0s autopkgtest [19:37:26]: starting date and time: 2025-01-09 19:37:26+0000 0s autopkgtest [19:37:26]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:37:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zna4o3po/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade python-gffutils --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.13.1-1~exp2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-21.secgroup --name adt-plucky-i386-python-gffutils-20250109-190220-juju-7f2275-prod-proposed-migration-environment-2-f538bec2-9a6a-4084-a7a5-454d527350fa --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 220s autopkgtest [19:41:06]: testbed dpkg architecture: amd64 220s autopkgtest [19:41:06]: testbed apt version: 2.9.18 221s autopkgtest [19:41:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 221s autopkgtest [19:41:07]: testbed release detected to be: None 222s autopkgtest [19:41:08]: updating testbed package index (apt update) 222s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 222s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 222s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 223s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 223s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [129 kB] 223s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 223s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [785 kB] 223s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 223s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [249 kB] 223s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [157 kB] 223s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 223s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 223s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [414 kB] 223s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1019 kB] 223s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3100 B] 223s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.4 kB] 223s Fetched 2909 kB in 1s (3029 kB/s) 224s Reading package lists... 225s + lsb_release --codename --short 225s + RELEASE=plucky 225s + cat 225s + [ plucky != trusty ] 225s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Calculating upgrade... 226s The following packages will be upgraded: 226s firmware-sof-signed 226s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 7093 kB of archives. 226s After this operation, 0 B of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu4 [7093 kB] 227s Fetched 7093 kB in 1s (8746 kB/s) 227s (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 ... 75804 files and directories currently installed.) 227s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu4_all.deb ... 227s Unpacking firmware-sof-signed (2024.06-1ubuntu4) over (2024.06-1ubuntu3) ... 227s Setting up firmware-sof-signed (2024.06-1ubuntu4) ... 228s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 228s + /usr/lib/apt/apt-helper analyze-pattern ?true 228s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ?obsolete 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 228s + grep -q trusty /etc/lsb-release 228s + [ ! -d /usr/share/doc/unattended-upgrades ] 228s + [ ! -d /usr/share/doc/lxd ] 228s + [ ! -d /usr/share/doc/lxd-client ] 228s + [ ! -d /usr/share/doc/snapd ] 228s + type iptables 228s + cat 228s + chmod 755 /etc/rc.local 228s + . /etc/rc.local 228s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 228s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 228s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 228s + uname -m 228s + [ x86_64 = ppc64le ] 228s + [ -d /run/systemd/system ] 228s + systemd-detect-virt --quiet --vm 228s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 228s + cat 228s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 228s + echo COMPRESS=lz4 228s autopkgtest [19:41:14]: upgrading testbed (apt dist-upgrade and autopurge) 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 229s Starting 2 pkgProblemResolver with broken count: 0 229s Done 230s Entering ResolveByKeep 230s 231s The following packages were automatically installed and are no longer required: 231s python3.12 python3.12-minimal 231s Use 'sudo apt autoremove' to remove them. 231s The following NEW packages will be installed: 231s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 231s The following packages will be upgraded: 231s libpython3-stdlib python3 python3-minimal 231s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 6118 kB of archives. 231s After this operation, 22.7 MB of additional disk space will be used. 231s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.1-2 [881 kB] 232s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.1-2 [2358 kB] 232s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.13.1-1~exp2 [27.6 kB] 232s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.13.1-1~exp2 [23.9 kB] 232s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [2088 kB] 232s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.1-2 [729 kB] 232s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.13.1-1~exp2 [10.2 kB] 232s Fetched 6118 kB in 1s (7059 kB/s) 232s Selecting previously unselected package libpython3.13-minimal:amd64. 232s (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 ... 75804 files and directories currently installed.) 232s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_amd64.deb ... 232s Unpacking libpython3.13-minimal:amd64 (3.13.1-2) ... 232s Selecting previously unselected package python3.13-minimal. 232s Preparing to unpack .../python3.13-minimal_3.13.1-2_amd64.deb ... 232s Unpacking python3.13-minimal (3.13.1-2) ... 232s Setting up libpython3.13-minimal:amd64 (3.13.1-2) ... 232s Setting up python3.13-minimal (3.13.1-2) ... 233s (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 ... 76124 files and directories currently installed.) 233s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_amd64.deb ... 233s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 233s Setting up python3-minimal (3.13.1-1~exp2) ... 233s (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 ... 76124 files and directories currently installed.) 233s Preparing to unpack .../python3_3.13.1-1~exp2_amd64.deb ... 233s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 233s Selecting previously unselected package libpython3.13-stdlib:amd64. 233s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_amd64.deb ... 233s Unpacking libpython3.13-stdlib:amd64 (3.13.1-2) ... 234s Selecting previously unselected package python3.13. 234s Preparing to unpack .../python3.13_3.13.1-2_amd64.deb ... 234s Unpacking python3.13 (3.13.1-2) ... 234s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_amd64.deb ... 234s Unpacking libpython3-stdlib:amd64 (3.13.1-1~exp2) over (3.12.8-1) ... 234s Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... 234s Setting up libpython3-stdlib:amd64 (3.13.1-1~exp2) ... 234s Setting up python3.13 (3.13.1-2) ... 235s Setting up python3 (3.13.1-1~exp2) ... 235s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 235s for fn in glob1(directory, "%s.*" % fname): 235s Processing triggers for man-db (2.13.0-1) ... 236s Processing triggers for systemd (257-2ubuntu1) ... 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 237s Starting pkgProblemResolver with broken count: 0 237s Starting 2 pkgProblemResolver with broken count: 0 237s Done 237s The following packages will be REMOVED: 237s python3.12* python3.12-minimal* 238s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 238s After this operation, 8926 kB disk space will be freed. 238s (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 ... 76541 files and directories currently installed.) 238s Removing python3.12 (3.12.8-3) ... 238s Removing python3.12-minimal (3.12.8-3) ... 238s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 238s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 238s Processing triggers for man-db (2.13.0-1) ... 239s Processing triggers for systemd (257-2ubuntu1) ... 239s (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 ... 76513 files and directories currently installed.) 239s Purging configuration files for python3.12-minimal (3.12.8-3) ... 239s autopkgtest [19:41:25]: rebooting testbed after setup commands that affected boot 273s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 280s autopkgtest [19:42:06]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 282s autopkgtest [19:42:08]: @@@@@@@@@@@@@@@@@@@@ apt-source python-gffutils 285s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (dsc) [2351 B] 285s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (tar) [1560 kB] 285s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (diff) [5024 B] 285s gpgv: Signature made Sat Apr 13 20:25:45 2024 UTC 285s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 285s gpgv: issuer "tchet@debian.org" 285s gpgv: Can't check signature: No public key 285s dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.13-1.dsc: no acceptable signature found 285s autopkgtest [19:42:11]: testing package python-gffutils version 0.13-1 285s autopkgtest [19:42:11]: build not needed 286s autopkgtest [19:42:12]: test run-unit-test: preparing testbed 286s Reading package lists... 287s Building dependency tree... 287s Reading state information... 287s Starting pkgProblemResolver with broken count: 0 287s Starting 2 pkgProblemResolver with broken count: 0 287s Done 288s The following NEW packages will be installed: 288s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 288s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 288s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 288s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 288s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 288s libxcb-shm0 libxrender1 python3-argcomplete python3-argh python3-biopython 288s python3-cairo python3-freetype python3-gffutils python3-importlib-metadata 288s python3-iniconfig python3-numpy python3-packaging python3-pil python3-pluggy 288s python3-pyfaidx python3-pytest python3-reportlab python3-rlpycairo 288s python3-simplejson sgml-base w3c-sgml-lib x11-common xfonts-encodings 288s xfonts-utils xml-core 288s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 288s Need to get 31.8 MB of archives. 288s After this operation, 120 MB of additional disk space will be used. 288s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 288s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 288s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 288s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 288s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 288s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 288s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 288s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 289s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 289s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 289s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 289s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 289s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 289s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 289s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 289s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 289s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 289s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-12ubuntu1 [909 kB] 289s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-12ubuntu1 [148 kB] 289s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 289s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.1.0-1 [541 kB] 289s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 289s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 289s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 289s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 289s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 289s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 289s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 289s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 289s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 289s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 289s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 289s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 289s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 289s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-argcomplete all 3.5.1-1ubuntu1 [35.6 kB] 289s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [5319 kB] 289s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu2 [217 kB] 289s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu2 [580 kB] 289s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 289s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 289s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 289s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 289s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 289s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 289s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 289s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-argh all 0.31.3-1 [27.0 kB] 289s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 289s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 289s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 289s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-simplejson amd64 3.19.3-1build1 [59.3 kB] 289s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gffutils all 0.13-1 [1081 kB] 289s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 289s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 289s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 290s Fetched 31.8 MB in 1s (21.4 MB/s) 290s Selecting previously unselected package sgml-base. 290s (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 ... 76513 files and directories currently installed.) 290s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 290s Unpacking sgml-base (1.31) ... 290s Selecting previously unselected package fonts-dejavu-mono. 290s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 290s Unpacking fonts-dejavu-mono (2.37-8) ... 290s Selecting previously unselected package fonts-dejavu-core. 290s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 290s Unpacking fonts-dejavu-core (2.37-8) ... 290s Selecting previously unselected package libfontenc1:amd64. 290s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 290s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 290s Selecting previously unselected package x11-common. 290s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 290s Unpacking x11-common (1:7.7+23ubuntu3) ... 290s Selecting previously unselected package xfonts-encodings. 290s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 290s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 290s Selecting previously unselected package xfonts-utils. 290s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ... 290s Unpacking xfonts-utils (1:7.7+7) ... 290s Selecting previously unselected package fonts-urw-base35. 290s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 290s Unpacking fonts-urw-base35 (20200910-8) ... 290s Selecting previously unselected package fontconfig-config. 290s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 290s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 291s Selecting previously unselected package libblas3:amd64. 291s Preparing to unpack .../09-libblas3_3.12.0-4_amd64.deb ... 291s Unpacking libblas3:amd64 (3.12.0-4) ... 291s Selecting previously unselected package libfontconfig1:amd64. 291s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 291s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 291s Selecting previously unselected package libpixman-1-0:amd64. 291s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_amd64.deb ... 291s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 291s Selecting previously unselected package libxcb-render0:amd64. 291s Preparing to unpack .../12-libxcb-render0_1.17.0-2_amd64.deb ... 291s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 291s Selecting previously unselected package libxcb-shm0:amd64. 291s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_amd64.deb ... 291s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 291s Selecting previously unselected package libxrender1:amd64. 291s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 291s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 291s Selecting previously unselected package libcairo2:amd64. 291s Preparing to unpack .../15-libcairo2_1.18.2-2_amd64.deb ... 291s Unpacking libcairo2:amd64 (1.18.2-2) ... 291s Selecting previously unselected package libdeflate0:amd64. 291s Preparing to unpack .../16-libdeflate0_1.22-1_amd64.deb ... 291s Unpacking libdeflate0:amd64 (1.22-1) ... 291s Selecting previously unselected package libgfortran5:amd64. 291s Preparing to unpack .../17-libgfortran5_14.2.0-12ubuntu1_amd64.deb ... 291s Unpacking libgfortran5:amd64 (14.2.0-12ubuntu1) ... 291s Selecting previously unselected package libgomp1:amd64. 291s Preparing to unpack .../18-libgomp1_14.2.0-12ubuntu1_amd64.deb ... 291s Unpacking libgomp1:amd64 (14.2.0-12ubuntu1) ... 291s Selecting previously unselected package libgraphite2-3:amd64. 291s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 291s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 291s Selecting previously unselected package libharfbuzz0b:amd64. 291s Preparing to unpack .../20-libharfbuzz0b_10.1.0-1_amd64.deb ... 291s Unpacking libharfbuzz0b:amd64 (10.1.0-1) ... 291s Selecting previously unselected package libimagequant0:amd64. 291s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 291s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 291s Selecting previously unselected package libjpeg-turbo8:amd64. 291s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 291s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 291s Selecting previously unselected package libjpeg8:amd64. 291s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 291s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 291s Selecting previously unselected package liblapack3:amd64. 291s Preparing to unpack .../24-liblapack3_3.12.0-4_amd64.deb ... 291s Unpacking liblapack3:amd64 (3.12.0-4) ... 291s Selecting previously unselected package liblcms2-2:amd64. 291s Preparing to unpack .../25-liblcms2-2_2.16-2_amd64.deb ... 291s Unpacking liblcms2-2:amd64 (2.16-2) ... 291s Selecting previously unselected package liblerc4:amd64. 291s Preparing to unpack .../26-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 291s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 291s Selecting previously unselected package libraqm0:amd64. 291s Preparing to unpack .../27-libraqm0_0.10.2-1_amd64.deb ... 291s Unpacking libraqm0:amd64 (0.10.2-1) ... 291s Selecting previously unselected package libsharpyuv0:amd64. 291s Preparing to unpack .../28-libsharpyuv0_1.4.0-0.1_amd64.deb ... 291s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 291s Selecting previously unselected package libjbig0:amd64. 291s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 291s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 291s Selecting previously unselected package libwebp7:amd64. 291s Preparing to unpack .../30-libwebp7_1.4.0-0.1_amd64.deb ... 291s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 291s Selecting previously unselected package libtiff6:amd64. 291s Preparing to unpack .../31-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 291s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 291s Selecting previously unselected package libwebpdemux2:amd64. 291s Preparing to unpack .../32-libwebpdemux2_1.4.0-0.1_amd64.deb ... 291s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 291s Selecting previously unselected package libwebpmux3:amd64. 291s Preparing to unpack .../33-libwebpmux3_1.4.0-0.1_amd64.deb ... 291s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 291s Selecting previously unselected package python3-argcomplete. 291s Preparing to unpack .../34-python3-argcomplete_3.5.1-1ubuntu1_all.deb ... 291s Unpacking python3-argcomplete (3.5.1-1ubuntu1) ... 291s Selecting previously unselected package python3-numpy. 291s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-12_amd64.deb ... 291s Unpacking python3-numpy (1:1.26.4+ds-12) ... 291s Selecting previously unselected package libopenjp2-7:amd64. 291s Preparing to unpack .../36-libopenjp2-7_2.5.0-2ubuntu2_amd64.deb ... 291s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu2) ... 291s Selecting previously unselected package python3-pil:amd64. 291s Preparing to unpack .../37-python3-pil_10.4.0-1ubuntu2_amd64.deb ... 291s Unpacking python3-pil:amd64 (10.4.0-1ubuntu2) ... 292s Selecting previously unselected package python3-cairo. 292s Preparing to unpack .../38-python3-cairo_1.26.1-2build1_amd64.deb ... 292s Unpacking python3-cairo (1.26.1-2build1) ... 292s Selecting previously unselected package python3-freetype. 292s Preparing to unpack .../39-python3-freetype_2.5.1-1_all.deb ... 292s Unpacking python3-freetype (2.5.1-1) ... 292s Selecting previously unselected package python3-rlpycairo. 292s Preparing to unpack .../40-python3-rlpycairo_0.3.0-3_all.deb ... 292s Unpacking python3-rlpycairo (0.3.0-3) ... 292s Selecting previously unselected package python3-reportlab. 292s Preparing to unpack .../41-python3-reportlab_4.2.5-1_all.deb ... 292s Unpacking python3-reportlab (4.2.5-1) ... 292s Selecting previously unselected package xml-core. 292s Preparing to unpack .../42-xml-core_0.19_all.deb ... 292s Unpacking xml-core (0.19) ... 292s Selecting previously unselected package w3c-sgml-lib. 292s Preparing to unpack .../43-w3c-sgml-lib_1.3-3_all.deb ... 292s Unpacking w3c-sgml-lib (1.3-3) ... 292s Selecting previously unselected package python3-biopython. 292s Preparing to unpack .../44-python3-biopython_1.84+dfsg-4build1_amd64.deb ... 292s Unpacking python3-biopython (1.84+dfsg-4build1) ... 292s Selecting previously unselected package python3-argh. 292s Preparing to unpack .../45-python3-argh_0.31.3-1_all.deb ... 292s Unpacking python3-argh (0.31.3-1) ... 292s Selecting previously unselected package python3-importlib-metadata. 292s Preparing to unpack .../46-python3-importlib-metadata_8.5.0-1_all.deb ... 292s Unpacking python3-importlib-metadata (8.5.0-1) ... 292s Selecting previously unselected package python3-packaging. 292s Preparing to unpack .../47-python3-packaging_24.2-1_all.deb ... 292s Unpacking python3-packaging (24.2-1) ... 292s Selecting previously unselected package python3-pyfaidx. 292s Preparing to unpack .../48-python3-pyfaidx_0.8.1.3-1_all.deb ... 292s Unpacking python3-pyfaidx (0.8.1.3-1) ... 292s Selecting previously unselected package python3-simplejson. 292s Preparing to unpack .../49-python3-simplejson_3.19.3-1build1_amd64.deb ... 292s Unpacking python3-simplejson (3.19.3-1build1) ... 292s Selecting previously unselected package python3-gffutils. 292s Preparing to unpack .../50-python3-gffutils_0.13-1_all.deb ... 292s Unpacking python3-gffutils (0.13-1) ... 292s Selecting previously unselected package python3-iniconfig. 292s Preparing to unpack .../51-python3-iniconfig_1.1.1-2_all.deb ... 292s Unpacking python3-iniconfig (1.1.1-2) ... 292s Selecting previously unselected package python3-pluggy. 292s Preparing to unpack .../52-python3-pluggy_1.5.0-1_all.deb ... 292s Unpacking python3-pluggy (1.5.0-1) ... 292s Selecting previously unselected package python3-pytest. 292s Preparing to unpack .../53-python3-pytest_8.3.4-1_all.deb ... 292s Unpacking python3-pytest (8.3.4-1) ... 292s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 292s Setting up liblcms2-2:amd64 (2.16-2) ... 292s Setting up python3-iniconfig (1.1.1-2) ... 292s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 292s Setting up python3-argh (0.31.3-1) ... 292s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 292s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 292s Setting up python3-importlib-metadata (8.5.0-1) ... 293s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 293s Setting up libxcb-render0:amd64 (1.17.0-2) ... 293s Setting up x11-common (1:7.7+23ubuntu3) ... 293s Setting up libdeflate0:amd64 (1.22-1) ... 293s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 293s Setting up libgomp1:amd64 (14.2.0-12ubuntu1) ... 293s Setting up python3-freetype (2.5.1-1) ... 293s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 293s Setting up python3-simplejson (3.19.3-1build1) ... 293s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 293s Setting up libblas3:amd64 (3.12.0-4) ... 293s 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 293s Setting up python3-packaging (24.2-1) ... 293s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 293s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 293s Setting up fonts-dejavu-mono (2.37-8) ... 293s Setting up fonts-dejavu-core (2.37-8) ... 293s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 293s Setting up libgfortran5:amd64 (14.2.0-12ubuntu1) ... 293s Setting up python3-pluggy (1.5.0-1) ... 293s Setting up libwebp7:amd64 (1.4.0-0.1) ... 293s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu2) ... 293s Setting up libharfbuzz0b:amd64 (10.1.0-1) ... 293s Setting up sgml-base (1.31) ... 293s Setting up python3-argcomplete (3.5.1-1ubuntu1) ... 293s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 293s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 293s Setting up python3-pyfaidx (0.8.1.3-1) ... 294s Setting up liblapack3:amd64 (3.12.0-4) ... 294s 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 294s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 294s Setting up python3-pytest (8.3.4-1) ... 294s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 294s Setting up xfonts-utils (1:7.7+7) ... 294s Setting up libraqm0:amd64 (0.10.2-1) ... 294s Setting up python3-numpy (1:1.26.4+ds-12) ... 295s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 295s Setting up xml-core (0.19) ... 295s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 295s Setting up fonts-urw-base35 (20200910-8) ... 296s Setting up libcairo2:amd64 (1.18.2-2) ... 296s Setting up python3-pil:amd64 (10.4.0-1ubuntu2) ... 296s Setting up python3-cairo (1.26.1-2build1) ... 296s Setting up python3-rlpycairo (0.3.0-3) ... 296s Setting up python3-reportlab (4.2.5-1) ... 297s Processing triggers for libc-bin (2.40-4ubuntu1) ... 297s Processing triggers for man-db (2.13.0-1) ... 298s Processing triggers for sgml-base (1.31) ... 298s Setting up w3c-sgml-lib (1.3-3) ... 321s Setting up python3-biopython (1.84+dfsg-4build1) ... 322s Setting up python3-gffutils (0.13-1) ... 323s autopkgtest [19:42:49]: testbed environment configured for cross-architecture building 323s autopkgtest [19:42:49]: test run-unit-test: [----------------------- 323s + pkg=python-gffutils 323s + [ /tmp/autopkgtest.Nl8ZKd/autopkgtest_tmp = ] 323s + cd /tmp/autopkgtest.Nl8ZKd/autopkgtest_tmp 323s + export HOME=/tmp/autopkgtest.Nl8ZKd/autopkgtest_tmp 323s + cp -r /usr/lib/python3/dist-packages/gffutils/test ./ 323s + pytest --doctest-modules -m not slow test 324s ============================= test session starts ============================== 324s platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 324s rootdir: /tmp/autopkgtest.Nl8ZKd/autopkgtest_tmp 324s plugins: typeguard-4.4.1 324s collected 110 items 324s 324s test/feature_test.py ........... [ 10%] 324s test/helpers_test.py .. [ 11%] 324s test/parser_test.py .................. [ 28%] 325s test/test_1.py ...........x..........s........... [ 59%] 325s test/test_biopython_integration.py . [ 60%] 326s test/test_cli.py . [ 60%] 326s test/test_issues.py ........................ [ 82%] 326s test/test_iterators.py .... [ 86%] 326s test/test_merge.py ......... [ 94%] 326s test/test_merge_all.py ...... [100%] 326s 326s =============================== warnings summary =============================== 326s test/performance_evaluation.py:190 326s /tmp/autopkgtest.Nl8ZKd/autopkgtest_tmp/test/performance_evaluation.py:190: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 326s @pytest.mark.slow 326s 326s test/performance_evaluation.py:208 326s /tmp/autopkgtest.Nl8ZKd/autopkgtest_tmp/test/performance_evaluation.py:208: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 326s @pytest.mark.slow 326s 326s test/test_1.py:485 326s test/test_1.py:485: PytestCollectionWarning: yield tests were removed in pytest 4.0 - test_region will be ignored 326s def test_region(): 326s 326s test/parser_test.py::test_parser_from_string 326s /usr/lib/python3/dist-packages/_pytest/python.py:163: PytestReturnNotNoneWarning: Expected None, but test/parser_test.py::test_parser_from_string returned True, which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? 326s warnings.warn( 326s 326s test/parser_test.py::test_inconsistent_dialect 326s test/test_1.py::test_disable_infer 326s test/test_issues.py::test_pr_172 326s /usr/lib/python3/dist-packages/gffutils/create.py:770: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation 326s warnings.warn( 326s 326s test/test_1.py::test_disable_infer 326s /usr/lib/python3/dist-packages/gffutils/create.py:763: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation 326s warnings.warn( 326s 326s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 326s ============ 108 passed, 1 skipped, 1 xfailed, 8 warnings in 2.66s ============= 327s autopkgtest [19:42:53]: test run-unit-test: -----------------------] 327s autopkgtest [19:42:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 327s run-unit-test PASS 328s autopkgtest [19:42:54]: @@@@@@@@@@@@@@@@@@@@ summary 328s run-unit-test PASS 382s nova [W] Skipping flock for amd64 382s Creating nova instance adt-plucky-i386-python-gffutils-20250109-190220-juju-7f2275-prod-proposed-migration-environment-2-f538bec2-9a6a-4084-a7a5-454d527350fa from image adt/ubuntu-plucky-amd64-server-20250109.img (UUID 47fb0aba-d15c-4240-a5df-62aa479e218d)... 382s nova [W] Timed out waiting for 8fdbff33-e765-4d32-92f0-34a6124c0c92 to get deleted.