0s autopkgtest [15:58:19]: starting date and time: 2024-07-26 15:58:19+0000 0s autopkgtest [15:58:19]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [15:58:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.laiarv72/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:googletest --apt-upgrade seqan-raptor --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=googletest/1.15.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-13.secgroup --name adt-oracular-arm64-seqan-raptor-20240726-155819-juju-7f2275-prod-proposed-migration-environment-2-f392194d-21aa-414e-aaa5-60b37d42a540 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 77s autopkgtest [15:59:36]: testbed dpkg architecture: arm64 77s autopkgtest [15:59:36]: testbed apt version: 2.9.6 77s autopkgtest [15:59:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 79s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 79s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 80s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB] 80s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 80s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [436 kB] 80s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [88.6 kB] 80s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2116 B] 80s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 80s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 80s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [482 kB] 80s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8752 B] 80s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [8744 B] 80s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 82s Fetched 1261 kB in 1s (933 kB/s) 82s Reading package lists... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 89s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 89s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 89s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 91s Reading package lists... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s Calculating upgrade... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s autopkgtest [15:59:55]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 96s autopkgtest [15:59:55]: @@@@@@@@@@@@@@@@@@@@ apt-source seqan-raptor 99s Get:1 http://ftpmaster.internal/ubuntu oracular/universe seqan-raptor 3.0.1+ds-5 (dsc) [2642 B] 99s Get:2 http://ftpmaster.internal/ubuntu oracular/universe seqan-raptor 3.0.1+ds-5 (tar) [3085 kB] 99s Get:3 http://ftpmaster.internal/ubuntu oracular/universe seqan-raptor 3.0.1+ds-5 (diff) [10.3 kB] 99s gpgv: Signature made Wed Sep 6 13:05:19 2023 UTC 99s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 99s gpgv: Can't check signature: No public key 99s dpkg-source: warning: cannot verify inline signature for ./seqan-raptor_3.0.1+ds-5.dsc: no acceptable signature found 100s autopkgtest [15:59:59]: testing package seqan-raptor version 3.0.1+ds-5 100s autopkgtest [15:59:59]: build not needed 103s autopkgtest [16:00:02]: test cwl: preparing testbed 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Starting pkgProblemResolver with broken count: 0 106s Starting 2 pkgProblemResolver with broken count: 0 106s Done 107s The following additional packages will be installed: 107s cwl-upgrader cwltool fontconfig fonts-glyphicons-halflings graphviz libann0 107s libcairo2 libcares2 libcdt5 libcgraph6 libdatrie1 libgts-0.7-5t64 libgvc6 107s libgvpr2 libice6 libjs-bootstrap liblab-gamut1 libltdl7 libnode115 107s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 107s libpixman-1-0 libsm6 libthai-data libthai0 libxaw7 libxcb-render0 107s libxcb-shm0 libxmu6 libxrender1 libxslt1.1 libxt6t64 libyaml-cpp0.8 107s node-acorn node-cjs-module-lexer node-undici node-xtend nodejs python3-arcp 107s python3-argcomplete python3-cachecontrol python3-coloredlogs 107s python3-cwl-utils python3-dateutil python3-filelock python3-humanfriendly 107s python3-isodate python3-lxml python3-mistune python3-msgpack 107s python3-mypy-extensions python3-networkx python3-packaging python3-prov 107s python3-psutil python3-pydot python3-rdflib python3-ruamel.yaml 107s python3-ruamel.yaml.clib python3-schema-salad python3-shellescape 107s python3-six python3-spython seqan-raptor seqan-raptor-doc x11-common 107s Suggested packages: 107s podman | docker.io | singularity-container cwltool-doc gsfonts graphviz-doc 107s npm node-corepack cwl-utils python-lxml-doc python3-gdal python3-matplotlib 107s python3-pygraphviz python3-scipy python-prov-doc python-rdflib-doc 107s singularity-container 107s Recommended packages: 107s fonts-liberation libgts-bin nodejs-doc python3-bs4 python3-cssselect 107s python3-html5lib python3-numpy python3-sparqlwrapper black 107s The following NEW packages will be installed: 107s autopkgtest-satdep cwl-upgrader cwltool fontconfig 107s fonts-glyphicons-halflings graphviz libann0 libcairo2 libcares2 libcdt5 107s libcgraph6 libdatrie1 libgts-0.7-5t64 libgvc6 libgvpr2 libice6 107s libjs-bootstrap liblab-gamut1 libltdl7 libnode115 libpango-1.0-0 107s libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpixman-1-0 libsm6 107s libthai-data libthai0 libxaw7 libxcb-render0 libxcb-shm0 libxmu6 libxrender1 107s libxslt1.1 libxt6t64 libyaml-cpp0.8 node-acorn node-cjs-module-lexer 107s node-undici node-xtend nodejs python3-arcp python3-argcomplete 107s python3-cachecontrol python3-coloredlogs python3-cwl-utils python3-dateutil 107s python3-filelock python3-humanfriendly python3-isodate python3-lxml 107s python3-mistune python3-msgpack python3-mypy-extensions python3-networkx 107s python3-packaging python3-prov python3-psutil python3-pydot python3-rdflib 107s python3-ruamel.yaml python3-ruamel.yaml.clib python3-schema-salad 107s python3-shellescape python3-six python3-spython seqan-raptor 107s seqan-raptor-doc x11-common 107s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 37.2 MB/37.2 MB of archives. 107s After this operation, 188 MB of additional disk space will be used. 107s Get:1 /tmp/autopkgtest.8m8bRX/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 107s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8-1build1 [126 kB] 107s Get:3 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 107s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-msgpack arm64 1.0.3-3build2 [77.9 kB] 107s Get:5 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cachecontrol all 0.14.0-1 [19.0 kB] 107s Get:6 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-mistune all 3.0.2-1 [32.8 kB] 107s Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-mypy-extensions all 1.0.0-1 [6148 B] 107s Get:8 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-isodate all 0.6.1-2 [24.3 kB] 107s Get:9 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-rdflib all 7.0.0-1 [405 kB] 107s Get:10 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-filelock all 3.15.4-1 [12.8 kB] 107s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 107s Get:12 http://ftpmaster.internal/ubuntu oracular/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 108s Get:13 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-schema-salad arm64 8.5.20240410123758-1 [958 kB] 108s Get:14 http://ftpmaster.internal/ubuntu oracular/universe arm64 cwl-upgrader all 1.2.11-1 [16.0 kB] 108s Get:15 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-argcomplete all 3.4.0-1 [34.6 kB] 108s Get:16 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-humanfriendly all 10.0-5 [70.5 kB] 108s Get:17 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 108s Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.1-1 [41.4 kB] 108s Get:19 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cwl-utils all 0.33-1 [119 kB] 108s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-six all 1.16.0-6 [13.0 kB] 108s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 108s Get:22 http://ftpmaster.internal/ubuntu oracular/main arm64 libxslt1.1 arm64 1.1.39-0exp1build1 [166 kB] 108s Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-lxml arm64 5.2.2-1 [1176 kB] 108s Get:24 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 108s Get:25 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-prov all 2.0.1-1 [95.5 kB] 108s Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-psutil arm64 5.9.8-2build2 [196 kB] 108s Get:27 http://ftpmaster.internal/ubuntu oracular/universe arm64 libann0 arm64 1.1.2+doc-9build1 [25.7 kB] 108s Get:28 http://ftpmaster.internal/ubuntu oracular/universe arm64 libcdt5 arm64 2.42.4-1 [20.5 kB] 108s Get:29 http://ftpmaster.internal/ubuntu oracular/universe arm64 libcgraph6 arm64 2.42.4-1 [45.0 kB] 108s Get:30 http://ftpmaster.internal/ubuntu oracular/universe arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2build1 [154 kB] 108s Get:31 http://ftpmaster.internal/ubuntu oracular/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] 108s Get:32 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 108s Get:33 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 108s Get:34 http://ftpmaster.internal/ubuntu oracular/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 108s Get:35 http://ftpmaster.internal/ubuntu oracular/main arm64 libcairo2 arm64 1.18.0-3build1 [555 kB] 108s Get:36 http://ftpmaster.internal/ubuntu oracular/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB] 108s Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB] 108s Get:38 http://ftpmaster.internal/ubuntu oracular/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 108s Get:39 http://ftpmaster.internal/ubuntu oracular/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 108s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 108s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 libpango-1.0-0 arm64 1.54.0+ds-1 [230 kB] 108s Get:42 http://ftpmaster.internal/ubuntu oracular/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-1 [41.7 kB] 108s Get:43 http://ftpmaster.internal/ubuntu oracular/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-1 [27.2 kB] 108s Get:44 http://ftpmaster.internal/ubuntu oracular/universe arm64 libpathplan4 arm64 2.42.4-1 [22.7 kB] 108s Get:45 http://ftpmaster.internal/ubuntu oracular/universe arm64 libgvc6 arm64 2.42.4-1 [692 kB] 108s Get:46 http://ftpmaster.internal/ubuntu oracular/universe arm64 libgvpr2 arm64 2.42.4-1 [185 kB] 108s Get:47 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblab-gamut1 arm64 2.42.4-1 [1832 kB] 108s Get:48 http://ftpmaster.internal/ubuntu oracular/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 108s Get:49 http://ftpmaster.internal/ubuntu oracular/main arm64 libice6 arm64 2:1.0.10-1build3 [41.1 kB] 108s Get:50 http://ftpmaster.internal/ubuntu oracular/main arm64 libsm6 arm64 2:1.2.3-1build3 [15.6 kB] 108s Get:51 http://ftpmaster.internal/ubuntu oracular/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 108s Get:52 http://ftpmaster.internal/ubuntu oracular/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 108s Get:53 http://ftpmaster.internal/ubuntu oracular/main arm64 libxaw7 arm64 2:1.0.14-1build2 [183 kB] 108s Get:54 http://ftpmaster.internal/ubuntu oracular/universe arm64 graphviz arm64 2.42.4-1 [610 kB] 108s Get:55 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pydot all 2.0.0-3 [24.9 kB] 108s Get:56 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-shellescape all 3.4.1-5 [5064 B] 108s Get:57 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-spython all 0.3.13-2 [56.2 kB] 108s Get:58 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-arcp all 0.2.1-6 [13.6 kB] 108s Get:59 http://ftpmaster.internal/ubuntu oracular/universe arm64 cwltool all 3.1.20240508115724-1 [509 kB] 108s Get:60 http://ftpmaster.internal/ubuntu oracular/main arm64 libcares2 arm64 1.32.3-1 [82.8 kB] 108s Get:61 http://ftpmaster.internal/ubuntu oracular/universe arm64 node-xtend all 4.0.2-3 [3902 B] 108s Get:62 http://ftpmaster.internal/ubuntu oracular/universe arm64 nodejs arm64 20.15.0+dfsg-1ubuntu3 [332 kB] 108s Get:63 http://ftpmaster.internal/ubuntu oracular/universe arm64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [115 kB] 108s Get:64 http://ftpmaster.internal/ubuntu oracular/universe arm64 node-cjs-module-lexer all 1.2.3+dfsg-1 [32.1 kB] 108s Get:65 http://ftpmaster.internal/ubuntu oracular/universe arm64 node-undici all 5.28.4+dfsg1+~cs23.12.11-2 [321 kB] 109s Get:66 http://ftpmaster.internal/ubuntu oracular/universe arm64 libnode115 arm64 20.15.0+dfsg-1ubuntu3 [12.6 MB] 109s Get:67 http://ftpmaster.internal/ubuntu oracular/main arm64 libyaml-cpp0.8 arm64 0.8.0+dfsg-6build1 [112 kB] 109s Get:68 http://ftpmaster.internal/ubuntu oracular/universe arm64 seqan-raptor arm64 3.0.1+ds-5 [648 kB] 109s Get:69 http://ftpmaster.internal/ubuntu oracular/universe arm64 seqan-raptor-doc all 3.0.1+ds-5 [1247 kB] 109s Fetched 37.2 MB in 2s (18.6 MB/s) 110s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 110s (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 ... 78607 files and directories currently installed.) 110s Preparing to unpack .../00-python3-ruamel.yaml.clib_0.2.8-1build1_arm64.deb ... 110s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8-1build1) ... 110s Selecting previously unselected package python3-ruamel.yaml. 110s Preparing to unpack .../01-python3-ruamel.yaml_0.17.21-1_all.deb ... 110s Unpacking python3-ruamel.yaml (0.17.21-1) ... 110s Selecting previously unselected package python3-msgpack. 110s Preparing to unpack .../02-python3-msgpack_1.0.3-3build2_arm64.deb ... 110s Unpacking python3-msgpack (1.0.3-3build2) ... 110s Selecting previously unselected package python3-cachecontrol. 110s Preparing to unpack .../03-python3-cachecontrol_0.14.0-1_all.deb ... 110s Unpacking python3-cachecontrol (0.14.0-1) ... 110s Selecting previously unselected package python3-mistune. 110s Preparing to unpack .../04-python3-mistune_3.0.2-1_all.deb ... 110s Unpacking python3-mistune (3.0.2-1) ... 110s Selecting previously unselected package python3-mypy-extensions. 110s Preparing to unpack .../05-python3-mypy-extensions_1.0.0-1_all.deb ... 110s Unpacking python3-mypy-extensions (1.0.0-1) ... 110s Selecting previously unselected package python3-isodate. 111s Preparing to unpack .../06-python3-isodate_0.6.1-2_all.deb ... 111s Unpacking python3-isodate (0.6.1-2) ... 111s Selecting previously unselected package python3-rdflib. 111s Preparing to unpack .../07-python3-rdflib_7.0.0-1_all.deb ... 111s Unpacking python3-rdflib (7.0.0-1) ... 111s Selecting previously unselected package python3-filelock. 111s Preparing to unpack .../08-python3-filelock_3.15.4-1_all.deb ... 111s Unpacking python3-filelock (3.15.4-1) ... 111s Selecting previously unselected package fonts-glyphicons-halflings. 111s Preparing to unpack .../09-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 111s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 111s Selecting previously unselected package libjs-bootstrap. 111s Preparing to unpack .../10-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 111s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 111s Selecting previously unselected package python3-schema-salad. 111s Preparing to unpack .../11-python3-schema-salad_8.5.20240410123758-1_arm64.deb ... 111s Unpacking python3-schema-salad (8.5.20240410123758-1) ... 111s Selecting previously unselected package cwl-upgrader. 111s Preparing to unpack .../12-cwl-upgrader_1.2.11-1_all.deb ... 111s Unpacking cwl-upgrader (1.2.11-1) ... 111s Selecting previously unselected package python3-argcomplete. 111s Preparing to unpack .../13-python3-argcomplete_3.4.0-1_all.deb ... 111s Unpacking python3-argcomplete (3.4.0-1) ... 111s Selecting previously unselected package python3-humanfriendly. 111s Preparing to unpack .../14-python3-humanfriendly_10.0-5_all.deb ... 111s Unpacking python3-humanfriendly (10.0-5) ... 111s Selecting previously unselected package python3-coloredlogs. 111s Preparing to unpack .../15-python3-coloredlogs_15.0.1-1_all.deb ... 111s Unpacking python3-coloredlogs (15.0.1-1) ... 111s Selecting previously unselected package python3-packaging. 111s Preparing to unpack .../16-python3-packaging_24.1-1_all.deb ... 111s Unpacking python3-packaging (24.1-1) ... 112s Selecting previously unselected package python3-cwl-utils. 112s Preparing to unpack .../17-python3-cwl-utils_0.33-1_all.deb ... 112s Unpacking python3-cwl-utils (0.33-1) ... 112s Selecting previously unselected package python3-six. 112s Preparing to unpack .../18-python3-six_1.16.0-6_all.deb ... 112s Unpacking python3-six (1.16.0-6) ... 112s Selecting previously unselected package python3-dateutil. 112s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ... 112s Unpacking python3-dateutil (2.9.0-2) ... 112s Selecting previously unselected package libxslt1.1:arm64. 112s Preparing to unpack .../20-libxslt1.1_1.1.39-0exp1build1_arm64.deb ... 112s Unpacking libxslt1.1:arm64 (1.1.39-0exp1build1) ... 112s Selecting previously unselected package python3-lxml:arm64. 112s Preparing to unpack .../21-python3-lxml_5.2.2-1_arm64.deb ... 112s Unpacking python3-lxml:arm64 (5.2.2-1) ... 112s Selecting previously unselected package python3-networkx. 112s Preparing to unpack .../22-python3-networkx_3.2.1-4ubuntu1_all.deb ... 112s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 113s Selecting previously unselected package python3-prov. 113s Preparing to unpack .../23-python3-prov_2.0.1-1_all.deb ... 113s Unpacking python3-prov (2.0.1-1) ... 113s Selecting previously unselected package python3-psutil. 113s Preparing to unpack .../24-python3-psutil_5.9.8-2build2_arm64.deb ... 113s Unpacking python3-psutil (5.9.8-2build2) ... 113s Selecting previously unselected package libann0. 113s Preparing to unpack .../25-libann0_1.1.2+doc-9build1_arm64.deb ... 113s Unpacking libann0 (1.1.2+doc-9build1) ... 113s Selecting previously unselected package libcdt5:arm64. 113s Preparing to unpack .../26-libcdt5_2.42.4-1_arm64.deb ... 113s Unpacking libcdt5:arm64 (2.42.4-1) ... 113s Selecting previously unselected package libcgraph6:arm64. 113s Preparing to unpack .../27-libcgraph6_2.42.4-1_arm64.deb ... 113s Unpacking libcgraph6:arm64 (2.42.4-1) ... 113s Selecting previously unselected package libgts-0.7-5t64:arm64. 113s Preparing to unpack .../28-libgts-0.7-5t64_0.7.6+darcs121130-5.2build1_arm64.deb ... 113s Unpacking libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2build1) ... 113s Selecting previously unselected package libpixman-1-0:arm64. 113s Preparing to unpack .../29-libpixman-1-0_0.42.2-1build1_arm64.deb ... 113s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ... 113s Selecting previously unselected package libxcb-render0:arm64. 113s Preparing to unpack .../30-libxcb-render0_1.17.0-2_arm64.deb ... 113s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 113s Selecting previously unselected package libxcb-shm0:arm64. 113s Preparing to unpack .../31-libxcb-shm0_1.17.0-2_arm64.deb ... 113s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 113s Selecting previously unselected package libxrender1:arm64. 113s Preparing to unpack .../32-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 113s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 113s Selecting previously unselected package libcairo2:arm64. 113s Preparing to unpack .../33-libcairo2_1.18.0-3build1_arm64.deb ... 113s Unpacking libcairo2:arm64 (1.18.0-3build1) ... 113s Selecting previously unselected package libltdl7:arm64. 113s Preparing to unpack .../34-libltdl7_2.4.7-7build1_arm64.deb ... 113s Unpacking libltdl7:arm64 (2.4.7-7build1) ... 114s Selecting previously unselected package fontconfig. 114s Preparing to unpack .../35-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ... 114s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 114s Selecting previously unselected package libthai-data. 114s Preparing to unpack .../36-libthai-data_0.1.29-2build1_all.deb ... 114s Unpacking libthai-data (0.1.29-2build1) ... 114s Selecting previously unselected package libdatrie1:arm64. 114s Preparing to unpack .../37-libdatrie1_0.2.13-3build1_arm64.deb ... 114s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 114s Selecting previously unselected package libthai0:arm64. 114s Preparing to unpack .../38-libthai0_0.1.29-2build1_arm64.deb ... 114s Unpacking libthai0:arm64 (0.1.29-2build1) ... 114s Selecting previously unselected package libpango-1.0-0:arm64. 114s Preparing to unpack .../39-libpango-1.0-0_1.54.0+ds-1_arm64.deb ... 114s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-1) ... 114s Selecting previously unselected package libpangoft2-1.0-0:arm64. 114s Preparing to unpack .../40-libpangoft2-1.0-0_1.54.0+ds-1_arm64.deb ... 114s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-1) ... 114s Selecting previously unselected package libpangocairo-1.0-0:arm64. 114s Preparing to unpack .../41-libpangocairo-1.0-0_1.54.0+ds-1_arm64.deb ... 114s Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-1) ... 114s Selecting previously unselected package libpathplan4:arm64. 114s Preparing to unpack .../42-libpathplan4_2.42.4-1_arm64.deb ... 114s Unpacking libpathplan4:arm64 (2.42.4-1) ... 114s Selecting previously unselected package libgvc6. 114s Preparing to unpack .../43-libgvc6_2.42.4-1_arm64.deb ... 114s Unpacking libgvc6 (2.42.4-1) ... 114s Selecting previously unselected package libgvpr2:arm64. 114s Preparing to unpack .../44-libgvpr2_2.42.4-1_arm64.deb ... 114s Unpacking libgvpr2:arm64 (2.42.4-1) ... 114s Selecting previously unselected package liblab-gamut1:arm64. 114s Preparing to unpack .../45-liblab-gamut1_2.42.4-1_arm64.deb ... 114s Unpacking liblab-gamut1:arm64 (2.42.4-1) ... 114s Selecting previously unselected package x11-common. 114s Preparing to unpack .../46-x11-common_1%3a7.7+23ubuntu3_all.deb ... 114s Unpacking x11-common (1:7.7+23ubuntu3) ... 114s Selecting previously unselected package libice6:arm64. 115s Preparing to unpack .../47-libice6_2%3a1.0.10-1build3_arm64.deb ... 115s Unpacking libice6:arm64 (2:1.0.10-1build3) ... 115s Selecting previously unselected package libsm6:arm64. 115s Preparing to unpack .../48-libsm6_2%3a1.2.3-1build3_arm64.deb ... 115s Unpacking libsm6:arm64 (2:1.2.3-1build3) ... 115s Selecting previously unselected package libxt6t64:arm64. 115s Preparing to unpack .../49-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 115s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 115s Selecting previously unselected package libxmu6:arm64. 115s Preparing to unpack .../50-libxmu6_2%3a1.1.3-3build2_arm64.deb ... 115s Unpacking libxmu6:arm64 (2:1.1.3-3build2) ... 115s Selecting previously unselected package libxaw7:arm64. 115s Preparing to unpack .../51-libxaw7_2%3a1.0.14-1build2_arm64.deb ... 115s Unpacking libxaw7:arm64 (2:1.0.14-1build2) ... 115s Selecting previously unselected package graphviz. 115s Preparing to unpack .../52-graphviz_2.42.4-1_arm64.deb ... 115s Unpacking graphviz (2.42.4-1) ... 115s Selecting previously unselected package python3-pydot. 115s Preparing to unpack .../53-python3-pydot_2.0.0-3_all.deb ... 115s Unpacking python3-pydot (2.0.0-3) ... 115s Selecting previously unselected package python3-shellescape. 115s Preparing to unpack .../54-python3-shellescape_3.4.1-5_all.deb ... 115s Unpacking python3-shellescape (3.4.1-5) ... 115s Selecting previously unselected package python3-spython. 115s Preparing to unpack .../55-python3-spython_0.3.13-2_all.deb ... 115s Unpacking python3-spython (0.3.13-2) ... 116s Selecting previously unselected package python3-arcp. 116s Preparing to unpack .../56-python3-arcp_0.2.1-6_all.deb ... 116s Unpacking python3-arcp (0.2.1-6) ... 116s Selecting previously unselected package cwltool. 116s Preparing to unpack .../57-cwltool_3.1.20240508115724-1_all.deb ... 116s Unpacking cwltool (3.1.20240508115724-1) ... 116s Selecting previously unselected package libcares2:arm64. 116s Preparing to unpack .../58-libcares2_1.32.3-1_arm64.deb ... 116s Unpacking libcares2:arm64 (1.32.3-1) ... 116s Selecting previously unselected package node-xtend. 116s Preparing to unpack .../59-node-xtend_4.0.2-3_all.deb ... 116s Unpacking node-xtend (4.0.2-3) ... 116s Selecting previously unselected package nodejs. 116s Preparing to unpack .../60-nodejs_20.15.0+dfsg-1ubuntu3_arm64.deb ... 116s Unpacking nodejs (20.15.0+dfsg-1ubuntu3) ... 116s Selecting previously unselected package node-acorn. 116s Preparing to unpack .../61-node-acorn_8.8.1+ds+~cs25.17.7-2_all.deb ... 116s Unpacking node-acorn (8.8.1+ds+~cs25.17.7-2) ... 116s Selecting previously unselected package node-cjs-module-lexer. 116s Preparing to unpack .../62-node-cjs-module-lexer_1.2.3+dfsg-1_all.deb ... 116s Unpacking node-cjs-module-lexer (1.2.3+dfsg-1) ... 117s Selecting previously unselected package node-undici. 117s Preparing to unpack .../63-node-undici_5.28.4+dfsg1+~cs23.12.11-2_all.deb ... 117s Unpacking node-undici (5.28.4+dfsg1+~cs23.12.11-2) ... 117s Selecting previously unselected package libnode115:arm64. 117s Preparing to unpack .../64-libnode115_20.15.0+dfsg-1ubuntu3_arm64.deb ... 117s Unpacking libnode115:arm64 (20.15.0+dfsg-1ubuntu3) ... 118s Selecting previously unselected package libyaml-cpp0.8:arm64. 118s Preparing to unpack .../65-libyaml-cpp0.8_0.8.0+dfsg-6build1_arm64.deb ... 118s Unpacking libyaml-cpp0.8:arm64 (0.8.0+dfsg-6build1) ... 118s Selecting previously unselected package seqan-raptor. 118s Preparing to unpack .../66-seqan-raptor_3.0.1+ds-5_arm64.deb ... 118s Unpacking seqan-raptor (3.0.1+ds-5) ... 118s Selecting previously unselected package seqan-raptor-doc. 118s Preparing to unpack .../67-seqan-raptor-doc_3.0.1+ds-5_all.deb ... 118s Unpacking seqan-raptor-doc (3.0.1+ds-5) ... 118s Selecting previously unselected package autopkgtest-satdep. 118s Preparing to unpack .../68-1-autopkgtest-satdep.deb ... 118s Unpacking autopkgtest-satdep (0) ... 118s Setting up python3-arcp (0.2.1-6) ... 118s Setting up libpixman-1-0:arm64 (0.42.2-1build1) ... 118s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 121s Regenerating fonts cache... done. 121s Setting up python3-filelock (3.15.4-1) ... 121s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 121s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 121s Setting up libxcb-render0:arm64 (1.17.0-2) ... 121s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 121s Setting up python3-mypy-extensions (1.0.0-1) ... 121s Setting up libyaml-cpp0.8:arm64 (0.8.0+dfsg-6build1) ... 121s Setting up liblab-gamut1:arm64 (2.42.4-1) ... 121s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8-1build1) ... 121s Setting up x11-common (1:7.7+23ubuntu3) ... 122s Setting up node-cjs-module-lexer (1.2.3+dfsg-1) ... 122s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 122s Setting up python3-networkx (3.2.1-4ubuntu1) ... 123s Setting up libcairo2:arm64 (1.18.0-3build1) ... 123s Setting up python3-psutil (5.9.8-2build2) ... 124s Setting up python3-six (1.16.0-6) ... 124s Setting up python3-isodate (0.6.1-2) ... 124s Setting up python3-packaging (24.1-1) ... 124s Setting up python3-humanfriendly (10.0-5) ... 125s Setting up python3-spython (0.3.13-2) ... 125s Setting up libpathplan4:arm64 (2.42.4-1) ... 125s Setting up libann0 (1.1.2+doc-9build1) ... 125s Setting up libcares2:arm64 (1.32.3-1) ... 125s Setting up libltdl7:arm64 (2.4.7-7build1) ... 125s Setting up python3-ruamel.yaml (0.17.21-1) ... 125s Setting up node-undici (5.28.4+dfsg1+~cs23.12.11-2) ... 125s Setting up python3-rdflib (7.0.0-1) ... 126s Setting up libxslt1.1:arm64 (1.1.39-0exp1build1) ... 126s Setting up libthai-data (0.1.29-2build1) ... 126s Setting up python3-dateutil (2.9.0-2) ... 126s Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2build1) ... 126s Setting up python3-msgpack (1.0.3-3build2) ... 127s Setting up libcdt5:arm64 (2.42.4-1) ... 127s Setting up libcgraph6:arm64 (2.42.4-1) ... 127s Setting up python3-cachecontrol (0.14.0-1) ... 127s Setting up python3-shellescape (3.4.1-5) ... 127s Setting up node-xtend (4.0.2-3) ... 127s Setting up seqan-raptor (3.0.1+ds-5) ... 127s Setting up python3-argcomplete (3.4.0-1) ... 127s Setting up python3-coloredlogs (15.0.1-1) ... 128s Setting up seqan-raptor-doc (3.0.1+ds-5) ... 128s Setting up python3-mistune (3.0.2-1) ... 128s Setting up libjs-bootstrap (3.4.1+dfsg-3) ... 128s Setting up libice6:arm64 (2:1.0.10-1build3) ... 128s Setting up python3-schema-salad (8.5.20240410123758-1) ... 128s Setting up libthai0:arm64 (0.1.29-2build1) ... 128s Setting up cwl-upgrader (1.2.11-1) ... 129s Setting up libgvpr2:arm64 (2.42.4-1) ... 129s Setting up python3-lxml:arm64 (5.2.2-1) ... 129s Setting up libsm6:arm64 (2:1.2.3-1build3) ... 129s Setting up libpango-1.0-0:arm64 (1.54.0+ds-1) ... 129s Setting up python3-cwl-utils (0.33-1) ... 130s Setting up python3-prov (2.0.1-1) ... 131s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 131s Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-1) ... 131s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-1) ... 131s Setting up libxmu6:arm64 (2:1.1.3-3build2) ... 131s Setting up libxaw7:arm64 (2:1.0.14-1build2) ... 131s Setting up libgvc6 (2.42.4-1) ... 131s Setting up graphviz (2.42.4-1) ... 131s Setting up python3-pydot (2.0.0-3) ... 131s Setting up cwltool (3.1.20240508115724-1) ... 132s Setting up libnode115:arm64 (20.15.0+dfsg-1ubuntu3) ... 132s Setting up nodejs (20.15.0+dfsg-1ubuntu3) ... 132s update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode 132s Setting up node-acorn (8.8.1+ds+~cs25.17.7-2) ... 132s Setting up autopkgtest-satdep (0) ... 132s Processing triggers for libc-bin (2.39-0ubuntu9) ... 132s Processing triggers for man-db (2.12.1-2) ... 140s (Reading database ... 86501 files and directories currently installed.) 140s Removing autopkgtest-satdep (0) ... 141s autopkgtest [16:00:40]: test cwl: [----------------------- 142s INFO /usr/bin/cwltool 3.1.20240508115724 142s INFO Resolved '/usr/share/commonwl/raptor-build.cwl' to 'file:///usr/share/commonwl/raptor-build.cwl' 145s INFO [job raptor-build.cwl] /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/3y51muos$ raptor \ 145s build \ 145s --input \ 145s input_bins_filepaths.txt \ 145s --output \ 145s 0_bins_window_19.index 145s ============= Timings ============= 145s Wall clock time [s]: 0.00 145s Peak memory usage [MiB]: 62.9 145s Determine IBF size [s]: 0.00 145s Index allocation [s]: 0.00 145s User bin I/O avg per thread [s]: 0.00 145s User bin I/O sum [s]: 0.00 145s Fill IBF avg per thread [s]: 0.00 145s Fill IBF sum [s]: 0.00 145s Store index [s]: 0.00 145s INFO [job raptor-build.cwl] completed success 145s INFO Final process status is success 146s "checksum": "sha1$098169f476fb949b0d08f2d1e05881049819b811", 146s INFO /usr/bin/cwltool 3.1.20240508115724 146s INFO Resolved '/usr/share/commonwl/raptor-build.cwl' to 'file:///usr/share/commonwl/raptor-build.cwl' 148s INFO [job raptor-build.cwl] /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lyvf7za8$ raptor \ 148s build \ 148s --input \ 148s input_bins_filepaths.txt \ 148s --output \ 148s 0_bins_window_19.index 148s ============= Timings ============= 148s Wall clock time [s]: 0.01 148s Peak memory usage [MiB]: 63.6 148s Determine IBF size [s]: 0.01 148s Index allocation [s]: 0.00 148s User bin I/O avg per thread [s]: 0.00 148s User bin I/O sum [s]: 0.00 148s Fill IBF avg per thread [s]: 0.00 148s Fill IBF sum [s]: 0.00 148s Store index [s]: 0.00 148s INFO [job raptor-build.cwl] completed success 148s INFO Final process status is success 149s "checksum": "sha1$64a4328eb3dab99bf6ecd38f84f4ae45fd01a4dd", 149s autopkgtest [16:00:48]: test cwl: -----------------------] 150s autopkgtest [16:00:49]: test cwl: - - - - - - - - - - results - - - - - - - - - - 150s cwl PASS 150s autopkgtest [16:00:49]: test run-unit-test: preparing testbed 228s autopkgtest [16:02:07]: testbed dpkg architecture: arm64 229s autopkgtest [16:02:08]: testbed apt version: 2.9.6 229s autopkgtest [16:02:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 231s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 231s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 231s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 231s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [436 kB] 231s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB] 231s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [88.6 kB] 231s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2116 B] 231s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 231s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 231s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [482 kB] 231s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8752 B] 231s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [8744 B] 231s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 233s Fetched 1261 kB in 1s (1182 kB/s) 233s Reading package lists... 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 236s Calculating upgrade... 237s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 238s Reading package lists... 238s Building dependency tree... 238s Reading state information... 238s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 242s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 242s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 242s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 242s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 244s Reading package lists... 244s Reading package lists... 245s Building dependency tree... 245s Reading state information... 245s Calculating upgrade... 246s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 246s Reading package lists... 246s Building dependency tree... 246s Reading state information... 246s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 251s Reading package lists... 251s Building dependency tree... 251s Reading state information... 251s Starting pkgProblemResolver with broken count: 0 251s Starting 2 pkgProblemResolver with broken count: 0 251s Done 252s The following additional packages will be installed: 252s cmake cmake-data cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 252s g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 252s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu googletest libasan8 252s libatomic1 libbz2-dev libcc1-0 libcereal-dev libgcc-14-dev libgtest-dev 252s libhwasan0 libisl23 libitm1 libjsoncpp25 liblsan0 libmpc3 libpkgconf3 252s librhash0 libseqan3-dev libsimde-dev libstdc++-14-dev libtsan2 libubsan1 252s libxxhash-dev libyaml-cpp-dev libyaml-cpp0.8 pkg-config pkgconf pkgconf-bin 252s rapidjson-dev seqan-raptor seqan-raptor-doc zlib1g-dev 252s Suggested packages: 252s cmake-doc cmake-format elpa-cmake-mode ninja-build cpp-doc gcc-14-locales 252s cpp-14-doc gcc-14-doc gcc-multilib manpages-dev autoconf automake libtool 252s flex bison gdb gcc-doc gdb-aarch64-linux-gnu libstdc++-14-doc rapidjson-doc 252s cwl-runner 252s Recommended packages: 252s bzip2-doc 252s The following NEW packages will be installed: 252s autopkgtest-satdep cmake cmake-data cpp cpp-14 cpp-14-aarch64-linux-gnu 252s cpp-aarch64-linux-gnu g++ g++-14 g++-14-aarch64-linux-gnu 252s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 252s gcc-aarch64-linux-gnu googletest libasan8 libatomic1 libbz2-dev libcc1-0 252s libcereal-dev libgcc-14-dev libgtest-dev libhwasan0 libisl23 libitm1 252s libjsoncpp25 liblsan0 libmpc3 libpkgconf3 librhash0 libseqan3-dev 252s libsimde-dev libstdc++-14-dev libtsan2 libubsan1 libxxhash-dev 252s libyaml-cpp-dev libyaml-cpp0.8 pkg-config pkgconf pkgconf-bin rapidjson-dev 252s seqan-raptor seqan-raptor-doc zlib1g-dev 252s 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. 252s Need to get 78.1 MB/78.1 MB of archives. 252s After this operation, 287 MB of additional disk space will be used. 252s Get:1 /tmp/autopkgtest.8m8bRX/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [780 B] 252s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libjsoncpp25 arm64 1.9.5-6build1 [78.2 kB] 252s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 librhash0 arm64 1.4.3-3build1 [126 kB] 252s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 cmake-data all 3.29.6-1 [2193 kB] 253s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 cmake arm64 3.29.6-1 [10.5 MB] 253s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 libisl23 arm64 0.26-3build1 [669 kB] 253s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libmpc3 arm64 1.3.1-1build1 [56.4 kB] 253s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp-14-aarch64-linux-gnu arm64 14.1.0-5ubuntu1 [10.6 MB] 253s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp-14 arm64 14.1.0-5ubuntu1 [1030 B] 253s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 253s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 253s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 libcc1-0 arm64 14.1.0-5ubuntu1 [49.6 kB] 253s Get:13 http://ftpmaster.internal/ubuntu oracular/main arm64 libitm1 arm64 14.1.0-5ubuntu1 [27.9 kB] 253s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libatomic1 arm64 14.1.0-5ubuntu1 [11.5 kB] 253s Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libasan8 arm64 14.1.0-5ubuntu1 [2894 kB] 253s Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 liblsan0 arm64 14.1.0-5ubuntu1 [1283 kB] 254s Get:17 http://ftpmaster.internal/ubuntu oracular/main arm64 libtsan2 arm64 14.1.0-5ubuntu1 [2685 kB] 254s Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 libubsan1 arm64 14.1.0-5ubuntu1 [1152 kB] 254s Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 libhwasan0 arm64 14.1.0-5ubuntu1 [1598 kB] 254s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 libgcc-14-dev arm64 14.1.0-5ubuntu1 [2596 kB] 254s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-14-aarch64-linux-gnu arm64 14.1.0-5ubuntu1 [20.9 MB] 255s Get:22 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-14 arm64 14.1.0-5ubuntu1 [506 kB] 255s Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 255s Get:24 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 255s Get:25 http://ftpmaster.internal/ubuntu oracular/main arm64 libstdc++-14-dev arm64 14.1.0-5ubuntu1 [2468 kB] 255s Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 g++-14-aarch64-linux-gnu arm64 14.1.0-5ubuntu1 [12.1 MB] 255s Get:27 http://ftpmaster.internal/ubuntu oracular/main arm64 g++-14 arm64 14.1.0-5ubuntu1 [18.0 kB] 255s Get:28 http://ftpmaster.internal/ubuntu oracular/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 255s Get:29 http://ftpmaster.internal/ubuntu oracular/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 255s Get:30 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 googletest all 1.15.0-1 [523 kB] 255s Get:31 http://ftpmaster.internal/ubuntu oracular/main arm64 libbz2-dev arm64 1.0.8-5.1 [35.8 kB] 255s Get:32 http://ftpmaster.internal/ubuntu oracular/universe arm64 rapidjson-dev all 1.1.0+dfsg2-7.2 [96.7 kB] 255s Get:33 http://ftpmaster.internal/ubuntu oracular/universe arm64 libcereal-dev arm64 1.3.2+dfsg-5 [222 kB] 255s Get:34 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 libgtest-dev arm64 1.15.0-1 [272 kB] 255s Get:35 http://ftpmaster.internal/ubuntu oracular/main arm64 libpkgconf3 arm64 1.8.1-3 [31.2 kB] 255s Get:36 http://ftpmaster.internal/ubuntu oracular/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1ubuntu2 [894 kB] 255s Get:37 http://ftpmaster.internal/ubuntu oracular/universe arm64 libseqan3-dev all 3.3.0+ds-1 [748 kB] 255s Get:38 http://ftpmaster.internal/ubuntu oracular/universe arm64 libsimde-dev all 0.8.2-1 [466 kB] 255s Get:39 http://ftpmaster.internal/ubuntu oracular/main arm64 libxxhash-dev arm64 0.8.2-2build1 [80.6 kB] 255s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 libyaml-cpp0.8 arm64 0.8.0+dfsg-6build1 [112 kB] 255s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 libyaml-cpp-dev arm64 0.8.0+dfsg-6build1 [189 kB] 255s Get:42 http://ftpmaster.internal/ubuntu oracular/main arm64 pkgconf-bin arm64 1.8.1-3 [20.7 kB] 255s Get:43 http://ftpmaster.internal/ubuntu oracular/main arm64 pkgconf arm64 1.8.1-3 [16.7 kB] 255s Get:44 http://ftpmaster.internal/ubuntu oracular/main arm64 pkg-config arm64 1.8.1-3 [7266 B] 255s Get:45 http://ftpmaster.internal/ubuntu oracular/universe arm64 seqan-raptor arm64 3.0.1+ds-5 [648 kB] 255s Get:46 http://ftpmaster.internal/ubuntu oracular/universe arm64 seqan-raptor-doc all 3.0.1+ds-5 [1247 kB] 256s Fetched 78.1 MB in 3s (23.3 MB/s) 256s Selecting previously unselected package libjsoncpp25:arm64. 256s (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 ... 78607 files and directories currently installed.) 256s Preparing to unpack .../00-libjsoncpp25_1.9.5-6build1_arm64.deb ... 256s Unpacking libjsoncpp25:arm64 (1.9.5-6build1) ... 256s Selecting previously unselected package librhash0:arm64. 257s Preparing to unpack .../01-librhash0_1.4.3-3build1_arm64.deb ... 257s Unpacking librhash0:arm64 (1.4.3-3build1) ... 257s Selecting previously unselected package cmake-data. 257s Preparing to unpack .../02-cmake-data_3.29.6-1_all.deb ... 257s Unpacking cmake-data (3.29.6-1) ... 257s Selecting previously unselected package cmake. 257s Preparing to unpack .../03-cmake_3.29.6-1_arm64.deb ... 257s Unpacking cmake (3.29.6-1) ... 258s Selecting previously unselected package libisl23:arm64. 258s Preparing to unpack .../04-libisl23_0.26-3build1_arm64.deb ... 258s Unpacking libisl23:arm64 (0.26-3build1) ... 258s Selecting previously unselected package libmpc3:arm64. 258s Preparing to unpack .../05-libmpc3_1.3.1-1build1_arm64.deb ... 258s Unpacking libmpc3:arm64 (1.3.1-1build1) ... 258s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 258s Preparing to unpack .../06-cpp-14-aarch64-linux-gnu_14.1.0-5ubuntu1_arm64.deb ... 258s Unpacking cpp-14-aarch64-linux-gnu (14.1.0-5ubuntu1) ... 258s Selecting previously unselected package cpp-14. 258s Preparing to unpack .../07-cpp-14_14.1.0-5ubuntu1_arm64.deb ... 258s Unpacking cpp-14 (14.1.0-5ubuntu1) ... 258s Selecting previously unselected package cpp-aarch64-linux-gnu. 259s Preparing to unpack .../08-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 259s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 259s Selecting previously unselected package cpp. 259s Preparing to unpack .../09-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 259s Unpacking cpp (4:14.1.0-2ubuntu1) ... 259s Selecting previously unselected package libcc1-0:arm64. 259s Preparing to unpack .../10-libcc1-0_14.1.0-5ubuntu1_arm64.deb ... 259s Unpacking libcc1-0:arm64 (14.1.0-5ubuntu1) ... 259s Selecting previously unselected package libitm1:arm64. 259s Preparing to unpack .../11-libitm1_14.1.0-5ubuntu1_arm64.deb ... 259s Unpacking libitm1:arm64 (14.1.0-5ubuntu1) ... 259s Selecting previously unselected package libatomic1:arm64. 259s Preparing to unpack .../12-libatomic1_14.1.0-5ubuntu1_arm64.deb ... 259s Unpacking libatomic1:arm64 (14.1.0-5ubuntu1) ... 259s Selecting previously unselected package libasan8:arm64. 259s Preparing to unpack .../13-libasan8_14.1.0-5ubuntu1_arm64.deb ... 259s Unpacking libasan8:arm64 (14.1.0-5ubuntu1) ... 259s Selecting previously unselected package liblsan0:arm64. 259s Preparing to unpack .../14-liblsan0_14.1.0-5ubuntu1_arm64.deb ... 259s Unpacking liblsan0:arm64 (14.1.0-5ubuntu1) ... 259s Selecting previously unselected package libtsan2:arm64. 260s Preparing to unpack .../15-libtsan2_14.1.0-5ubuntu1_arm64.deb ... 260s Unpacking libtsan2:arm64 (14.1.0-5ubuntu1) ... 260s Selecting previously unselected package libubsan1:arm64. 260s Preparing to unpack .../16-libubsan1_14.1.0-5ubuntu1_arm64.deb ... 260s Unpacking libubsan1:arm64 (14.1.0-5ubuntu1) ... 260s Selecting previously unselected package libhwasan0:arm64. 260s Preparing to unpack .../17-libhwasan0_14.1.0-5ubuntu1_arm64.deb ... 260s Unpacking libhwasan0:arm64 (14.1.0-5ubuntu1) ... 260s Selecting previously unselected package libgcc-14-dev:arm64. 260s Preparing to unpack .../18-libgcc-14-dev_14.1.0-5ubuntu1_arm64.deb ... 260s Unpacking libgcc-14-dev:arm64 (14.1.0-5ubuntu1) ... 260s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 260s Preparing to unpack .../19-gcc-14-aarch64-linux-gnu_14.1.0-5ubuntu1_arm64.deb ... 260s Unpacking gcc-14-aarch64-linux-gnu (14.1.0-5ubuntu1) ... 261s Selecting previously unselected package gcc-14. 261s Preparing to unpack .../20-gcc-14_14.1.0-5ubuntu1_arm64.deb ... 261s Unpacking gcc-14 (14.1.0-5ubuntu1) ... 261s Selecting previously unselected package gcc-aarch64-linux-gnu. 261s Preparing to unpack .../21-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 261s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 261s Selecting previously unselected package gcc. 261s Preparing to unpack .../22-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 261s Unpacking gcc (4:14.1.0-2ubuntu1) ... 261s Selecting previously unselected package libstdc++-14-dev:arm64. 261s Preparing to unpack .../23-libstdc++-14-dev_14.1.0-5ubuntu1_arm64.deb ... 261s Unpacking libstdc++-14-dev:arm64 (14.1.0-5ubuntu1) ... 261s Selecting previously unselected package g++-14-aarch64-linux-gnu. 261s Preparing to unpack .../24-g++-14-aarch64-linux-gnu_14.1.0-5ubuntu1_arm64.deb ... 261s Unpacking g++-14-aarch64-linux-gnu (14.1.0-5ubuntu1) ... 262s Selecting previously unselected package g++-14. 262s Preparing to unpack .../25-g++-14_14.1.0-5ubuntu1_arm64.deb ... 262s Unpacking g++-14 (14.1.0-5ubuntu1) ... 262s Selecting previously unselected package g++-aarch64-linux-gnu. 262s Preparing to unpack .../26-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 262s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 262s Selecting previously unselected package g++. 262s Preparing to unpack .../27-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 262s Unpacking g++ (4:14.1.0-2ubuntu1) ... 262s Selecting previously unselected package googletest. 262s Preparing to unpack .../28-googletest_1.15.0-1_all.deb ... 262s Unpacking googletest (1.15.0-1) ... 262s Selecting previously unselected package libbz2-dev:arm64. 262s Preparing to unpack .../29-libbz2-dev_1.0.8-5.1_arm64.deb ... 262s Unpacking libbz2-dev:arm64 (1.0.8-5.1) ... 262s Selecting previously unselected package rapidjson-dev. 262s Preparing to unpack .../30-rapidjson-dev_1.1.0+dfsg2-7.2_all.deb ... 262s Unpacking rapidjson-dev (1.1.0+dfsg2-7.2) ... 262s Selecting previously unselected package libcereal-dev. 262s Preparing to unpack .../31-libcereal-dev_1.3.2+dfsg-5_arm64.deb ... 262s Unpacking libcereal-dev (1.3.2+dfsg-5) ... 262s Selecting previously unselected package libgtest-dev:arm64. 262s Preparing to unpack .../32-libgtest-dev_1.15.0-1_arm64.deb ... 262s Unpacking libgtest-dev:arm64 (1.15.0-1) ... 262s Selecting previously unselected package libpkgconf3:arm64. 262s Preparing to unpack .../33-libpkgconf3_1.8.1-3_arm64.deb ... 262s Unpacking libpkgconf3:arm64 (1.8.1-3) ... 262s Selecting previously unselected package zlib1g-dev:arm64. 262s Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu2_arm64.deb ... 262s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu2) ... 262s Selecting previously unselected package libseqan3-dev. 262s Preparing to unpack .../35-libseqan3-dev_3.3.0+ds-1_all.deb ... 262s Unpacking libseqan3-dev (3.3.0+ds-1) ... 262s Selecting previously unselected package libsimde-dev. 262s Preparing to unpack .../36-libsimde-dev_0.8.2-1_all.deb ... 262s Unpacking libsimde-dev (0.8.2-1) ... 262s Selecting previously unselected package libxxhash-dev:arm64. 262s Preparing to unpack .../37-libxxhash-dev_0.8.2-2build1_arm64.deb ... 262s Unpacking libxxhash-dev:arm64 (0.8.2-2build1) ... 262s Selecting previously unselected package libyaml-cpp0.8:arm64. 262s Preparing to unpack .../38-libyaml-cpp0.8_0.8.0+dfsg-6build1_arm64.deb ... 262s Unpacking libyaml-cpp0.8:arm64 (0.8.0+dfsg-6build1) ... 262s Selecting previously unselected package libyaml-cpp-dev:arm64. 262s Preparing to unpack .../39-libyaml-cpp-dev_0.8.0+dfsg-6build1_arm64.deb ... 262s Unpacking libyaml-cpp-dev:arm64 (0.8.0+dfsg-6build1) ... 262s Selecting previously unselected package pkgconf-bin. 262s Preparing to unpack .../40-pkgconf-bin_1.8.1-3_arm64.deb ... 262s Unpacking pkgconf-bin (1.8.1-3) ... 262s Selecting previously unselected package pkgconf:arm64. 262s Preparing to unpack .../41-pkgconf_1.8.1-3_arm64.deb ... 263s Unpacking pkgconf:arm64 (1.8.1-3) ... 263s Selecting previously unselected package pkg-config:arm64. 263s Preparing to unpack .../42-pkg-config_1.8.1-3_arm64.deb ... 263s Unpacking pkg-config:arm64 (1.8.1-3) ... 263s Selecting previously unselected package seqan-raptor. 263s Preparing to unpack .../43-seqan-raptor_3.0.1+ds-5_arm64.deb ... 263s Unpacking seqan-raptor (3.0.1+ds-5) ... 263s Selecting previously unselected package seqan-raptor-doc. 263s Preparing to unpack .../44-seqan-raptor-doc_3.0.1+ds-5_all.deb ... 263s Unpacking seqan-raptor-doc (3.0.1+ds-5) ... 263s Selecting previously unselected package autopkgtest-satdep. 263s Preparing to unpack .../45-2-autopkgtest-satdep.deb ... 263s Unpacking autopkgtest-satdep (0) ... 263s Setting up libsimde-dev (0.8.2-1) ... 263s Setting up libyaml-cpp0.8:arm64 (0.8.0+dfsg-6build1) ... 263s Setting up libyaml-cpp-dev:arm64 (0.8.0+dfsg-6build1) ... 263s Setting up googletest (1.15.0-1) ... 263s Setting up rapidjson-dev (1.1.0+dfsg2-7.2) ... 263s Setting up libpkgconf3:arm64 (1.8.1-3) ... 263s Setting up libmpc3:arm64 (1.3.1-1build1) ... 263s Setting up libatomic1:arm64 (14.1.0-5ubuntu1) ... 263s Setting up libjsoncpp25:arm64 (1.9.5-6build1) ... 263s Setting up pkgconf-bin (1.8.1-3) ... 263s Setting up libxxhash-dev:arm64 (0.8.2-2build1) ... 263s Setting up libubsan1:arm64 (14.1.0-5ubuntu1) ... 263s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu2) ... 263s Setting up libhwasan0:arm64 (14.1.0-5ubuntu1) ... 263s Setting up librhash0:arm64 (1.4.3-3build1) ... 263s Setting up libasan8:arm64 (14.1.0-5ubuntu1) ... 263s Setting up cmake-data (3.29.6-1) ... 263s Setting up libtsan2:arm64 (14.1.0-5ubuntu1) ... 263s Setting up libisl23:arm64 (0.26-3build1) ... 263s Setting up seqan-raptor (3.0.1+ds-5) ... 263s Setting up seqan-raptor-doc (3.0.1+ds-5) ... 263s Setting up libcc1-0:arm64 (14.1.0-5ubuntu1) ... 263s Setting up liblsan0:arm64 (14.1.0-5ubuntu1) ... 263s Setting up libitm1:arm64 (14.1.0-5ubuntu1) ... 263s Setting up libbz2-dev:arm64 (1.0.8-5.1) ... 263s Setting up libgtest-dev:arm64 (1.15.0-1) ... 263s Setting up libcereal-dev (1.3.2+dfsg-5) ... 263s Setting up pkgconf:arm64 (1.8.1-3) ... 263s Setting up pkg-config:arm64 (1.8.1-3) ... 263s Setting up cpp-14-aarch64-linux-gnu (14.1.0-5ubuntu1) ... 263s Setting up cmake (3.29.6-1) ... 263s Setting up libgcc-14-dev:arm64 (14.1.0-5ubuntu1) ... 263s Setting up libstdc++-14-dev:arm64 (14.1.0-5ubuntu1) ... 263s Setting up libseqan3-dev (3.3.0+ds-1) ... 263s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 263s Setting up cpp-14 (14.1.0-5ubuntu1) ... 263s Setting up cpp (4:14.1.0-2ubuntu1) ... 263s Setting up gcc-14-aarch64-linux-gnu (14.1.0-5ubuntu1) ... 263s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 263s Setting up g++-14-aarch64-linux-gnu (14.1.0-5ubuntu1) ... 263s Setting up gcc-14 (14.1.0-5ubuntu1) ... 263s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 263s Setting up g++-14 (14.1.0-5ubuntu1) ... 263s Setting up gcc (4:14.1.0-2ubuntu1) ... 263s Setting up g++ (4:14.1.0-2ubuntu1) ... 263s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 263s Setting up autopkgtest-satdep (0) ... 263s Processing triggers for man-db (2.12.1-2) ... 264s Processing triggers for libc-bin (2.39-0ubuntu9) ... 269s (Reading database ... 85619 files and directories currently installed.) 269s Removing autopkgtest-satdep (0) ... 273s autopkgtest [16:02:52]: test run-unit-test: [----------------------- 274s + pkg=seqan-raptor 274s + export LC_ALL=C.UTF-8 274s + LC_ALL=C.UTF-8 274s + '[' /tmp/autopkgtest.8m8bRX/autopkgtest_tmp = '' ']' 274s + cp -r CHANGELOG.md CMakeLists.txt CODE_OF_CONDUCT.md INSTALL.md LICENSE.md README.md build_system debian doc include lib src test util workflow /tmp/autopkgtest.8m8bRX/autopkgtest_tmp 274s + export 'CXXFLAGS=-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/sharg-parser/include/ -I/tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/submodules/lemon/include/' 274s + CXXFLAGS='-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/sharg-parser/include/ -I/tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/submodules/lemon/include/' 274s + cd /tmp/autopkgtest.8m8bRX/autopkgtest_tmp 274s + patch -p1 274s patching file test/raptor-test.cmake 274s + cd /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/test/unit 274s + cmake -DRAPTOR_SUBMODULES_DIR=/tmp/autopkgtest.8m8bRX/autopkgtest_tmp/test/unit/../../lib -DRAPTOR_NATIVE_BUILD=OFF . 274s -- The CXX compiler identification is GNU 14.1.0 274s -- The C compiler identification is GNU 14.1.0 274s -- Detecting CXX compiler ABI info 275s -- Detecting CXX compiler ABI info - done 275s -- Check for working CXX compiler: /usr/bin/c++ - skipped 275s -- Detecting CXX compile features 275s -- Detecting CXX compile features - done 275s -- Detecting C compiler ABI info 275s -- Detecting C compiler ABI info - done 275s -- Check for working C compiler: /usr/bin/cc - skipped 275s -- Detecting C compile features 275s -- Detecting C compile features - done 275s -- Finding RAPTOR and checking requirements: 275s -- RAPTOR include dir found: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include 275s -- Detected as running from a repository checkout… 275s -- …adding submodule include: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/chopper/include 275s -- …adding submodule include: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/robin-hood-hashing/src/include 275s -- …adding submodule include: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/sharg-parser/include 275s -- …adding submodule include: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/sharg-parser/test/include 275s -- …adding submodule include: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/lib/submodules/lemon/include 275s -- C++ Standard-20 support: via -std=c++20 276s -- OpenMP Support: via -fopenmp 276s -- SIMD-OpenMP Support: via -fopenmp-simd 277s -- Suppressing GCC 4 warnings: via -Wno-psabi 277s -- Optimize build: disabled 278s -- Link Time Optimization: enabled 278s -- Binary-stripping: via -s 278s -- Thread support: builtin 278s -- Optional dependency: ZLIB-1.3 found 278s -- Optional dependency: BZip2-1.0.8 found 278s -- Optional dependency: libexecinfo found 278s -- Found Raptor: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include 278s -- Finding program ccache 278s -- Finding program ccache - Failed 281s -- You can run `make` to build the application. 281s -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") 281s -- Checking for module 'libxxhash' 281s -- Found libxxhash, version 0.8.2 282s -- Test dependency: Google Test 1.15.0 found. 282s -- Configuring done (7.7s) 282s -- Generating done (0.1s) 282s -- Build files have been written to: /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/test/unit 282s + make 282s [ 1%] Building CXX object src/upgrade/CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o 283s In file included from /usr/include/seqan3/core/concept/cereal.hpp:17, 283s from /usr/include/seqan3/utility/container/dynamic_bitset.hpp:17, 283s from /usr/include/seqan3/search/kmer_index/shape.hpp:16, 283s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include/raptor/argument_parsing/build_arguments.hpp:18, 283s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include/raptor/argument_parsing/compute_bin_size.hpp:15, 283s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/src/upgrade/raptor_upgrade.cpp:13: 283s /usr/include/seqan3/core/platform.hpp:85:17: note: ‘#pragma message: Your compiler is newer than the latest supported compiler of this SeqAn version (gcc-13). It might be that SeqAn does not compile due to this. You can disable this warning by setting -DSEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC.’ 283s 85 | "Your compiler is newer than the latest supported compiler of this SeqAn version (gcc-13). It might be that SeqAn does not compile due to this. You can disable this warning by setting -DSEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC." 283s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288s In file included from /usr/include/cereal/archives/json.hpp:67, 288s from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp:17, 288s from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp:21, 288s from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp:13, 288s from /usr/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp:18, 288s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include/raptor/hierarchical_interleaved_bloom_filter.hpp:17, 288s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include/raptor/index.hpp:18, 288s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/include/raptor/upgrade/index_upgrader.hpp:16, 288s from /tmp/autopkgtest.8m8bRX/autopkgtest_tmp/src/upgrade/raptor_upgrade.cpp:16: 288s /usr/include/rapidjson/document.h: In member function ‘rapidjson::GenericStringRef& rapidjson::GenericStringRef::operator=(const rapidjson::GenericStringRef&)’: 288s /usr/include/rapidjson/document.h:319:82: error: assignment of read-only member ‘rapidjson::GenericStringRef::length’ 288s 319 | GenericStringRef& operator=(const GenericStringRef& rhs) { s = rhs.s; length = rhs.length; } 288s | ~~~~~~~^~~~~~~~~~~~ 297s make[2]: *** [src/upgrade/CMakeFiles/raptor_upgrade.dir/build.make:76: src/upgrade/CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o] Error 1 297s make[1]: *** [CMakeFiles/Makefile2:750: src/upgrade/CMakeFiles/raptor_upgrade.dir/all] Error 2 297s make: *** [Makefile:146: all] Error 2 298s autopkgtest [16:03:17]: test run-unit-test: -----------------------] 298s run-unit-test FAIL non-zero exit status 2 298s autopkgtest [16:03:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 299s autopkgtest [16:03:18]: @@@@@@@@@@@@@@@@@@@@ summary 299s cwl PASS 299s run-unit-test FAIL non-zero exit status 2 304s nova [W] Skipping flock in bos03-arm64 304s Creating nova instance adt-oracular-arm64-seqan-raptor-20240726-155819-juju-7f2275-prod-proposed-migration-environment-2-f392194d-21aa-414e-aaa5-60b37d42a540 from image adt/ubuntu-oracular-arm64-server-20240726.img (UUID 33caccb7-bc3b-4ecc-9e17-59d67995dc9e)... 304s nova [W] Skipping flock in bos03-arm64 304s Creating nova instance adt-oracular-arm64-seqan-raptor-20240726-155819-juju-7f2275-prod-proposed-migration-environment-2-f392194d-21aa-414e-aaa5-60b37d42a540 from image adt/ubuntu-oracular-arm64-server-20240726.img (UUID 33caccb7-bc3b-4ecc-9e17-59d67995dc9e)...