0s autopkgtest [13:30:28]: starting date and time: 2024-11-13 13:30:28+0000
  0s autopkgtest [13:30:28]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [13:30:28]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1i4zxs4f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:libxml2 --apt-upgrade openbabel --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=libxml2/2.12.7+dfsg+really2.9.14-0.2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-34.secgroup --name adt-plucky-arm64-openbabel-20241113-133028-juju-7f2275-prod-proposed-migration-environment-15-c1aacaee-8f5c-4d71-9a4f-ce5d9026db2e --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 75s autopkgtest [13:31:43]: testbed dpkg architecture: arm64
 75s autopkgtest [13:31:43]: testbed apt version: 2.9.8
 75s autopkgtest [13:31:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB]
 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB]
 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [124 kB]
 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [682 kB]
 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.9 kB]
 77s Fetched 2042 kB in 1s (2215 kB/s)
 78s Reading package lists...
 80s Reading package lists...
 81s Building dependency tree...
 81s Reading state information...
 82s Calculating upgrade...
 83s The following packages will be upgraded:
 83s   libxml2
 83s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 83s Need to get 737 kB of archives.
 83s After this operation, 385 kB of additional disk space will be used.
 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2build1 [737 kB]
 84s Fetched 737 kB in 1s (1437 kB/s)
 84s (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 ... 79924 files and directories currently installed.)
 84s Preparing to unpack .../libxml2_2.12.7+dfsg+really2.9.14-0.2build1_arm64.deb ...
 84s Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2build1) over (2.12.7+dfsg-3) ...
 84s Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2build1) ...
 84s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 87s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 87s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 88s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 88s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 89s Reading package lists...
 89s Reading package lists...
 90s Building dependency tree...
 90s Reading state information...
 91s Calculating upgrade...
 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 92s Reading package lists...
 93s Building dependency tree...
 93s Reading state information...
 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 98s autopkgtest [13:32:06]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
 98s autopkgtest [13:32:06]: @@@@@@@@@@@@@@@@@@@@ apt-source openbabel
104s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openbabel 3.1.1+dfsg-11ubuntu1 (dsc) [2896 B]
104s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openbabel 3.1.1+dfsg-11ubuntu1 (tar) [21.8 MB]
104s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openbabel 3.1.1+dfsg-11ubuntu1 (diff) [22.0 kB]
105s gpgv: Signature made Mon Oct 21 10:43:56 2024 UTC
105s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
105s gpgv: Can't check signature: No public key
105s dpkg-source: warning: cannot verify inline signature for ./openbabel_3.1.1+dfsg-11ubuntu1.dsc: no acceptable signature found
107s dpkg-source: warning: diff 'src/debian/patches/2315.patch' patches file src/src/CMakeLists.txt more than once
107s dpkg-source: warning: diff 'src/debian/patches/2315.patch' patches file src/CMakeLists.txt more than once
107s dpkg-source: warning: diff 'src/debian/patches/2315.patch' patches file src/OpenBabel3Config.cmake.in more than once
107s autopkgtest [13:32:15]: testing package openbabel version 3.1.1+dfsg-11ubuntu1
108s autopkgtest [13:32:16]: build not needed
116s autopkgtest [13:32:24]: test python3: preparing testbed
118s Reading package lists...
118s Building dependency tree...
118s Reading state information...
119s Starting pkgProblemResolver with broken count: 0
119s Starting 2 pkgProblemResolver with broken count: 0
119s Done
119s The following additional packages will be installed:
119s   adwaita-icon-theme at-spi2-common dconf-gsettings-backend dconf-service
119s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
119s   gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme
119s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
119s   libavahi-common-data libavahi-common3 libboost-iostreams1.83.0
119s   libcairo-gobject2 libcairo2 libchemistry-openbabel-perl libcolord2
119s   libcups2t64 libdatrie1 libdconf1 libdeflate0 libepoxy0 libfontconfig1
119s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgomp1 libgraphite2-3
119s   libgtk-3-0t64 libgtk-3-common libharfbuzz0b libice6 libinchi1 libjbig0
119s   libjpeg-turbo8 libjpeg8 libjs-jquery liblcms2-2 liblerc4 libmaeparser1
119s   libnotify4 libopenbabel-dev libopenbabel-doc libopenbabel7 libpango-1.0-0
119s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre2-32-0 libpixman-1-0
119s   libsharpyuv0 libsm6 libthai-data libthai0 libtiff6 libwayland-client0
119s   libwayland-cursor0 libwayland-egl1 libwebp7 libwxbase3.2-1t64
119s   libwxgtk3.2-1t64 libxcb-render0 libxcb-shm0 libxcomposite1 libxcursor1
119s   libxdamage1 libxfixes3 libxi6 libxinerama1 libxrandr2 libxrender1 libxtst6
119s   openbabel openbabel-gui python3-openbabel ubuntu-mono x11-common
119s Suggested packages:
119s   adwaita-icon-theme-legacy colord cups-common gvfs liblcms2-utils
119s   notification-daemon
119s Recommended packages:
119s   librsvg2-common at-spi2-core libgdk-pixbuf2.0-bin libgtk-3-bin
119s   javascript-common
119s The following NEW packages will be installed:
119s   adwaita-icon-theme at-spi2-common autopkgtest-satdep dconf-gsettings-backend
119s   dconf-service fontconfig fontconfig-config fonts-dejavu-core
119s   fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme
119s   humanity-icon-theme libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64
119s   libavahi-client3 libavahi-common-data libavahi-common3
119s   libboost-iostreams1.83.0 libcairo-gobject2 libcairo2
119s   libchemistry-openbabel-perl libcolord2 libcups2t64 libdatrie1 libdconf1
119s   libdeflate0 libepoxy0 libfontconfig1 libgdk-pixbuf-2.0-0
119s   libgdk-pixbuf2.0-common libgomp1 libgraphite2-3 libgtk-3-0t64
119s   libgtk-3-common libharfbuzz0b libice6 libinchi1 libjbig0 libjpeg-turbo8
119s   libjpeg8 libjs-jquery liblcms2-2 liblerc4 libmaeparser1 libnotify4
119s   libopenbabel-dev libopenbabel-doc libopenbabel7 libpango-1.0-0
119s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre2-32-0 libpixman-1-0
119s   libsharpyuv0 libsm6 libthai-data libthai0 libtiff6 libwayland-client0
119s   libwayland-cursor0 libwayland-egl1 libwebp7 libwxbase3.2-1t64
119s   libwxgtk3.2-1t64 libxcb-render0 libxcb-shm0 libxcomposite1 libxcursor1
119s   libxdamage1 libxfixes3 libxi6 libxinerama1 libxrandr2 libxrender1 libxtst6
119s   openbabel openbabel-gui python3-openbabel ubuntu-mono x11-common
119s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded.
119s Need to get 29.4 MB/29.4 MB of archives.
119s After this operation, 157 MB of additional disk space will be used.
119s Get:1 /tmp/autopkgtest.r6PFaE/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [748 B]
120s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B]
120s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
120s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
120s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
120s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
120s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
120s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
120s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
120s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
120s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1 [145 kB]
120s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.16.5+ds-1 [51.7 kB]
120s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-1 [13.5 kB]
120s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 humanity-icon-theme all 0.6.16 [1282 kB]
121s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB]
121s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 47.0-2 [525 kB]
121s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 at-spi2-common all 2.54.0-1 [8774 B]
121s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-4build2 [39.8 kB]
121s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-4build2 [26.9 kB]
121s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-4build2 [22.0 kB]
121s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
121s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
121s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
121s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
121s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB]
122s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk1.0-0t64 arm64 2.54.0-1 [55.0 kB]
122s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB]
122s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libatspi2.0-0t64 arm64 2.54.0-1 [80.2 kB]
122s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk-bridge2.0-0t64 arm64 2.54.0-1 [66.6 kB]
122s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-13ubuntu6 [29.6 kB]
122s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-13ubuntu6 [23.3 kB]
122s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-13ubuntu6 [27.2 kB]
122s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-3.2ubuntu2 [259 kB]
122s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
122s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
122s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
122s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
122s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
122s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.2-2 [127 kB]
122s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
122s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 libinchi1 arm64 1.03+dfsg-4build1 [451 kB]
122s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB]
122s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenbabel7 arm64 3.1.1+dfsg-11ubuntu1 [3178 kB]
122s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libchemistry-openbabel-perl arm64 3.1.1+dfsg-11ubuntu1 [690 kB]
122s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
122s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolord2 arm64 1.4.7-1build2 [149 kB]
122s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.10-1ubuntu2 [271 kB]
123s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
123s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB]
123s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
123s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
123s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
123s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
123s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [234 kB]
123s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [48.9 kB]
123s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [27.5 kB]
123s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.0-1 [26.7 kB]
123s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-cursor0 arm64 1.23.0-1 [10.6 kB]
123s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.0-1 [5636 B]
123s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B]
123s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB]
123s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.2-1 [21.2 kB]
123s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B]
123s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B]
123s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB]
123s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-common all 3.24.43-3ubuntu2 [1202 kB]
123s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-0t64 arm64 3.24.43-3ubuntu2 [2898 kB]
123s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
123s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
123s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
123s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libnotify4 arm64 0.8.3-1build2 [25.4 kB]
123s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenbabel-dev arm64 3.1.1+dfsg-11ubuntu1 [181 kB]
123s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenbabel-doc all 3.1.1+dfsg-11ubuntu1 [5610 kB]
123s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu3 [187 kB]
124s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
124s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxbase3.2-1t64 arm64 3.2.5+dfsg-1 [865 kB]
124s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libxtst6 arm64 2:1.2.3-1.1build1 [13.0 kB]
124s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwxgtk3.2-1t64 arm64 3.2.5+dfsg-1 [4352 kB]
124s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 openbabel arm64 3.1.1+dfsg-11ubuntu1 [125 kB]
124s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 openbabel-gui arm64 3.1.1+dfsg-11ubuntu1 [84.8 kB]
124s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openbabel arm64 3.1.1+dfsg-11ubuntu1 [607 kB]
124s Fetched 29.4 MB in 4s (6700 kB/s)
124s Selecting previously unselected package libgdk-pixbuf2.0-common.
124s (Reading database ... 
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(Reading database ... 79924 files and directories currently installed.)
124s Preparing to unpack .../00-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ...
124s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
124s Selecting previously unselected package libjpeg-turbo8:arm64.
124s Preparing to unpack .../01-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ...
124s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
124s Selecting previously unselected package libjpeg8:arm64.
125s Preparing to unpack .../02-libjpeg8_8c-2ubuntu11_arm64.deb ...
125s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
125s Selecting previously unselected package libdeflate0:arm64.
125s Preparing to unpack .../03-libdeflate0_1.22-1_arm64.deb ...
125s Unpacking libdeflate0:arm64 (1.22-1) ...
125s Selecting previously unselected package libjbig0:arm64.
125s Preparing to unpack .../04-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
125s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ...
125s Selecting previously unselected package liblerc4:arm64.
125s Preparing to unpack .../05-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ...
125s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
125s Selecting previously unselected package libsharpyuv0:arm64.
125s Preparing to unpack .../06-libsharpyuv0_1.4.0-0.1_arm64.deb ...
125s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ...
125s Selecting previously unselected package libwebp7:arm64.
125s Preparing to unpack .../07-libwebp7_1.4.0-0.1_arm64.deb ...
125s Unpacking libwebp7:arm64 (1.4.0-0.1) ...
125s Selecting previously unselected package libtiff6:arm64.
125s Preparing to unpack .../08-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
125s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
125s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
125s Preparing to unpack .../09-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_arm64.deb ...
125s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1) ...
125s Selecting previously unselected package gtk-update-icon-cache.
125s Preparing to unpack .../10-gtk-update-icon-cache_4.16.5+ds-1_arm64.deb ...
125s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
125s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed.
125s Unpacking gtk-update-icon-cache (4.16.5+ds-1) ...
125s Selecting previously unselected package hicolor-icon-theme.
125s Preparing to unpack .../11-hicolor-icon-theme_0.18-1_all.deb ...
125s Unpacking hicolor-icon-theme (0.18-1) ...
125s Selecting previously unselected package humanity-icon-theme.
126s Preparing to unpack .../12-humanity-icon-theme_0.6.16_all.deb ...
126s Unpacking humanity-icon-theme (0.6.16) ...
126s Selecting previously unselected package ubuntu-mono.
126s Preparing to unpack .../13-ubuntu-mono_24.04-0ubuntu1_all.deb ...
126s Unpacking ubuntu-mono (24.04-0ubuntu1) ...
127s Selecting previously unselected package adwaita-icon-theme.
127s Preparing to unpack .../14-adwaita-icon-theme_47.0-2_all.deb ...
127s Unpacking adwaita-icon-theme (47.0-2) ...
128s Selecting previously unselected package at-spi2-common.
128s Preparing to unpack .../15-at-spi2-common_2.54.0-1_all.deb ...
128s Unpacking at-spi2-common (2.54.0-1) ...
128s Selecting previously unselected package libdconf1:arm64.
128s Preparing to unpack .../16-libdconf1_0.40.0-4build2_arm64.deb ...
128s Unpacking libdconf1:arm64 (0.40.0-4build2) ...
128s Selecting previously unselected package dconf-service.
128s Preparing to unpack .../17-dconf-service_0.40.0-4build2_arm64.deb ...
128s Unpacking dconf-service (0.40.0-4build2) ...
128s Selecting previously unselected package dconf-gsettings-backend:arm64.
128s Preparing to unpack .../18-dconf-gsettings-backend_0.40.0-4build2_arm64.deb ...
128s Unpacking dconf-gsettings-backend:arm64 (0.40.0-4build2) ...
128s Selecting previously unselected package fonts-dejavu-mono.
128s Preparing to unpack .../19-fonts-dejavu-mono_2.37-8_all.deb ...
128s Unpacking fonts-dejavu-mono (2.37-8) ...
128s Selecting previously unselected package fonts-dejavu-core.
128s Preparing to unpack .../20-fonts-dejavu-core_2.37-8_all.deb ...
128s Unpacking fonts-dejavu-core (2.37-8) ...
128s Selecting previously unselected package fontconfig-config.
128s Preparing to unpack .../21-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
128s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
128s Selecting previously unselected package libfontconfig1:arm64.
128s Preparing to unpack .../22-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ...
128s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
128s Selecting previously unselected package fontconfig.
128s Preparing to unpack .../23-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ...
128s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
128s Selecting previously unselected package libatk1.0-0t64:arm64.
128s Preparing to unpack .../24-libatk1.0-0t64_2.54.0-1_arm64.deb ...
128s Unpacking libatk1.0-0t64:arm64 (2.54.0-1) ...
128s Selecting previously unselected package libxi6:arm64.
128s Preparing to unpack .../25-libxi6_2%3a1.8.2-1_arm64.deb ...
128s Unpacking libxi6:arm64 (2:1.8.2-1) ...
128s Selecting previously unselected package libatspi2.0-0t64:arm64.
128s Preparing to unpack .../26-libatspi2.0-0t64_2.54.0-1_arm64.deb ...
128s Unpacking libatspi2.0-0t64:arm64 (2.54.0-1) ...
128s Selecting previously unselected package libatk-bridge2.0-0t64:arm64.
128s Preparing to unpack .../27-libatk-bridge2.0-0t64_2.54.0-1_arm64.deb ...
128s Unpacking libatk-bridge2.0-0t64:arm64 (2.54.0-1) ...
128s Selecting previously unselected package libavahi-common-data:arm64.
128s Preparing to unpack .../28-libavahi-common-data_0.8-13ubuntu6_arm64.deb ...
128s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu6) ...
128s Selecting previously unselected package libavahi-common3:arm64.
128s Preparing to unpack .../29-libavahi-common3_0.8-13ubuntu6_arm64.deb ...
128s Unpacking libavahi-common3:arm64 (0.8-13ubuntu6) ...
128s Selecting previously unselected package libavahi-client3:arm64.
128s Preparing to unpack .../30-libavahi-client3_0.8-13ubuntu6_arm64.deb ...
128s Unpacking libavahi-client3:arm64 (0.8-13ubuntu6) ...
128s Selecting previously unselected package libboost-iostreams1.83.0:arm64.
128s Preparing to unpack .../31-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_arm64.deb ...
128s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
128s Selecting previously unselected package libpixman-1-0:arm64.
128s Preparing to unpack .../32-libpixman-1-0_0.44.0-3_arm64.deb ...
128s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
128s Selecting previously unselected package libxcb-render0:arm64.
128s Preparing to unpack .../33-libxcb-render0_1.17.0-2_arm64.deb ...
128s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
128s Selecting previously unselected package libxcb-shm0:arm64.
128s Preparing to unpack .../34-libxcb-shm0_1.17.0-2_arm64.deb ...
128s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
128s Selecting previously unselected package libxrender1:arm64.
128s Preparing to unpack .../35-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
128s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
128s Selecting previously unselected package libcairo2:arm64.
128s Preparing to unpack .../36-libcairo2_1.18.2-2_arm64.deb ...
128s Unpacking libcairo2:arm64 (1.18.2-2) ...
128s Selecting previously unselected package libcairo-gobject2:arm64.
128s Preparing to unpack .../37-libcairo-gobject2_1.18.2-2_arm64.deb ...
128s Unpacking libcairo-gobject2:arm64 (1.18.2-2) ...
128s Selecting previously unselected package libgomp1:arm64.
128s Preparing to unpack .../38-libgomp1_14.2.0-8ubuntu1_arm64.deb ...
128s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ...
128s Selecting previously unselected package libinchi1.
128s Preparing to unpack .../39-libinchi1_1.03+dfsg-4build1_arm64.deb ...
128s Unpacking libinchi1 (1.03+dfsg-4build1) ...
128s Selecting previously unselected package libmaeparser1:arm64.
128s Preparing to unpack .../40-libmaeparser1_1.3.1-1build1_arm64.deb ...
128s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ...
128s Selecting previously unselected package libopenbabel7.
128s Preparing to unpack .../41-libopenbabel7_3.1.1+dfsg-11ubuntu1_arm64.deb ...
128s Unpacking libopenbabel7 (3.1.1+dfsg-11ubuntu1) ...
128s Selecting previously unselected package libchemistry-openbabel-perl.
128s Preparing to unpack .../42-libchemistry-openbabel-perl_3.1.1+dfsg-11ubuntu1_arm64.deb ...
128s Unpacking libchemistry-openbabel-perl (3.1.1+dfsg-11ubuntu1) ...
129s Selecting previously unselected package liblcms2-2:arm64.
129s Preparing to unpack .../43-liblcms2-2_2.16-2_arm64.deb ...
129s Unpacking liblcms2-2:arm64 (2.16-2) ...
129s Selecting previously unselected package libcolord2:arm64.
129s Preparing to unpack .../44-libcolord2_1.4.7-1build2_arm64.deb ...
129s Unpacking libcolord2:arm64 (1.4.7-1build2) ...
129s Selecting previously unselected package libcups2t64:arm64.
129s Preparing to unpack .../45-libcups2t64_2.4.10-1ubuntu2_arm64.deb ...
129s Unpacking libcups2t64:arm64 (2.4.10-1ubuntu2) ...
129s Selecting previously unselected package libdatrie1:arm64.
129s Preparing to unpack .../46-libdatrie1_0.2.13-3build1_arm64.deb ...
129s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
129s Selecting previously unselected package libepoxy0:arm64.
129s Preparing to unpack .../47-libepoxy0_1.5.10-2_arm64.deb ...
129s Unpacking libepoxy0:arm64 (1.5.10-2) ...
129s Selecting previously unselected package libgraphite2-3:arm64.
129s Preparing to unpack .../48-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
129s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
129s Selecting previously unselected package libharfbuzz0b:arm64.
129s Preparing to unpack .../49-libharfbuzz0b_10.0.1-1_arm64.deb ...
129s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ...
129s Selecting previously unselected package libthai-data.
129s Preparing to unpack .../50-libthai-data_0.1.29-2build1_all.deb ...
129s Unpacking libthai-data (0.1.29-2build1) ...
129s Selecting previously unselected package libthai0:arm64.
129s Preparing to unpack .../51-libthai0_0.1.29-2build1_arm64.deb ...
129s Unpacking libthai0:arm64 (0.1.29-2build1) ...
129s Selecting previously unselected package libpango-1.0-0:arm64.
129s Preparing to unpack .../52-libpango-1.0-0_1.54.0+ds-3_arm64.deb ...
129s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-3) ...
129s Selecting previously unselected package libpangoft2-1.0-0:arm64.
129s Preparing to unpack .../53-libpangoft2-1.0-0_1.54.0+ds-3_arm64.deb ...
129s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
129s Selecting previously unselected package libpangocairo-1.0-0:arm64.
129s Preparing to unpack .../54-libpangocairo-1.0-0_1.54.0+ds-3_arm64.deb ...
129s Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ...
129s Selecting previously unselected package libwayland-client0:arm64.
129s Preparing to unpack .../55-libwayland-client0_1.23.0-1_arm64.deb ...
129s Unpacking libwayland-client0:arm64 (1.23.0-1) ...
129s Selecting previously unselected package libwayland-cursor0:arm64.
129s Preparing to unpack .../56-libwayland-cursor0_1.23.0-1_arm64.deb ...
129s Unpacking libwayland-cursor0:arm64 (1.23.0-1) ...
129s Selecting previously unselected package libwayland-egl1:arm64.
129s Preparing to unpack .../57-libwayland-egl1_1.23.0-1_arm64.deb ...
129s Unpacking libwayland-egl1:arm64 (1.23.0-1) ...
129s Selecting previously unselected package libxcomposite1:arm64.
129s Preparing to unpack .../58-libxcomposite1_1%3a0.4.6-1_arm64.deb ...
129s Unpacking libxcomposite1:arm64 (1:0.4.6-1) ...
129s Selecting previously unselected package libxfixes3:arm64.
129s Preparing to unpack .../59-libxfixes3_1%3a6.0.0-2build1_arm64.deb ...
129s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ...
129s Selecting previously unselected package libxcursor1:arm64.
129s Preparing to unpack .../60-libxcursor1_1%3a1.2.2-1_arm64.deb ...
129s Unpacking libxcursor1:arm64 (1:1.2.2-1) ...
129s Selecting previously unselected package libxdamage1:arm64.
129s Preparing to unpack .../61-libxdamage1_1%3a1.1.6-1build1_arm64.deb ...
129s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ...
129s Selecting previously unselected package libxinerama1:arm64.
129s Preparing to unpack .../62-libxinerama1_2%3a1.1.4-3build1_arm64.deb ...
129s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ...
129s Selecting previously unselected package libxrandr2:arm64.
129s Preparing to unpack .../63-libxrandr2_2%3a1.5.4-1_arm64.deb ...
129s Unpacking libxrandr2:arm64 (2:1.5.4-1) ...
129s Selecting previously unselected package libgtk-3-common.
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129s Unpacking libgtk-3-common (3.24.43-3ubuntu2) ...
130s Selecting previously unselected package libgtk-3-0t64:arm64.
130s Preparing to unpack .../65-libgtk-3-0t64_3.24.43-3ubuntu2_arm64.deb ...
130s Unpacking libgtk-3-0t64:arm64 (3.24.43-3ubuntu2) ...
130s Selecting previously unselected package x11-common.
130s Preparing to unpack .../66-x11-common_1%3a7.7+23ubuntu3_all.deb ...
130s Unpacking x11-common (1:7.7+23ubuntu3) ...
130s Selecting previously unselected package libice6:arm64.
130s Preparing to unpack .../67-libice6_2%3a1.1.1-1_arm64.deb ...
130s Unpacking libice6:arm64 (2:1.1.1-1) ...
130s Selecting previously unselected package libjs-jquery.
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130s Selecting previously unselected package libnotify4:arm64.
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130s Selecting previously unselected package libopenbabel-dev.
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130s Selecting previously unselected package libopenbabel-doc.
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130s Selecting previously unselected package libpcre2-32-0:arm64.
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130s Selecting previously unselected package libwxbase3.2-1t64:arm64.
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130s Selecting previously unselected package libwxgtk3.2-1t64:arm64.
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130s Unpacking libwxgtk3.2-1t64:arm64 (3.2.5+dfsg-1) ...
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131s Unpacking openbabel (3.1.1+dfsg-11ubuntu1) ...
131s Selecting previously unselected package openbabel-gui.
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131s Selecting previously unselected package python3-openbabel.
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131s Unpacking python3-openbabel (3.1.1+dfsg-11ubuntu1) ...
131s Selecting previously unselected package autopkgtest-satdep.
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131s Unpacking autopkgtest-satdep (0) ...
131s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
131s Setting up liblcms2-2:arm64 (2.16-2) ...
131s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
131s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
131s Setting up libxdamage1:arm64 (1:1.1.6-1build1) ...
131s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
131s Setting up hicolor-icon-theme (0.18-1) ...
131s Setting up libxi6:arm64 (2:1.8.2-1) ...
131s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
131s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
131s Setting up libxcb-render0:arm64 (1.17.0-2) ...
131s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
131s Setting up x11-common (1:7.7+23ubuntu3) ...
131s Setting up libdeflate0:arm64 (1.22-1) ...
131s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
131s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ...
131s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
131s Setting up libcolord2:arm64 (1.4.7-1build2) ...
131s Setting up libdconf1:arm64 (0.40.0-4build2) ...
131s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu3) ...
131s Setting up libepoxy0:arm64 (1.5.10-2) ...
131s Setting up libxfixes3:arm64 (1:6.0.0-2build1) ...
131s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
131s Setting up libavahi-common-data:arm64 (0.8-13ubuntu6) ...
131s Setting up libatspi2.0-0t64:arm64 (2.54.0-1) ...
131s Setting up libxinerama1:arm64 (2:1.1.4-3build1) ...
131s Setting up fonts-dejavu-mono (2.37-8) ...
131s Setting up libxrandr2:arm64 (2:1.5.4-1) ...
131s Setting up fonts-dejavu-core (2.37-8) ...
131s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
131s Setting up libwebp7:arm64 (1.4.0-0.1) ...
131s Setting up at-spi2-common (2.54.0-1) ...
131s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
131s Setting up libthai-data (0.1.29-2build1) ...
131s Setting up libwayland-egl1:arm64 (1.23.0-1) ...
131s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
131s Setting up libwxbase3.2-1t64:arm64 (3.2.5+dfsg-1) ...
131s Setting up libxcomposite1:arm64 (1:0.4.6-1) ...
131s Setting up libinchi1 (1.03+dfsg-4build1) ...
131s Setting up libwayland-client0:arm64 (1.23.0-1) ...
131s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
131s Setting up libice6:arm64 (2:1.1.1-1) ...
131s Setting up libatk1.0-0t64:arm64 (2.54.0-1) ...
131s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
132s Setting up libxtst6:arm64 (2:1.2.3-1.1build1) ...
132s Setting up libxcursor1:arm64 (1:1.2.2-1) ...
132s Setting up libavahi-common3:arm64 (0.8-13ubuntu6) ...
132s Setting up dconf-service (0.40.0-4build2) ...
132s Setting up libopenbabel-doc (3.1.1+dfsg-11ubuntu1) ...
132s Setting up libmaeparser1:arm64 (1.3.1-1build1) ...
132s Setting up libthai0:arm64 (0.1.29-2build1) ...
132s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
132s Setting up libwayland-cursor0:arm64 (1.23.0-1) ...
132s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1) ...
132s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
132s Setting up libsm6:arm64 (2:1.2.4-1) ...
132s Setting up libavahi-client3:arm64 (0.8-13ubuntu6) ...
132s Setting up libatk-bridge2.0-0t64:arm64 (2.54.0-1) ...
132s Setting up gtk-update-icon-cache (4.16.5+ds-1) ...
132s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
134s Regenerating fonts cache... done.
134s Setting up dconf-gsettings-backend:arm64 (0.40.0-4build2) ...
134s Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ...
134s Setting up libcairo2:arm64 (1.18.2-2) ...
134s Setting up libnotify4:arm64 (0.8.3-1build2) ...
134s Setting up libcairo-gobject2:arm64 (1.18.2-2) ...
134s Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
134s Setting up libcups2t64:arm64 (2.4.10-1ubuntu2) ...
134s Setting up libgtk-3-common (3.24.43-3ubuntu2) ...
134s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ...
134s Setting up libopenbabel7 (3.1.1+dfsg-11ubuntu1) ...
134s Setting up libopenbabel-dev (3.1.1+dfsg-11ubuntu1) ...
134s Setting up libchemistry-openbabel-perl (3.1.1+dfsg-11ubuntu1) ...
134s Setting up python3-openbabel (3.1.1+dfsg-11ubuntu1) ...
134s Setting up openbabel (3.1.1+dfsg-11ubuntu1) ...
134s Setting up adwaita-icon-theme (47.0-2) ...
134s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
134s Setting up humanity-icon-theme (0.6.16) ...
134s Setting up ubuntu-mono (24.04-0ubuntu1) ...
134s Processing triggers for man-db (2.12.1-3) ...
134s Processing triggers for libglib2.0-0t64:arm64 (2.82.1-0ubuntu1) ...
134s Setting up libgtk-3-0t64:arm64 (3.24.43-3ubuntu2) ...
134s Setting up libwxgtk3.2-1t64:arm64 (3.2.5+dfsg-1) ...
134s Processing triggers for libc-bin (2.40-1ubuntu3) ...
134s Setting up openbabel-gui (3.1.1+dfsg-11ubuntu1) ...
134s Setting up autopkgtest-satdep (0) ...
142s (Reading database ... 95339 files and directories currently installed.)
142s Removing autopkgtest-satdep (0) ...
143s autopkgtest [13:32:51]: test python3: [-----------------------
143s Running test/testRInChI.py ...
143s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testRInChI.py:1: SyntaxWarning: invalid escape sequence '\P'
143s   """Test OpenBabel executables from Python
143s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testbabel.py:1: SyntaxWarning: invalid escape sequence '\P'
143s   """Test OpenBabel executables from Python
143s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testbabel.py:101: SyntaxWarning: invalid escape sequence '\d'
143s   pat = "(-?\d.*) molecule(?:s?) converted"
144s ..
144s ----------------------------------------------------------------------
144s Ran 2 tests in 1.188s
144s 
144s OK
144s Running test/test_pybel.py ...
144s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/test_pybel.py:1: SyntaxWarning: invalid escape sequence '\P'
144s   """Test OpenBabel Python bindings
144s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testbindings.py:1: SyntaxWarning: invalid escape sequence '\P'
144s   """Test OpenBabel Python bindings
145s .........................==============================
145s *** Open Babel Warning  in WriteMolecule
145s   No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D.
145s .....==============================
145s *** Open Babel Error  in SMARTSError
145s   SMARTS Error:
145s [#NOEL][#NOEL]
145s   ^
145s 
145s ....
145s ----------------------------------------------------------------------
145s Ran 34 tests in 0.425s
145s 
145s OK
145s Running test/testbabel.py ...
145s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testbabel.py:1: SyntaxWarning: invalid escape sequence '\P'
145s   """Test OpenBabel executables from Python
145s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testbabel.py:101: SyntaxWarning: invalid escape sequence '\d'
145s   pat = "(-?\d.*) molecule(?:s?) converted"
147s ......./usr/lib/python3.12/subprocess.py:1010: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
147s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
147s /usr/lib/python3.12/subprocess.py:1016: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
147s   self.stdout = io.open(c2pread, 'rb', bufsize)
147s /usr/lib/python3.12/subprocess.py:1021: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
147s   self.stderr = io.open(errread, 'rb', bufsize)
149s ......
149s ----------------------------------------------------------------------
149s Ran 13 tests in 3.887s
149s 
149s OK
149s Running test/testbindings.py ...
149s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testbindings.py:1: SyntaxWarning: invalid escape sequence '\P'
149s   """Test OpenBabel Python bindings
149s ...==============================
149s *** Open Babel Warning  in WriteMolecule
149s   No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D.
149s ....==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Too many greater-than signs in SMILES string
149s 
149s ==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Too many greater-than signs in SMILES string
149s 
149s ==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Too many greater-than signs in SMILES string
149s 
149s ==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Invalid reaction SMILES string: only a single '>' sign found (two required to be valid).
149s ==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Invalid reaction SMILES string: only a single '>' sign found (two required to be valid).
149s ==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Invalid reaction SMILES string: only a single '>' sign found (two required to be valid).
149s ..==============================
149s *** Open Babel Warning  in IsValid
149s   The molecule is not marked as a reaction. Use SetIsReaction().
149s ==============================
149s *** Open Babel Warning  in IsValid
149s   Reaction roles should be in the range 0 to 3 inclusive.
149s ==============================
149s *** Open Babel Warning  in IsValid
149s   Reaction component Ids should all be non-zero positive integers.
149s ==============================
149s *** Open Babel Warning  in IsValid
149s   The molecule contains an atom that is missing a reaction component Id. Use SetComponentId().
149s ==============================
149s *** Open Babel Warning  in IsValid
149s   A reaction component Id has been stored using a data type that is not an OBPairInteger.
149s ==============================
149s *** Open Babel Warning  in IsValid
149s   The molecule contains a connected component that contains atoms with different reaction component Ids. All atoms in a particular connected component should have the same value.
149s ==============================
149s *** Open Babel Warning  in IsValid
149s   The molecule contains a connected component that contains atoms with different reaction roles. All atoms in a particular connected component should have the same role.
149s ...........==============================
149s *** Open Babel Warning  in ReadMolecule
149s   WARNING: Problem interpreting the valence field of an atom
149s The valence field specifies a valence 0 that is
149s less than the observed explicit valence 1.
149s 
149s .==============================
149s *** Open Babel Warning  in WriteMolecule
149s   No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D.
149s ..........==============================
149s *** Open Babel Error  in ParseComplex
149s   SMILES string contains a character '#' which is invalid
149s ==============================
149s *** Open Babel Error  in ParseComplex
149s   Element number must be <= 255)
149s ==============================
149s *** Open Babel Error  in ParseComplex
149s   SMILES string contains a character '#' which is invalid
149s ..==============================
149s *** Open Babel Warning  in ParseRingBond
149s   Warning: Tetrahedral stereo specified for atom with more than 4 connections.
149s ==============================
149s *** Open Babel Warning  in ParseSmiles
149s   Failed to kekulize aromatic SMILES
149s 
197s .../tmp/autopkgtest.r6PFaE/build.gbN/src/debian/tests/python3: line 9:  3585 Killed                  python3 ${TEST}
197s Ignoring test/testbindings.py on arm64 ...
197s Running test/testcdjsonformat.py ...
197s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testcdjsonformat.py:1: SyntaxWarning: invalid escape sequence '\P'
197s   """Test ChemDoodle JSON format using the OpenBabel Python bindings
198s ..........
198s ----------------------------------------------------------------------
198s Ran 10 tests in 0.012s
198s 
198s OK
198s Running test/testdistgeom.py ...
198s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testdistgeom.py:1: SyntaxWarning: invalid escape sequence '\P'
198s   """Test OpenBabel executables from Python
198s /usr/lib/python3.12/subprocess.py:1010: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
198s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
198s /usr/lib/python3.12/subprocess.py:1016: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
198s   self.stdout = io.open(c2pread, 'rb', bufsize)
198s /usr/lib/python3.12/subprocess.py:1021: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
198s   self.stderr = io.open(errread, 'rb', bufsize)
233s .
233s ----------------------------------------------------------------------
233s Ran 1 test in 35.316s
233s 
233s OK
233s Running test/testexample.py ...
233s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testexample.py:1: SyntaxWarning: invalid escape sequence '\P'
233s   """Example test that uses the OpenBabel Python bindings
233s ..
233s ----------------------------------------------------------------------
233s Ran 2 tests in 0.001s
233s 
233s OK
233s Running test/testfastsearch.py ...
233s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testfastsearch.py:1: SyntaxWarning: invalid escape sequence '\P'
233s   """Test OpenBabel executables from Python
233s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testfastsearch.py:30: SyntaxWarning: invalid escape sequence '\C'
233s   smiles = """C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC
233s .
233s ----------------------------------------------------------------------
233s Ran 1 test in 0.078s
233s 
233s OK
233s Running test/testkekule.py ...
233s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testkekule.py:1: SyntaxWarning: invalid escape sequence '\P'
233s   """Test OpenBabel executables from Python
233s /usr/lib/python3.12/subprocess.py:1010: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
233s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
233s /usr/lib/python3.12/subprocess.py:1016: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
233s   self.stdout = io.open(c2pread, 'rb', bufsize)
233s /usr/lib/python3.12/subprocess.py:1021: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
233s   self.stderr = io.open(errread, 'rb', bufsize)
234s ...
234s ----------------------------------------------------------------------
234s Ran 3 tests in 0.572s
234s 
234s OK
234s Running test/testobconv_writers.py ...
234s ..........................................................................................F..................................................
234s ======================================================================
234s FAIL: test_default (__main__.TestPCJSON.test_default)
234s ----------------------------------------------------------------------
234s Traceback (most recent call last):
234s   File "/tmp/autopkgtest.r6PFaE/build.gbN/src/test/testobconv_writers.py", line 2761, in test_default
234s     self.assertWriters(self.fmt, """\
234s   File "/tmp/autopkgtest.r6PFaE/build.gbN/src/test/testobconv_writers.py", line 258, in assertWriters
234s     test_write_string(self, mol, conv, expected_output, normalize)
234s   File "/tmp/autopkgtest.r6PFaE/build.gbN/src/test/testobconv_writers.py", line 165, in test_write_string
234s     test_case.assertMultiLineEqual(output.replace("\r\n", "\n"), expected_output.replace("\r\n", "\n"))
234s AssertionError: '{\n [1926 chars]102014\n              ],\n              "y": [[1070 chars]]\n}' != '{\n [1926 chars]102012\n              ],\n              "y": [[1070 chars]]\n}'
234s   {
234s     "PC_Compounds": [
234s       {
234s         "atoms": {
234s           "aids": [
234s             1,
234s             2,
234s             3,
234s             4,
234s             5,
234s             6,
234s             7,
234s             8,
234s             9,
234s             10,
234s             11,
234s             12,
234s             13
234s           ],
234s           "element": [
234s             6,
234s             6,
234s             6,
234s             6,
234s             6,
234s             6,
234s             8,
234s             1,
234s             1,
234s             1,
234s             1,
234s             1,
234s             1
234s           ]
234s         },
234s         "bonds": {
234s           "aid1": [
234s             1,
234s             1,
234s             2,
234s             3,
234s             4,
234s             5,
234s             6,
234s             1,
234s             2,
234s             3,
234s             4,
234s             5,
234s             7
234s           ],
234s           "aid2": [
234s             6,
234s             2,
234s             3,
234s             4,
234s             5,
234s             6,
234s             7,
234s             8,
234s             9,
234s             10,
234s             11,
234s             12,
234s             13
234s           ],
234s           "order": [
234s             2,
234s             1,
234s             2,
234s             1,
234s             2,
234s             1,
234s             1,
234s             1,
234s             1,
234s             1,
234s             1,
234s             1,
234s             1
234s           ]
234s         },
234s         "coords": [
234s           {
234s             "type": [
234s               1
234s             ],
234s             "aids": [
234s               1,
234s               2,
234s               3,
234s               4,
234s               5,
234s               6,
234s               7,
234s               8,
234s               9,
234s               10,
234s               11,
234s               12,
234s               13
234s             ],
234s             "conformers": [
234s               {
234s                 "x": [
234s                   1.5846,
234s                   1.5703,
234s                   2.4295,
234s                   3.3031,
234s                   3.3175,
234s                   0.0,
234s                   -1.0005,
234s                   2.313816216007316,
234s                   0.669250157347277,
234s                   2.4146659588503769,
234s                   4.189331679349326,
234s                   4.052466878708012,
234s -                 -1.4648575597102014
234s ?                                   ^
234s +                 -1.4648575597102012
234s ?                                   ^
234s                 ],
234s                 "y": [
234s                   1.5846,
234s                   1.5703,
234s                   2.4295,
234s                   3.3031,
234s                   3.3175,
234s                   0.0,
234s                   -1.0005,
234s                   2.313816216007316,
234s                   0.669250157347277,
234s                   2.4146659588503769,
234s                   4.189331679349326,
234s                   4.052466878708012,
234s -                 -1.4648575597102014
234s ?                                   ^
234s +                 -1.4648575597102012
234s ?                                   ^
234s                 ],
234s                 "style": {
234s                   "annotation": [
234s                     8,
234s                     8,
234s                     8,
234s                     8,
234s                     8,
234s                     8
234s                   ],
234s                   "aid1": [
234s                     1,
234s                     1,
234s                     2,
234s                     3,
234s                     4,
234s                     5
234s                   ],
234s                   "aid2": [
234s                     6,
234s                     2,
234s                     3,
234s                     4,
234s                     5,
234s                     6
234s                   ]
234s                 }
234s               }
234s             ]
234s           }
234s         ],
234s         "charge": 0
234s       }
234s     ]
234s   }
234s 
234s 
234s ----------------------------------------------------------------------
234s Ran 141 tests in 0.172s
234s 
234s FAILED (failures=1)
234s Ignoring test/testobconv_writers.py on arm64 ...
234s Running test/testpcjsonformat.py ...
234s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testpcjsonformat.py:1: SyntaxWarning: invalid escape sequence '\P'
234s   """Test PubChem JSON format using the OpenBabel Python bindings
234s .................
234s ----------------------------------------------------------------------
234s Ran 17 tests in 0.019s
234s 
234s OK
234s Running test/testpdbformat.py ...
234s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testpdbformat.py:1: SyntaxWarning: invalid escape sequence '\P'
234s   """Test OpenBabel executables from Python
235s /usr/lib/python3.12/subprocess.py:1010: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
235s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
235s /usr/lib/python3.12/subprocess.py:1016: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
235s   self.stdout = io.open(c2pread, 'rb', bufsize)
235s /usr/lib/python3.12/subprocess.py:1021: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
235s   self.stderr = io.open(errread, 'rb', bufsize)
235s .
235s ----------------------------------------------------------------------
235s Ran 1 test in 0.026s
235s 
235s OK
235s Skipping test/testroundtrip.py ...
235s Running test/testsmartssym.py ...
235s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testsmartssym.py:1: SyntaxWarning: invalid escape sequence '\P'
235s   """Test OpenBabel executables from Python
235s /usr/lib/python3.12/subprocess.py:1010: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
235s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
235s /usr/lib/python3.12/subprocess.py:1016: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
235s   self.stdout = io.open(c2pread, 'rb', bufsize)
235s /usr/lib/python3.12/subprocess.py:1021: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
235s   self.stderr = io.open(errread, 'rb', bufsize)
236s ....
236s ----------------------------------------------------------------------
236s Ran 4 tests in 1.146s
236s 
236s OK
236s Skipping test/testsym.py ...
236s Running test/testunique.py ...
236s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testunique.py:1: SyntaxWarning: invalid escape sequence '\P'
236s   """Test OpenBabel executables from Python
236s /tmp/autopkgtest.r6PFaE/build.gbN/src/test/testunique.py:26: SyntaxWarning: invalid escape sequence '\F'
236s   self.smiles = """C	methane
236s /usr/lib/python3.12/subprocess.py:1010: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
236s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
236s /usr/lib/python3.12/subprocess.py:1016: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
236s   self.stdout = io.open(c2pread, 'rb', bufsize)
236s /usr/lib/python3.12/subprocess.py:1021: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
236s   self.stderr = io.open(errread, 'rb', bufsize)
236s .
236s ----------------------------------------------------------------------
236s Ran 1 test in 0.277s
236s 
236s OK
237s autopkgtest [13:34:25]: test python3: -----------------------]
237s autopkgtest [13:34:25]: test python3:  - - - - - - - - - - results - - - - - - - - - -
237s python3              PASS
238s autopkgtest [13:34:26]: @@@@@@@@@@@@@@@@@@@@ summary
238s python3              PASS
265s nova [W] Skipping flock in bos03-arm64
265s Creating nova instance adt-plucky-arm64-openbabel-20241113-133028-juju-7f2275-prod-proposed-migration-environment-15-c1aacaee-8f5c-4d71-9a4f-ce5d9026db2e from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...