1004s return _bootstrap._gcd_import(name[level:], package, level) 1004s tests/test_contigs.py:1: in 1004s from pyensembl import genome_for_reference_name 1004s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 1004s from .database import Database 1004s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 1004s import datacache 1004s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 1004s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 1004s /usr/lib/python3/dist-packages/datacache/download.py:24: in 1004s import pandas as pd 1004s /usr/lib/python3/dist-packages/pandas/__init__.py:16: in 1004s raise ImportError( 1004s E ImportError: Unable to import required dependencies: 1004s E pytz: No module named '_sysconfigdata__i386-linux-gnu' 1004s =============================== warnings summary =============================== 1004s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 1004s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 1004s EPOCH = datetime.datetime.utcfromtimestamp(0) 1004s 1004s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 1004s /usr/lib/python3/dist-packages/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 1004s import pkg_resources 1004s 1004s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871 1004s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 1004s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 1004s declare_namespace(pkg) 1004s 1004s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:65 1004s /usr/lib/python3/dist-packages/pyensembl/shell.py:65: DeprecationWarning: Nesting argument groups is deprecated. 1004s release_group = root_group.add_argument_group() 1004s 1004s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:87 1004s /usr/lib/python3/dist-packages/pyensembl/shell.py:87: DeprecationWarning: Nesting argument groups is deprecated. 1004s path_group = root_group.add_argument_group() 1004s 1004s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1004s =========================== short test summary info ============================ 1004s ERROR tests/test_contigs.py 1004s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 1004s ================= 97 deselected, 5 warnings, 1 error in 0.63s ================== 1004s E: pybuild pybuild:391: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.JO8XuK/autopkgtest_tmp/build; python3.12 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' 1004s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p 3.12 returned exit code 13 1004s make: *** [/tmp/_E7FuSUL7P/run:4: pybuild-autopkgtest] Error 25 1004s pybuild-autopkgtest: error: /tmp/_E7FuSUL7P/run pybuild-autopkgtest returned exit code 2 1005s autopkgtest [23:42:12]: test pybuild-autopkgtest: -----------------------] 1005s autopkgtest [23:42:12]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1005s pybuild-autopkgtest FAIL non-zero exit status 25 1005s autopkgtest [23:42:12]: @@@@@@@@@@@@@@@@@@@@ summary 1005s run-unit-test PASS 1005s pybuild-autopkgtest FAIL non-zero exit status 25 1034s Creating nova instance adt-noble-i386-pyensembl-20240324-232527-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240324.img (UUID 4e56ccec-954f-4884-8b9c-3e1a29e50308)...