0s autopkgtest [13:58:49]: starting date and time: 2025-01-17 13:58:49+0000 0s autopkgtest [13:58:49]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:58:49]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.aitjl0r4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:rdkit,src:boost1.83,src:python3-defaults --apt-upgrade rdkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=rdkit/202409.4-1 boost1.83/1.83.0-4ubuntu2 python3-defaults/3.13.1-1~exp2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-28.secgroup --name adt-plucky-arm64-rdkit-20250117-135849-juju-7f2275-prod-proposed-migration-environment-15-ba908c29-d404-4e05-8c68-97b0621ed4f8 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 155s autopkgtest [14:01:24]: testbed dpkg architecture: arm64 155s autopkgtest [14:01:24]: testbed apt version: 2.9.18 155s autopkgtest [14:01:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s autopkgtest [14:01:24]: testbed release detected to be: None 156s autopkgtest [14:01:25]: updating testbed package index (apt update) 157s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 157s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 157s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 157s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 157s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.7 kB] 157s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 157s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [877 kB] 157s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 157s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [318 kB] 157s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 157s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [1079 kB] 157s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 158s Fetched 2618 kB in 1s (2520 kB/s) 159s Reading package lists... 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 161s Calculating upgrade... 161s The following packages will be upgraded: 161s libgudev-1.0-0 usb.ids 161s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 238 kB of archives. 161s After this operation, 1024 B of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 usb.ids all 2025.01.14-1 [223 kB] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgudev-1.0-0 arm64 1:238-6 [14.9 kB] 162s Fetched 238 kB in 0s (481 kB/s) 163s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80204 files and directories currently installed.) 163s Preparing to unpack .../usb.ids_2025.01.14-1_all.deb ... 163s Unpacking usb.ids (2025.01.14-1) over (2024.12.04-1) ... 163s Preparing to unpack .../libgudev-1.0-0_1%3a238-6_arm64.deb ... 163s Unpacking libgudev-1.0-0:arm64 (1:238-6) over (1:238-5ubuntu1) ... 163s Setting up usb.ids (2025.01.14-1) ... 163s Setting up libgudev-1.0-0:arm64 (1:238-6) ... 163s Processing triggers for libc-bin (2.40-4ubuntu1) ... 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 165s autopkgtest [14:01:34]: upgrading testbed (apt dist-upgrade and autopurge) 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 167s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 167s Starting 2 pkgProblemResolver with broken count: 0 167s Done 168s Entering ResolveByKeep 168s 169s The following packages were automatically installed and are no longer required: 169s python3.12 python3.12-minimal 169s Use 'sudo apt autoremove' to remove them. 169s The following NEW packages will be installed: 169s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 169s The following packages will be upgraded: 169s libpython3-stdlib python3 python3-minimal 169s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 169s Need to get 5992 kB of archives. 169s After this operation, 24.3 MB of additional disk space will be used. 169s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.1-2 [879 kB] 170s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.1-2 [2262 kB] 170s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.13.1-1~exp2 [27.6 kB] 170s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.13.1-1~exp2 [23.9 kB] 170s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [2061 kB] 170s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.1-2 [729 kB] 170s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.13.1-1~exp2 [10.2 kB] 171s Fetched 5992 kB in 1s (6969 kB/s) 171s Selecting previously unselected package libpython3.13-minimal:arm64. 171s (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 ... 80204 files and directories currently installed.) 171s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_arm64.deb ... 171s Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... 171s Selecting previously unselected package python3.13-minimal. 171s Preparing to unpack .../python3.13-minimal_3.13.1-2_arm64.deb ... 171s Unpacking python3.13-minimal (3.13.1-2) ... 171s Setting up libpython3.13-minimal:arm64 (3.13.1-2) ... 171s Setting up python3.13-minimal (3.13.1-2) ... 173s (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 ... 80524 files and directories currently installed.) 173s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_arm64.deb ... 173s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 173s Setting up python3-minimal (3.13.1-1~exp2) ... 173s (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 ... 80524 files and directories currently installed.) 173s Preparing to unpack .../python3_3.13.1-1~exp2_arm64.deb ... 173s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 173s Selecting previously unselected package libpython3.13-stdlib:arm64. 173s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_arm64.deb ... 173s Unpacking libpython3.13-stdlib:arm64 (3.13.1-2) ... 173s Selecting previously unselected package python3.13. 173s Preparing to unpack .../python3.13_3.13.1-2_arm64.deb ... 173s Unpacking python3.13 (3.13.1-2) ... 174s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_arm64.deb ... 174s Unpacking libpython3-stdlib:arm64 (3.13.1-1~exp2) over (3.12.8-1) ... 174s Setting up libpython3.13-stdlib:arm64 (3.13.1-2) ... 174s Setting up libpython3-stdlib:arm64 (3.13.1-1~exp2) ... 174s Setting up python3.13 (3.13.1-2) ... 175s Setting up python3 (3.13.1-1~exp2) ... 175s /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. 175s for fn in glob1(directory, "%s.*" % fname): 176s Processing triggers for man-db (2.13.0-1) ... 177s Processing triggers for systemd (257-2ubuntu1) ... 177s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 179s The following packages will be REMOVED: 179s python3.12* python3.12-minimal* 180s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 180s After this operation, 8710 kB disk space will be freed. 180s (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 ... 80941 files and directories currently installed.) 180s Removing python3.12 (3.12.8-3) ... 180s Removing python3.12-minimal (3.12.8-3) ... 180s /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. 180s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 181s Processing triggers for man-db (2.13.0-1) ... 181s Processing triggers for systemd (257-2ubuntu1) ... 182s (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 ... 80913 files and directories currently installed.) 182s Purging configuration files for python3.12-minimal (3.12.8-3) ... 185s autopkgtest [14:01:54]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 185s autopkgtest [14:01:54]: @@@@@@@@@@@@@@@@@@@@ apt-source rdkit 192s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe rdkit 202409.4-1 (dsc) [3024 B] 192s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe rdkit 202409.4-1 (tar) [63.4 MB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe rdkit 202409.4-1 (diff) [39.7 kB] 193s gpgv: Signature made Wed Jan 15 17:30:33 2025 UTC 193s gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 193s gpgv: Can't check signature: No public key 193s dpkg-source: warning: cannot verify inline signature for ./rdkit_202409.4-1.dsc: no acceptable signature found 196s autopkgtest [14:02:05]: testing package rdkit version 202409.4-1 197s autopkgtest [14:02:06]: build not needed 207s autopkgtest [14:02:16]: test installcheck: preparing testbed 207s Reading package lists... 208s Building dependency tree... 208s Reading state information... 208s Starting pkgProblemResolver with broken count: 0 208s Starting 2 pkgProblemResolver with broken count: 0 208s Done 209s The following NEW packages will be installed: 209s fontconfig-config fonts-freefont-ttf libblas3 libboost-iostreams1.83.0 209s libboost-numpy1.83.0 libboost-python1.83.0 libboost-serialization1.83.0 209s libcairo2 libcoordgen3 libfontconfig1 libgfortran5 libinchi1.07 209s libio-pty-perl libipc-run-perl libjs-jquery libjs-underscore libjson-perl 209s liblapack3 libmaeparser1 libpixman-1-0 libpq5 librdkit-dev librdkit1t64 209s libxcb-render0 libxcb-shm0 libxrender1 libxslt1.1 postgresql-17 209s postgresql-17-rdkit postgresql-client-17 postgresql-client-common 209s postgresql-common python3-numpy python3-rdkit rdkit-data rdkit-doc ssl-cert 209s 0 upgraded, 37 newly installed, 0 to remove and 0 not upgraded. 209s Need to get 63.1 MB of archives. 209s After this operation, 326 MB of additional disk space will be used. 209s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 210s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-pty-perl arm64 1:1.20-1build3 [31.3 kB] 210s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libipc-run-perl all 20231003.0-2 [91.5 kB] 210s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-client-common all 267 [37.1 kB] 210s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 ssl-cert all 1.1.3ubuntu1 [18.7 kB] 210s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-common all 267 [162 kB] 210s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 210s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 210s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 210s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-4ubuntu2 [259 kB] 210s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libboost-python1.83.0 arm64 1.83.0-4ubuntu2 [323 kB] 210s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4ubuntu2 [242 kB] 210s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libboost-serialization1.83.0 arm64 1.83.0-4ubuntu2 [338 kB] 210s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 210s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 210s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 210s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 210s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 210s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 210s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB] 210s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 210s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libinchi1.07 arm64 1.07.1+dfsg-6 [574 kB] 210s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 211s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 211s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 211s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB] 211s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpq5 arm64 17.2-1 [141 kB] 211s Get:28 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit1t64 arm64 202409.4-1 [5376 kB] 211s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit-dev arm64 202409.4-1 [346 kB] 211s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 211s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-client-17 arm64 17.2-1 [1318 kB] 211s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-17 arm64 17.2-1 [15.5 MB] 213s Get:33 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 postgresql-17-rdkit arm64 202409.4-1 [121 kB] 213s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 213s Get:35 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-data all 202409.4-1 [12.6 MB] 214s Get:36 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-rdkit arm64 202409.4-1 [4656 kB] 214s Get:37 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-doc all 202409.4-1 [6325 kB] 215s Preconfiguring packages ... 215s Fetched 63.1 MB in 5s (12.0 MB/s) 216s Selecting previously unselected package libjson-perl. 216s (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 ... 80913 files and directories currently installed.) 216s Preparing to unpack .../00-libjson-perl_4.10000-1_all.deb ... 216s Unpacking libjson-perl (4.10000-1) ... 216s Selecting previously unselected package libio-pty-perl. 216s Preparing to unpack .../01-libio-pty-perl_1%3a1.20-1build3_arm64.deb ... 216s Unpacking libio-pty-perl (1:1.20-1build3) ... 216s Selecting previously unselected package libipc-run-perl. 216s Preparing to unpack .../02-libipc-run-perl_20231003.0-2_all.deb ... 216s Unpacking libipc-run-perl (20231003.0-2) ... 216s Selecting previously unselected package postgresql-client-common. 216s Preparing to unpack .../03-postgresql-client-common_267_all.deb ... 216s Unpacking postgresql-client-common (267) ... 216s Selecting previously unselected package ssl-cert. 216s Preparing to unpack .../04-ssl-cert_1.1.3ubuntu1_all.deb ... 216s Unpacking ssl-cert (1.1.3ubuntu1) ... 216s Selecting previously unselected package postgresql-common. 216s Preparing to unpack .../05-postgresql-common_267_all.deb ... 216s Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common' 216s Unpacking postgresql-common (267) ... 216s Selecting previously unselected package fonts-freefont-ttf. 216s Preparing to unpack .../06-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 216s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 216s Selecting previously unselected package fontconfig-config. 216s Preparing to unpack .../07-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 216s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 216s Selecting previously unselected package libblas3:arm64. 216s Preparing to unpack .../08-libblas3_3.12.0-4_arm64.deb ... 216s Unpacking libblas3:arm64 (3.12.0-4) ... 216s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 216s Preparing to unpack .../09-libboost-iostreams1.83.0_1.83.0-4ubuntu2_arm64.deb ... 216s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-4ubuntu2) ... 216s Selecting previously unselected package libboost-python1.83.0. 216s Preparing to unpack .../10-libboost-python1.83.0_1.83.0-4ubuntu2_arm64.deb ... 216s Unpacking libboost-python1.83.0 (1.83.0-4ubuntu2) ... 216s Selecting previously unselected package libboost-numpy1.83.0. 216s Preparing to unpack .../11-libboost-numpy1.83.0_1.83.0-4ubuntu2_arm64.deb ... 216s Unpacking libboost-numpy1.83.0 (1.83.0-4ubuntu2) ... 216s Selecting previously unselected package libboost-serialization1.83.0:arm64. 217s Preparing to unpack .../12-libboost-serialization1.83.0_1.83.0-4ubuntu2_arm64.deb ... 217s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-4ubuntu2) ... 217s Selecting previously unselected package libfontconfig1:arm64. 217s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 217s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 217s Selecting previously unselected package libpixman-1-0:arm64. 217s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_arm64.deb ... 217s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 217s Selecting previously unselected package libxcb-render0:arm64. 217s Preparing to unpack .../15-libxcb-render0_1.17.0-2_arm64.deb ... 217s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 217s Selecting previously unselected package libxcb-shm0:arm64. 217s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_arm64.deb ... 217s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 217s Selecting previously unselected package libxrender1:arm64. 217s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 217s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 217s Selecting previously unselected package libcairo2:arm64. 217s Preparing to unpack .../18-libcairo2_1.18.2-2_arm64.deb ... 217s Unpacking libcairo2:arm64 (1.18.2-2) ... 217s Selecting previously unselected package libcoordgen3:arm64. 217s Preparing to unpack .../19-libcoordgen3_3.0.2-1_arm64.deb ... 217s Unpacking libcoordgen3:arm64 (3.0.2-1) ... 217s Selecting previously unselected package libgfortran5:arm64. 217s Preparing to unpack .../20-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 217s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 217s Selecting previously unselected package libinchi1.07. 217s Preparing to unpack .../21-libinchi1.07_1.07.1+dfsg-6_arm64.deb ... 217s Unpacking libinchi1.07 (1.07.1+dfsg-6) ... 217s Selecting previously unselected package libjs-jquery. 217s Preparing to unpack .../22-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 217s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 217s Selecting previously unselected package libjs-underscore. 217s Preparing to unpack .../23-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 217s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 217s Selecting previously unselected package liblapack3:arm64. 217s Preparing to unpack .../24-liblapack3_3.12.0-4_arm64.deb ... 217s Unpacking liblapack3:arm64 (3.12.0-4) ... 217s Selecting previously unselected package libmaeparser1:arm64. 217s Preparing to unpack .../25-libmaeparser1_1.3.1-1build1_arm64.deb ... 217s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ... 217s Selecting previously unselected package libpq5:arm64. 217s Preparing to unpack .../26-libpq5_17.2-1_arm64.deb ... 217s Unpacking libpq5:arm64 (17.2-1) ... 217s Selecting previously unselected package librdkit1t64. 217s Preparing to unpack .../27-librdkit1t64_202409.4-1_arm64.deb ... 217s Unpacking librdkit1t64 (202409.4-1) ... 218s Selecting previously unselected package librdkit-dev. 218s Preparing to unpack .../28-librdkit-dev_202409.4-1_arm64.deb ... 218s Unpacking librdkit-dev (202409.4-1) ... 218s Selecting previously unselected package libxslt1.1:arm64. 218s Preparing to unpack .../29-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 218s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 218s Selecting previously unselected package postgresql-client-17. 218s Preparing to unpack .../30-postgresql-client-17_17.2-1_arm64.deb ... 218s Unpacking postgresql-client-17 (17.2-1) ... 218s Selecting previously unselected package postgresql-17. 218s Preparing to unpack .../31-postgresql-17_17.2-1_arm64.deb ... 218s Unpacking postgresql-17 (17.2-1) ... 219s Selecting previously unselected package postgresql-17-rdkit. 219s Preparing to unpack .../32-postgresql-17-rdkit_202409.4-1_arm64.deb ... 219s Unpacking postgresql-17-rdkit (202409.4-1) ... 219s Selecting previously unselected package python3-numpy. 219s Preparing to unpack .../33-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 219s Unpacking python3-numpy (1:1.26.4+ds-12) ... 219s Selecting previously unselected package rdkit-data. 219s Preparing to unpack .../34-rdkit-data_202409.4-1_all.deb ... 219s Unpacking rdkit-data (202409.4-1) ... 220s Selecting previously unselected package python3-rdkit. 220s Preparing to unpack .../35-python3-rdkit_202409.4-1_arm64.deb ... 220s Unpacking python3-rdkit (202409.4-1) ... 220s Selecting previously unselected package rdkit-doc. 220s Preparing to unpack .../36-rdkit-doc_202409.4-1_all.deb ... 220s Unpacking rdkit-doc (202409.4-1) ... 221s Setting up libboost-python1.83.0 (1.83.0-4ubuntu2) ... 221s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 221s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 221s Setting up libio-pty-perl (1:1.20-1build3) ... 221s Setting up libxcb-render0:arm64 (1.17.0-2) ... 221s Setting up libpq5:arm64 (17.2-1) ... 221s Setting up fonts-freefont-ttf (20211204+svn4273-2) ... 221s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 221s Setting up rdkit-data (202409.4-1) ... 221s Setting up libboost-serialization1.83.0:arm64 (1.83.0-4ubuntu2) ... 221s Setting up libboost-numpy1.83.0 (1.83.0-4ubuntu2) ... 221s Setting up libblas3:arm64 (3.12.0-4) ... 221s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 221s Setting up ssl-cert (1.1.3ubuntu1) ... 222s Created symlink '/etc/systemd/system/multi-user.target.wants/ssl-cert.service' → '/usr/lib/systemd/system/ssl-cert.service'. 222s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-4ubuntu2) ... 222s Setting up libipc-run-perl (20231003.0-2) ... 222s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 222s Setting up libjson-perl (4.10000-1) ... 222s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 222s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 222s Setting up libcoordgen3:arm64 (3.0.2-1) ... 222s Setting up libinchi1.07 (1.07.1+dfsg-6) ... 222s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 222s Setting up postgresql-client-common (267) ... 222s Setting up liblapack3:arm64 (3.12.0-4) ... 222s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 222s Setting up postgresql-client-17 (17.2-1) ... 223s update-alternatives: using /usr/share/postgresql/17/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode 223s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 224s Setting up rdkit-doc (202409.4-1) ... 224s Setting up libmaeparser1:arm64 (1.3.1-1build1) ... 224s Setting up postgresql-common (267) ... 224s Creating config file /etc/postgresql-common/createcluster.conf with new version 225s Building PostgreSQL dictionaries from installed myspell/hunspell packages... 225s Removing obsolete dictionary files: 226s Created symlink '/etc/systemd/system/multi-user.target.wants/postgresql.service' → '/usr/lib/systemd/system/postgresql.service'. 226s Setting up python3-numpy (1:1.26.4+ds-12) ... 229s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 229s Setting up postgresql-17 (17.2-1) ... 230s Creating new PostgreSQL cluster 17/main ... 230s /usr/lib/postgresql/17/bin/initdb -D /var/lib/postgresql/17/main --auth-local peer --auth-host scram-sha-256 --no-instructions 230s The files belonging to this database system will be owned by user "postgres". 230s This user must also own the server process. 230s 230s The database cluster will be initialized with locale "C.UTF-8". 230s The default database encoding has accordingly been set to "UTF8". 230s The default text search configuration will be set to "english". 230s 230s Data page checksums are disabled. 230s 230s fixing permissions on existing directory /var/lib/postgresql/17/main ... ok 230s creating subdirectories ... ok 230s selecting dynamic shared memory implementation ... posix 230s selecting default "max_connections" ... 100 230s selecting default "shared_buffers" ... 128MB 230s selecting default time zone ... Etc/UTC 230s creating configuration files ... ok 230s running bootstrap script ... ok 231s performing post-bootstrap initialization ... ok 231s syncing data to disk ... ok 235s Setting up libcairo2:arm64 (1.18.2-2) ... 235s Setting up librdkit1t64 (202409.4-1) ... 235s Setting up postgresql-17-rdkit (202409.4-1) ... 235s Setting up python3-rdkit (202409.4-1) ... 236s Setting up librdkit-dev (202409.4-1) ... 236s Processing triggers for man-db (2.13.0-1) ... 237s Processing triggers for libc-bin (2.40-4ubuntu1) ... 240s autopkgtest [14:02:49]: test installcheck: [----------------------- 240s ### PostgreSQL 17 installcheck ### 240s Creating new PostgreSQL cluster 17/regress ... 243s make: Entering directory '/tmp/autopkgtest.oMhfzY/build.nEK/src/Code/PgSQL/rdkit' 243s echo "# +++ regress install-check in +++" && /usr/lib/postgresql/17/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=/tmp/autopkgtest.oMhfzY/build.nEK/src --bindir='/usr/lib/postgresql/17/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 bfpgin sfpgist slfpgist fps reaction fmcs query xqm 243s # +++ regress install-check in +++ 243s # using postmaster on localhost, port 5433 247s ok 1 - rdkit-91 3234 ms 247s ok 2 - props 194 ms 248s ok 3 - btree 577 ms 249s ok 4 - molgist 1550 ms 249s ok 5 - bfpgist-91 148 ms 249s ok 6 - bfpgin 258 ms 250s ok 7 - sfpgist 120 ms 250s ok 8 - slfpgist 103 ms 250s ok 9 - fps 148 ms 253s ok 10 - reaction 3224 ms 253s ok 11 - fmcs 342 ms 254s ok 12 - query 71 ms 254s ok 13 - xqm 383 ms 254s 1..13 254s # All 13 tests passed. 254s make: Leaving directory '/tmp/autopkgtest.oMhfzY/build.nEK/src/Code/PgSQL/rdkit' 254s Dropping cluster 17/regress ... 254s ### End 17 installcheck ### 254s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 254s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 255s autopkgtest [14:03:04]: test installcheck: -----------------------] 255s autopkgtest [14:03:04]: test installcheck: - - - - - - - - - - results - - - - - - - - - - 255s installcheck PASS 256s autopkgtest [14:03:05]: test importcheck: preparing testbed 449s autopkgtest [14:06:18]: testbed dpkg architecture: arm64 449s autopkgtest [14:06:18]: testbed apt version: 2.9.18 449s autopkgtest [14:06:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 449s autopkgtest [14:06:18]: testbed release detected to be: plucky 450s autopkgtest [14:06:19]: updating testbed package index (apt update) 450s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 451s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 451s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 451s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 451s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 451s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.7 kB] 451s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [877 kB] 451s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 451s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [318 kB] 451s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 451s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [1079 kB] 451s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 451s Fetched 2618 kB in 1s (2603 kB/s) 452s Reading package lists... 453s Reading package lists... 453s Building dependency tree... 453s Reading state information... 454s Calculating upgrade... 454s The following packages will be upgraded: 454s libgudev-1.0-0 usb.ids 455s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 455s Need to get 238 kB of archives. 455s After this operation, 1024 B of additional disk space will be used. 455s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 usb.ids all 2025.01.14-1 [223 kB] 455s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgudev-1.0-0 arm64 1:238-6 [14.9 kB] 456s Fetched 238 kB in 1s (421 kB/s) 456s (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 ... 80204 files and directories currently installed.) 456s Preparing to unpack .../usb.ids_2025.01.14-1_all.deb ... 456s Unpacking usb.ids (2025.01.14-1) over (2024.12.04-1) ... 456s Preparing to unpack .../libgudev-1.0-0_1%3a238-6_arm64.deb ... 456s Unpacking libgudev-1.0-0:arm64 (1:238-6) over (1:238-5ubuntu1) ... 456s Setting up usb.ids (2025.01.14-1) ... 456s Setting up libgudev-1.0-0:arm64 (1:238-6) ... 456s Processing triggers for libc-bin (2.40-4ubuntu1) ... 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 458s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 458s autopkgtest [14:06:27]: upgrading testbed (apt dist-upgrade and autopurge) 458s Reading package lists... 458s Building dependency tree... 458s Reading state information... 459s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 459s Starting 2 pkgProblemResolver with broken count: 0 459s Done 460s Entering ResolveByKeep 460s 461s The following packages were automatically installed and are no longer required: 461s python3.12 python3.12-minimal 461s Use 'sudo apt autoremove' to remove them. 461s The following NEW packages will be installed: 461s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 461s The following packages will be upgraded: 461s libpython3-stdlib python3 python3-minimal 461s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 461s Need to get 5992 kB of archives. 461s After this operation, 24.3 MB of additional disk space will be used. 461s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.1-2 [879 kB] 461s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.1-2 [2262 kB] 462s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.13.1-1~exp2 [27.6 kB] 462s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.13.1-1~exp2 [23.9 kB] 462s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [2061 kB] 462s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.1-2 [729 kB] 462s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.13.1-1~exp2 [10.2 kB] 463s Fetched 5992 kB in 2s (3274 kB/s) 463s Selecting previously unselected package libpython3.13-minimal:arm64. 463s (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 ... 80204 files and directories currently installed.) 463s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_arm64.deb ... 463s Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... 463s Selecting previously unselected package python3.13-minimal. 463s Preparing to unpack .../python3.13-minimal_3.13.1-2_arm64.deb ... 463s Unpacking python3.13-minimal (3.13.1-2) ... 463s Setting up libpython3.13-minimal:arm64 (3.13.1-2) ... 463s Setting up python3.13-minimal (3.13.1-2) ... 464s (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 ... 80524 files and directories currently installed.) 464s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_arm64.deb ... 464s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 464s Setting up python3-minimal (3.13.1-1~exp2) ... 465s (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 ... 80524 files and directories currently installed.) 465s Preparing to unpack .../python3_3.13.1-1~exp2_arm64.deb ... 465s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 465s Selecting previously unselected package libpython3.13-stdlib:arm64. 465s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_arm64.deb ... 465s Unpacking libpython3.13-stdlib:arm64 (3.13.1-2) ... 465s Selecting previously unselected package python3.13. 465s Preparing to unpack .../python3.13_3.13.1-2_arm64.deb ... 465s Unpacking python3.13 (3.13.1-2) ... 465s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_arm64.deb ... 465s Unpacking libpython3-stdlib:arm64 (3.13.1-1~exp2) over (3.12.8-1) ... 465s Setting up libpython3.13-stdlib:arm64 (3.13.1-2) ... 465s Setting up libpython3-stdlib:arm64 (3.13.1-1~exp2) ... 465s Setting up python3.13 (3.13.1-2) ... 466s Setting up python3 (3.13.1-1~exp2) ... 466s /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. 466s for fn in glob1(directory, "%s.*" % fname): 467s Processing triggers for man-db (2.13.0-1) ... 467s Processing triggers for systemd (257-2ubuntu1) ... 468s Reading package lists... 468s Building dependency tree... 468s Reading state information... 469s Starting pkgProblemResolver with broken count: 0 469s Starting 2 pkgProblemResolver with broken count: 0 469s Done 470s The following packages will be REMOVED: 470s python3.12* python3.12-minimal* 470s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 470s After this operation, 8710 kB disk space will be freed. 470s (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 ... 80941 files and directories currently installed.) 470s Removing python3.12 (3.12.8-3) ... 470s Removing python3.12-minimal (3.12.8-3) ... 471s /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. 471s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 471s Processing triggers for man-db (2.13.0-1) ... 471s Processing triggers for systemd (257-2ubuntu1) ... 471s (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 ... 80913 files and directories currently installed.) 471s Purging configuration files for python3.12-minimal (3.12.8-3) ... 475s Reading package lists... 475s Building dependency tree... 475s Reading state information... 476s Starting pkgProblemResolver with broken count: 0 476s Starting 2 pkgProblemResolver with broken count: 0 476s Done 477s The following NEW packages will be installed: 477s fontconfig-config fonts-freefont-ttf libblas3 libboost-iostreams1.83.0 477s libboost-numpy1.83.0 libboost-python1.83.0 libboost-serialization1.83.0 477s libcairo2 libcoordgen3 libfontconfig1 libgfortran5 libinchi1.07 477s libio-pty-perl libipc-run-perl libjs-jquery libjs-underscore libjson-perl 477s liblapack3 libmaeparser1 libpixman-1-0 libpq5 librdkit-dev librdkit1t64 477s libxcb-render0 libxcb-shm0 libxrender1 libxslt1.1 postgresql-17 477s postgresql-17-rdkit postgresql-client-17 postgresql-client-common 477s postgresql-common python3-numpy python3-rdkit rdkit-data rdkit-doc ssl-cert 477s 0 upgraded, 37 newly installed, 0 to remove and 0 not upgraded. 477s Need to get 63.1 MB of archives. 477s After this operation, 326 MB of additional disk space will be used. 477s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 477s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-pty-perl arm64 1:1.20-1build3 [31.3 kB] 477s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libipc-run-perl all 20231003.0-2 [91.5 kB] 477s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-client-common all 267 [37.1 kB] 477s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 ssl-cert all 1.1.3ubuntu1 [18.7 kB] 477s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-common all 267 [162 kB] 477s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 478s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 478s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 478s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-4ubuntu2 [259 kB] 478s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libboost-python1.83.0 arm64 1.83.0-4ubuntu2 [323 kB] 478s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-4ubuntu2 [242 kB] 478s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libboost-serialization1.83.0 arm64 1.83.0-4ubuntu2 [338 kB] 478s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 478s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 478s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 478s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 478s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 478s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 478s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB] 478s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 478s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libinchi1.07 arm64 1.07.1+dfsg-6 [574 kB] 478s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 478s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 478s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 478s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB] 478s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpq5 arm64 17.2-1 [141 kB] 478s Get:28 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit1t64 arm64 202409.4-1 [5376 kB] 478s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit-dev arm64 202409.4-1 [346 kB] 478s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 478s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-client-17 arm64 17.2-1 [1318 kB] 479s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-17 arm64 17.2-1 [15.5 MB] 479s Get:33 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 postgresql-17-rdkit arm64 202409.4-1 [121 kB] 479s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 479s Get:35 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-data all 202409.4-1 [12.6 MB] 480s Get:36 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-rdkit arm64 202409.4-1 [4656 kB] 480s Get:37 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-doc all 202409.4-1 [6325 kB] 480s Preconfiguring packages ... 481s Fetched 63.1 MB in 3s (19.4 MB/s) 481s Selecting previously unselected package libjson-perl. 481s (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 ... 80913 files and directories currently installed.) 481s Preparing to unpack .../00-libjson-perl_4.10000-1_all.deb ... 481s Unpacking libjson-perl (4.10000-1) ... 481s Selecting previously unselected package libio-pty-perl. 481s Preparing to unpack .../01-libio-pty-perl_1%3a1.20-1build3_arm64.deb ... 481s Unpacking libio-pty-perl (1:1.20-1build3) ... 481s Selecting previously unselected package libipc-run-perl. 481s Preparing to unpack .../02-libipc-run-perl_20231003.0-2_all.deb ... 481s Unpacking libipc-run-perl (20231003.0-2) ... 481s Selecting previously unselected package postgresql-client-common. 481s Preparing to unpack .../03-postgresql-client-common_267_all.deb ... 481s Unpacking postgresql-client-common (267) ... 481s Selecting previously unselected package ssl-cert. 481s Preparing to unpack .../04-ssl-cert_1.1.3ubuntu1_all.deb ... 481s Unpacking ssl-cert (1.1.3ubuntu1) ... 481s Selecting previously unselected package postgresql-common. 481s Preparing to unpack .../05-postgresql-common_267_all.deb ... 481s Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common' 481s Unpacking postgresql-common (267) ... 481s Selecting previously unselected package fonts-freefont-ttf. 481s Preparing to unpack .../06-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 481s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 481s Selecting previously unselected package fontconfig-config. 481s Preparing to unpack .../07-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 482s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 482s Selecting previously unselected package libblas3:arm64. 482s Preparing to unpack .../08-libblas3_3.12.0-4_arm64.deb ... 482s Unpacking libblas3:arm64 (3.12.0-4) ... 482s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 482s Preparing to unpack .../09-libboost-iostreams1.83.0_1.83.0-4ubuntu2_arm64.deb ... 482s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-4ubuntu2) ... 482s Selecting previously unselected package libboost-python1.83.0. 482s Preparing to unpack .../10-libboost-python1.83.0_1.83.0-4ubuntu2_arm64.deb ... 482s Unpacking libboost-python1.83.0 (1.83.0-4ubuntu2) ... 482s Selecting previously unselected package libboost-numpy1.83.0. 482s Preparing to unpack .../11-libboost-numpy1.83.0_1.83.0-4ubuntu2_arm64.deb ... 482s Unpacking libboost-numpy1.83.0 (1.83.0-4ubuntu2) ... 482s Selecting previously unselected package libboost-serialization1.83.0:arm64. 482s Preparing to unpack .../12-libboost-serialization1.83.0_1.83.0-4ubuntu2_arm64.deb ... 482s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-4ubuntu2) ... 482s Selecting previously unselected package libfontconfig1:arm64. 482s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 482s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 482s Selecting previously unselected package libpixman-1-0:arm64. 482s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_arm64.deb ... 482s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 482s Selecting previously unselected package libxcb-render0:arm64. 482s Preparing to unpack .../15-libxcb-render0_1.17.0-2_arm64.deb ... 482s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 482s Selecting previously unselected package libxcb-shm0:arm64. 482s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_arm64.deb ... 482s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 482s Selecting previously unselected package libxrender1:arm64. 482s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 482s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 482s Selecting previously unselected package libcairo2:arm64. 482s Preparing to unpack .../18-libcairo2_1.18.2-2_arm64.deb ... 482s Unpacking libcairo2:arm64 (1.18.2-2) ... 482s Selecting previously unselected package libcoordgen3:arm64. 482s Preparing to unpack .../19-libcoordgen3_3.0.2-1_arm64.deb ... 482s Unpacking libcoordgen3:arm64 (3.0.2-1) ... 483s Selecting previously unselected package libgfortran5:arm64. 483s Preparing to unpack .../20-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 483s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 483s Selecting previously unselected package libinchi1.07. 483s Preparing to unpack .../21-libinchi1.07_1.07.1+dfsg-6_arm64.deb ... 483s Unpacking libinchi1.07 (1.07.1+dfsg-6) ... 483s Selecting previously unselected package libjs-jquery. 483s Preparing to unpack .../22-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 483s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 483s Selecting previously unselected package libjs-underscore. 483s Preparing to unpack .../23-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 483s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 483s Selecting previously unselected package liblapack3:arm64. 483s Preparing to unpack .../24-liblapack3_3.12.0-4_arm64.deb ... 483s Unpacking liblapack3:arm64 (3.12.0-4) ... 483s Selecting previously unselected package libmaeparser1:arm64. 483s Preparing to unpack .../25-libmaeparser1_1.3.1-1build1_arm64.deb ... 483s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ... 483s Selecting previously unselected package libpq5:arm64. 483s Preparing to unpack .../26-libpq5_17.2-1_arm64.deb ... 483s Unpacking libpq5:arm64 (17.2-1) ... 483s Selecting previously unselected package librdkit1t64. 483s Preparing to unpack .../27-librdkit1t64_202409.4-1_arm64.deb ... 483s Unpacking librdkit1t64 (202409.4-1) ... 483s Selecting previously unselected package librdkit-dev. 483s Preparing to unpack .../28-librdkit-dev_202409.4-1_arm64.deb ... 483s Unpacking librdkit-dev (202409.4-1) ... 483s Selecting previously unselected package libxslt1.1:arm64. 483s Preparing to unpack .../29-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 483s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 483s Selecting previously unselected package postgresql-client-17. 483s Preparing to unpack .../30-postgresql-client-17_17.2-1_arm64.deb ... 483s Unpacking postgresql-client-17 (17.2-1) ... 483s Selecting previously unselected package postgresql-17. 483s Preparing to unpack .../31-postgresql-17_17.2-1_arm64.deb ... 483s Unpacking postgresql-17 (17.2-1) ... 484s Selecting previously unselected package postgresql-17-rdkit. 484s Preparing to unpack .../32-postgresql-17-rdkit_202409.4-1_arm64.deb ... 484s Unpacking postgresql-17-rdkit (202409.4-1) ... 484s Selecting previously unselected package python3-numpy. 484s Preparing to unpack .../33-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 484s Unpacking python3-numpy (1:1.26.4+ds-12) ... 484s Selecting previously unselected package rdkit-data. 484s Preparing to unpack .../34-rdkit-data_202409.4-1_all.deb ... 484s Unpacking rdkit-data (202409.4-1) ... 485s Selecting previously unselected package python3-rdkit. 485s Preparing to unpack .../35-python3-rdkit_202409.4-1_arm64.deb ... 485s Unpacking python3-rdkit (202409.4-1) ... 485s Selecting previously unselected package rdkit-doc. 485s Preparing to unpack .../36-rdkit-doc_202409.4-1_all.deb ... 485s Unpacking rdkit-doc (202409.4-1) ... 486s Setting up libboost-python1.83.0 (1.83.0-4ubuntu2) ... 486s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 486s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 486s Setting up libio-pty-perl (1:1.20-1build3) ... 486s Setting up libxcb-render0:arm64 (1.17.0-2) ... 486s Setting up libpq5:arm64 (17.2-1) ... 486s Setting up fonts-freefont-ttf (20211204+svn4273-2) ... 486s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 486s Setting up rdkit-data (202409.4-1) ... 486s Setting up libboost-serialization1.83.0:arm64 (1.83.0-4ubuntu2) ... 486s Setting up libboost-numpy1.83.0 (1.83.0-4ubuntu2) ... 486s Setting up libblas3:arm64 (3.12.0-4) ... 486s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 486s Setting up ssl-cert (1.1.3ubuntu1) ... 486s Created symlink '/etc/systemd/system/multi-user.target.wants/ssl-cert.service' → '/usr/lib/systemd/system/ssl-cert.service'. 487s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-4ubuntu2) ... 487s Setting up libipc-run-perl (20231003.0-2) ... 487s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 487s Setting up libjson-perl (4.10000-1) ... 487s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 487s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 487s Setting up libcoordgen3:arm64 (3.0.2-1) ... 487s Setting up libinchi1.07 (1.07.1+dfsg-6) ... 487s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 487s Setting up postgresql-client-common (267) ... 487s Setting up liblapack3:arm64 (3.12.0-4) ... 487s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 487s Setting up postgresql-client-17 (17.2-1) ... 487s update-alternatives: using /usr/share/postgresql/17/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode 487s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 488s Setting up rdkit-doc (202409.4-1) ... 488s Setting up libmaeparser1:arm64 (1.3.1-1build1) ... 488s Setting up postgresql-common (267) ... 488s Creating config file /etc/postgresql-common/createcluster.conf with new version 488s Building PostgreSQL dictionaries from installed myspell/hunspell packages... 488s Removing obsolete dictionary files: 489s Created symlink '/etc/systemd/system/multi-user.target.wants/postgresql.service' → '/usr/lib/systemd/system/postgresql.service'. 489s Setting up python3-numpy (1:1.26.4+ds-12) ... 492s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 492s Setting up postgresql-17 (17.2-1) ... 492s Creating new PostgreSQL cluster 17/main ... 492s /usr/lib/postgresql/17/bin/initdb -D /var/lib/postgresql/17/main --auth-local peer --auth-host scram-sha-256 --no-instructions 492s The files belonging to this database system will be owned by user "postgres". 492s This user must also own the server process. 492s 492s The database cluster will be initialized with locale "C.UTF-8". 492s The default database encoding has accordingly been set to "UTF8". 492s The default text search configuration will be set to "english". 492s 492s Data page checksums are disabled. 492s 492s fixing permissions on existing directory /var/lib/postgresql/17/main ... ok 492s creating subdirectories ... ok 492s selecting dynamic shared memory implementation ... posix 492s selecting default "max_connections" ... 100 492s selecting default "shared_buffers" ... 128MB 492s selecting default time zone ... Etc/UTC 492s creating configuration files ... ok 492s running bootstrap script ... ok 493s performing post-bootstrap initialization ... ok 493s syncing data to disk ... ok 497s Setting up libcairo2:arm64 (1.18.2-2) ... 497s Setting up librdkit1t64 (202409.4-1) ... 497s Setting up postgresql-17-rdkit (202409.4-1) ... 497s Setting up python3-rdkit (202409.4-1) ... 497s Setting up librdkit-dev (202409.4-1) ... 497s Processing triggers for man-db (2.13.0-1) ... 499s Processing triggers for libc-bin (2.40-4ubuntu1) ... 527s autopkgtest [14:07:36]: test importcheck: [----------------------- 528s autopkgtest [14:07:37]: test importcheck: -----------------------] 529s importcheck PASS 529s autopkgtest [14:07:38]: test importcheck: - - - - - - - - - - results - - - - - - - - - - 529s autopkgtest [14:07:38]: @@@@@@@@@@@@@@@@@@@@ summary 529s installcheck PASS 529s importcheck PASS 559s nova [W] Using flock in prodstack6-arm64 559s flock: timeout while waiting to get lock 559s Creating nova instance adt-plucky-arm64-rdkit-20250117-135849-juju-7f2275-prod-proposed-migration-environment-15-ba908c29-d404-4e05-8c68-97b0621ed4f8 from image adt/ubuntu-plucky-arm64-server-20250117.img (UUID 16a981e8-12f4-4912-806e-ebb4c2361146)... 559s nova [W] Timed out waiting for 2a37ceb4-07e1-4b32-9425-77e42db4e4e7 to get deleted. 559s nova [W] Using flock in prodstack6-arm64 559s Creating nova instance adt-plucky-arm64-rdkit-20250117-135849-juju-7f2275-prod-proposed-migration-environment-15-ba908c29-d404-4e05-8c68-97b0621ed4f8 from image adt/ubuntu-plucky-arm64-server-20250117.img (UUID 16a981e8-12f4-4912-806e-ebb4c2361146)... 559s nova [W] Timed out waiting for e1f69cf0-91ee-4b3a-bb98-0a79b651a929 to get deleted.