0s autopkgtest [07:16:45]: starting date and time: 2024-03-17 07:16:45+0000 0s autopkgtest [07:16:45]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [07:16:45]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.05hbpysd/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:nodejs,src:libuv1,src:openssl --apt-upgrade seqan-raptor --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=nodejs/18.19.1+dfsg-6ubuntu1 libuv1/1.48.0-1.1 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-22.secgroup --name adt-noble-arm64-seqan-raptor-20240317-071645-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 89s autopkgtest [07:18:14]: testbed dpkg architecture: arm64 90s autopkgtest [07:18:15]: testbed apt version: 2.7.12 90s autopkgtest [07:18:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 91s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 91s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [482 kB] 91s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 91s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 91s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [652 kB] 91s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 91s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 91s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 91s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4029 kB] 91s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 91s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.4 kB] 91s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 93s Fetched 9149 kB in 2s (4501 kB/s) 93s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s The following packages will be REMOVED: 97s libssl3 97s The following NEW packages will be installed: 97s libssl3t64 97s The following packages will be upgraded: 97s openssl 98s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 98s Need to get 2753 kB of archives. 98s After this operation, 72.7 kB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 98s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 99s Fetched 2753 kB in 1s (4044 kB/s) 99s (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 ... 74758 files and directories currently installed.) 99s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 99s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 99s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 99s wget depends on libssl3 (>= 3.0.0). 99s u-boot-tools depends on libssl3 (>= 3.0.0). 99s tnftp depends on libssl3 (>= 3.0.0). 99s tcpdump depends on libssl3 (>= 3.0.0). 99s systemd-resolved depends on libssl3 (>= 3.0.0). 99s systemd depends on libssl3 (>= 3.0.0). 99s sudo depends on libssl3 (>= 3.0.0). 99s sbsigntool depends on libssl3 (>= 3.0.0). 99s rsync depends on libssl3 (>= 3.0.0). 99s python3-cryptography depends on libssl3 (>= 3.0.0). 99s openssh-server depends on libssl3 (>= 3.0.10). 99s openssh-client depends on libssl3 (>= 3.0.10). 99s mtd-utils depends on libssl3 (>= 3.0.0). 99s mokutil depends on libssl3 (>= 3.0.0). 99s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 99s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 99s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 99s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 99s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 99s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 99s libnvme1 depends on libssl3 (>= 3.0.0). 99s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 99s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 99s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 99s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 99s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 99s kmod depends on libssl3 (>= 3.0.0). 99s dhcpcd-base depends on libssl3 (>= 3.0.0). 99s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 99s 99s (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 ... 74758 files and directories currently installed.) 99s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 99s Selecting previously unselected package libssl3t64:arm64. 99s (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 ... 74747 files and directories currently installed.) 99s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 99s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 99s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 99s Setting up openssl (3.0.13-0ubuntu1) ... 99s Processing triggers for man-db (2.12.0-3) ... 100s Processing triggers for libc-bin (2.39-0ubuntu2) ... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s sh: Attempting to set up Debian/Ubuntu apt sources automatically 102s sh: Distribution appears to be Ubuntu 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s eatmydata is already the newest version (131-1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s dbus is already the newest version (1.14.10-4ubuntu1). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s rng-tools-debian is already the newest version (2.4). 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s The following packages will be REMOVED: 108s cloud-init* python3-configobj* python3-debconf* 108s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 108s After this operation, 3252 kB disk space will be freed. 108s (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 ... 74760 files and directories currently installed.) 108s Removing cloud-init (24.1.1-0ubuntu1) ... 109s Removing python3-configobj (5.0.8-3) ... 109s Removing python3-debconf (1.5.86) ... 109s Processing triggers for man-db (2.12.0-3) ... 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 ... 74371 files and directories currently installed.) 110s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 111s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 111s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 111s invoke-rc.d: policy-rc.d denied execution of try-restart. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s linux-generic is already the newest version (6.8.0-11.11+1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 113s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 113s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 115s Reading package lists... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [07:18:42]: rebooting testbed after setup commands that affected boot 150s autopkgtest [07:19:15]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 152s autopkgtest [07:19:17]: @@@@@@@@@@@@@@@@@@@@ apt-source seqan-raptor 156s Get:1 http://ftpmaster.internal/ubuntu noble/universe seqan-raptor 3.0.1+ds-5 (dsc) [2642 B] 156s Get:2 http://ftpmaster.internal/ubuntu noble/universe seqan-raptor 3.0.1+ds-5 (tar) [3085 kB] 156s Get:3 http://ftpmaster.internal/ubuntu noble/universe seqan-raptor 3.0.1+ds-5 (diff) [10.3 kB] 156s gpgv: Signature made Wed Sep 6 13:05:19 2023 UTC 156s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 156s gpgv: Can't check signature: No public key 156s dpkg-source: warning: cannot verify inline signature for ./seqan-raptor_3.0.1+ds-5.dsc: no acceptable signature found 157s autopkgtest [07:19:22]: testing package seqan-raptor version 3.0.1+ds-5 157s autopkgtest [07:19:22]: build not needed 158s autopkgtest [07:19:23]: test cwl: preparing testbed 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s The following additional packages will be installed: 161s cwl-upgrader cwltool fontconfig fontconfig-config fonts-dejavu-core 161s fonts-dejavu-mono fonts-glyphicons-halflings graphviz libann0 libc-ares2 161s libcairo2 libcdt5 libcgraph6 libdatrie1 libdeflate0 libfontconfig1 libgd3 161s libgomp1 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libice6 161s libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap liblab-gamut1 liblerc4 161s libltdl7 libnode108 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 161s libpathplan4 libpixman-1-0 libsharpyuv0 libsm6 libthai-data libthai0 161s libtiff6 libwebp7 libxaw7 libxcb-render0 libxcb-shm0 libxmu6 libxpm4 161s libxrender1 libxslt1.1 libxt6 libyaml-cpp0.8 node-acorn node-busboy 161s node-cjs-module-lexer node-undici node-xtend nodejs python3-arcp 161s python3-argcomplete python3-cachecontrol python3-coloredlogs 161s python3-cwl-utils python3-dateutil python3-distutils python3-filelock 161s python3-humanfriendly python3-isodate python3-lib2to3 python3-lxml 161s python3-mistune python3-msgpack python3-mypy-extensions python3-networkx 161s python3-packaging python3-prov python3-psutil python3-pydot python3-rdflib 161s python3-ruamel.yaml python3-ruamel.yaml.clib python3-schema-salad 161s python3-setuptools python3-shellescape python3-spython seqan-raptor 161s seqan-raptor-doc x11-common 161s Suggested packages: 161s podman | docker.io | singularity-container gsfonts graphviz-doc libgd-tools 161s npm cwl-utils python-lxml-doc python-networkx-doc python3-gdal 161s python3-matplotlib python3-pygraphviz python3-scipy python-prov-doc 161s python-rdflib-doc python-setuptools-doc singularity-container 161s Recommended packages: 161s fonts-liberation2 libgts-bin nodejs-doc python3-bs4 python3-cssselect 161s python3-html5lib python3-numpy python3-sparqlwrapper black 161s The following NEW packages will be installed: 161s autopkgtest-satdep cwl-upgrader cwltool fontconfig fontconfig-config 161s fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings graphviz 161s libann0 libc-ares2 libcairo2 libcdt5 libcgraph6 libdatrie1 libdeflate0 161s libfontconfig1 libgd3 libgomp1 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2 161s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 161s liblab-gamut1 liblerc4 libltdl7 libnode108 libpango-1.0-0 161s libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpixman-1-0 161s libsharpyuv0 libsm6 libthai-data libthai0 libtiff6 libwebp7 libxaw7 161s libxcb-render0 libxcb-shm0 libxmu6 libxpm4 libxrender1 libxslt1.1 libxt6 161s libyaml-cpp0.8 node-acorn node-busboy node-cjs-module-lexer node-undici 161s node-xtend nodejs python3-arcp python3-argcomplete python3-cachecontrol 161s python3-coloredlogs python3-cwl-utils python3-dateutil python3-distutils 161s python3-filelock python3-humanfriendly python3-isodate python3-lib2to3 161s python3-lxml python3-mistune python3-msgpack python3-mypy-extensions 161s python3-networkx python3-packaging python3-prov python3-psutil python3-pydot 161s python3-rdflib python3-ruamel.yaml python3-ruamel.yaml.clib 161s python3-schema-salad python3-setuptools python3-shellescape python3-spython 161s seqan-raptor seqan-raptor-doc x11-common 161s 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 30.9 MB/30.9 MB of archives. 161s After this operation, 140 MB of additional disk space will be used. 161s Get:1 /tmp/autopkgtest.fy7WQs/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 161s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8-1 [187 kB] 162s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 162s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3-msgpack arm64 1.0.3-3build1 [93.0 kB] 162s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cachecontrol all 0.14.0-1 [19.0 kB] 162s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mistune all 3.0.2-1 [32.8 kB] 162s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mypy-extensions all 1.0.0-1 [6148 B] 162s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-isodate all 0.6.1-2 [24.3 kB] 162s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rdflib all 6.1.1-3 [362 kB] 162s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-filelock all 3.13.1-1 [10.8 kB] 162s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 162s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 162s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-schema-salad arm64 8.5.20240102191335-1 [1433 kB] 162s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 cwl-upgrader all 1.2.11-1 [16.0 kB] 162s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-argcomplete all 3.1.4-1 [33.5 kB] 162s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-humanfriendly all 10.0-3 [70.4 kB] 162s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 162s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 162s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cwl-utils all 0.32-1 [118 kB] 162s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 162s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB] 162s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 162s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 162s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-prov all 2.0.0-2 [96.3 kB] 162s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-psutil arm64 5.9.8-1 [196 kB] 162s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libann0 arm64 1.1.2+doc-9 [25.1 kB] 162s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libcdt5 arm64 2.42.2-8build1 [20.3 kB] 162s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libcgraph6 arm64 2.42.2-8build1 [44.8 kB] 162s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 162s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 162s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 162s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 162s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 162s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 162s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 162s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 162s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 162s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 162s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 162s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 162s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxpm4 arm64 1:3.5.17-1 [34.5 kB] 162s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libgd3 arm64 2.3.3-9ubuntu1 [119 kB] 162s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 libgts-0.7-5 arm64 0.7.6+darcs121130-5 [157 kB] 162s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 162s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 162s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 162s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 162s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 162s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl7 arm64 2.4.7-7 [40.3 kB] 162s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 162s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 162s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 162s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 162s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 162s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 162s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 162s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 162s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 162s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 libpathplan4 arm64 2.42.2-8build1 [22.6 kB] 162s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 libgvc6 arm64 2.42.2-8build1 [692 kB] 162s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 libgvpr2 arm64 2.42.2-8build1 [187 kB] 162s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 liblab-gamut1 arm64 2.42.2-8build1 [1860 kB] 162s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 162s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 162s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 162s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 162s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxmu6 arm64 2:1.1.3-3 [48.9 kB] 162s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxaw7 arm64 2:1.0.14-1 [184 kB] 162s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 graphviz arm64 2.42.2-8build1 [613 kB] 162s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pydot all 1.4.2-2 [24.4 kB] 162s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-shellescape all 3.4.1-5 [5064 B] 162s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-spython all 0.3.13-2 [56.2 kB] 162s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-arcp all 0.2.1-6 [13.6 kB] 162s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 162s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 162s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] 162s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 cwltool all 3.1.20240112164112-2 [509 kB] 162s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 162s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libc-ares2 arm64 1.27.0-1 [74.1 kB] 162s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 node-xtend all 4.0.2-3 [3902 B] 162s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 nodejs arm64 18.19.1+dfsg-2ubuntu4 [306 kB] 162s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [115 kB] 163s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 node-cjs-module-lexer all 1.2.3+dfsg-1 [32.1 kB] 163s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 node-busboy all 1.6.0+~cs2.6.0-2 [17.3 kB] 163s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 node-undici all 5.26.3+dfsg1+~cs23.10.12-2 [325 kB] 163s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 libnode108 arm64 18.19.1+dfsg-2ubuntu4 [11.2 MB] 163s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libyaml-cpp0.8 arm64 0.8.0+dfsg-6 [112 kB] 163s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 seqan-raptor arm64 3.0.1+ds-5 [648 kB] 163s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 seqan-raptor-doc all 3.0.1+ds-5 [1247 kB] 164s Fetched 30.9 MB in 2s (16.0 MB/s) 164s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 164s (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 ... 74316 files and directories currently installed.) 164s Preparing to unpack .../00-python3-ruamel.yaml.clib_0.2.8-1_arm64.deb ... 164s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8-1) ... 164s Selecting previously unselected package python3-ruamel.yaml. 164s Preparing to unpack .../01-python3-ruamel.yaml_0.17.21-1_all.deb ... 164s Unpacking python3-ruamel.yaml (0.17.21-1) ... 164s Selecting previously unselected package python3-msgpack. 164s Preparing to unpack .../02-python3-msgpack_1.0.3-3build1_arm64.deb ... 164s Unpacking python3-msgpack (1.0.3-3build1) ... 164s Selecting previously unselected package python3-cachecontrol. 164s Preparing to unpack .../03-python3-cachecontrol_0.14.0-1_all.deb ... 164s Unpacking python3-cachecontrol (0.14.0-1) ... 164s Selecting previously unselected package python3-mistune. 164s Preparing to unpack .../04-python3-mistune_3.0.2-1_all.deb ... 164s Unpacking python3-mistune (3.0.2-1) ... 164s Selecting previously unselected package python3-mypy-extensions. 164s Preparing to unpack .../05-python3-mypy-extensions_1.0.0-1_all.deb ... 164s Unpacking python3-mypy-extensions (1.0.0-1) ... 164s Selecting previously unselected package python3-isodate. 164s Preparing to unpack .../06-python3-isodate_0.6.1-2_all.deb ... 164s Unpacking python3-isodate (0.6.1-2) ... 164s Selecting previously unselected package python3-rdflib. 164s Preparing to unpack .../07-python3-rdflib_6.1.1-3_all.deb ... 164s Unpacking python3-rdflib (6.1.1-3) ... 164s Selecting previously unselected package python3-filelock. 164s Preparing to unpack .../08-python3-filelock_3.13.1-1_all.deb ... 164s Unpacking python3-filelock (3.13.1-1) ... 164s Selecting previously unselected package fonts-glyphicons-halflings. 164s Preparing to unpack .../09-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 164s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 164s Selecting previously unselected package libjs-bootstrap. 164s Preparing to unpack .../10-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 164s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 164s Selecting previously unselected package python3-schema-salad. 164s Preparing to unpack .../11-python3-schema-salad_8.5.20240102191335-1_arm64.deb ... 164s Unpacking python3-schema-salad (8.5.20240102191335-1) ... 164s Selecting previously unselected package cwl-upgrader. 164s Preparing to unpack .../12-cwl-upgrader_1.2.11-1_all.deb ... 164s Unpacking cwl-upgrader (1.2.11-1) ... 164s Selecting previously unselected package python3-argcomplete. 164s Preparing to unpack .../13-python3-argcomplete_3.1.4-1_all.deb ... 164s Unpacking python3-argcomplete (3.1.4-1) ... 164s Selecting previously unselected package python3-humanfriendly. 164s Preparing to unpack .../14-python3-humanfriendly_10.0-3_all.deb ... 164s Unpacking python3-humanfriendly (10.0-3) ... 164s Selecting previously unselected package python3-coloredlogs. 164s Preparing to unpack .../15-python3-coloredlogs_15.0.1-1_all.deb ... 164s Unpacking python3-coloredlogs (15.0.1-1) ... 164s Selecting previously unselected package python3-packaging. 164s Preparing to unpack .../16-python3-packaging_23.2-1_all.deb ... 164s Unpacking python3-packaging (23.2-1) ... 164s Selecting previously unselected package python3-cwl-utils. 165s Preparing to unpack .../17-python3-cwl-utils_0.32-1_all.deb ... 165s Unpacking python3-cwl-utils (0.32-1) ... 165s Selecting previously unselected package python3-dateutil. 165s Preparing to unpack .../18-python3-dateutil_2.8.2-3_all.deb ... 165s Unpacking python3-dateutil (2.8.2-3) ... 165s Selecting previously unselected package libxslt1.1:arm64. 165s Preparing to unpack .../19-libxslt1.1_1.1.35-1_arm64.deb ... 165s Unpacking libxslt1.1:arm64 (1.1.35-1) ... 165s Selecting previously unselected package python3-lxml:arm64. 165s Preparing to unpack .../20-python3-lxml_5.1.0-1_arm64.deb ... 165s Unpacking python3-lxml:arm64 (5.1.0-1) ... 165s Selecting previously unselected package python3-networkx. 165s Preparing to unpack .../21-python3-networkx_2.8.8-1ubuntu1_all.deb ... 165s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 165s Selecting previously unselected package python3-prov. 165s Preparing to unpack .../22-python3-prov_2.0.0-2_all.deb ... 165s Unpacking python3-prov (2.0.0-2) ... 165s Selecting previously unselected package python3-psutil. 165s Preparing to unpack .../23-python3-psutil_5.9.8-1_arm64.deb ... 165s Unpacking python3-psutil (5.9.8-1) ... 165s Selecting previously unselected package libann0. 165s Preparing to unpack .../24-libann0_1.1.2+doc-9_arm64.deb ... 165s Unpacking libann0 (1.1.2+doc-9) ... 165s Selecting previously unselected package libcdt5:arm64. 165s Preparing to unpack .../25-libcdt5_2.42.2-8build1_arm64.deb ... 165s Unpacking libcdt5:arm64 (2.42.2-8build1) ... 165s Selecting previously unselected package libcgraph6:arm64. 165s Preparing to unpack .../26-libcgraph6_2.42.2-8build1_arm64.deb ... 165s Unpacking libcgraph6:arm64 (2.42.2-8build1) ... 165s Selecting previously unselected package fonts-dejavu-mono. 165s Preparing to unpack .../27-fonts-dejavu-mono_2.37-8_all.deb ... 165s Unpacking fonts-dejavu-mono (2.37-8) ... 165s Selecting previously unselected package fonts-dejavu-core. 165s Preparing to unpack .../28-fonts-dejavu-core_2.37-8_all.deb ... 166s Unpacking fonts-dejavu-core (2.37-8) ... 166s Selecting previously unselected package fontconfig-config. 166s Preparing to unpack .../29-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 166s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 166s Selecting previously unselected package libfontconfig1:arm64. 166s Preparing to unpack .../30-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 166s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 166s Selecting previously unselected package libjpeg-turbo8:arm64. 166s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 166s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 166s Selecting previously unselected package libjpeg8:arm64. 166s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_arm64.deb ... 166s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 166s Selecting previously unselected package libdeflate0:arm64. 166s Preparing to unpack .../33-libdeflate0_1.19-1_arm64.deb ... 166s Unpacking libdeflate0:arm64 (1.19-1) ... 166s Selecting previously unselected package libjbig0:arm64. 166s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 166s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 166s Selecting previously unselected package liblerc4:arm64. 166s Preparing to unpack .../35-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 166s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 166s Selecting previously unselected package libsharpyuv0:arm64. 166s Preparing to unpack .../36-libsharpyuv0_1.3.2-0.4_arm64.deb ... 166s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 166s Selecting previously unselected package libwebp7:arm64. 166s Preparing to unpack .../37-libwebp7_1.3.2-0.4_arm64.deb ... 166s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 166s Selecting previously unselected package libtiff6:arm64. 167s Preparing to unpack .../38-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 167s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 167s Selecting previously unselected package libxpm4:arm64. 167s Preparing to unpack .../39-libxpm4_1%3a3.5.17-1_arm64.deb ... 167s Unpacking libxpm4:arm64 (1:3.5.17-1) ... 167s Selecting previously unselected package libgd3:arm64. 167s Preparing to unpack .../40-libgd3_2.3.3-9ubuntu1_arm64.deb ... 167s Unpacking libgd3:arm64 (2.3.3-9ubuntu1) ... 167s Selecting previously unselected package libgts-0.7-5:arm64. 167s Preparing to unpack .../41-libgts-0.7-5_0.7.6+darcs121130-5_arm64.deb ... 167s Unpacking libgts-0.7-5:arm64 (0.7.6+darcs121130-5) ... 167s Selecting previously unselected package libpixman-1-0:arm64. 167s Preparing to unpack .../42-libpixman-1-0_0.42.2-1_arm64.deb ... 167s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 167s Selecting previously unselected package libxcb-render0:arm64. 167s Preparing to unpack .../43-libxcb-render0_1.15-1_arm64.deb ... 167s Unpacking libxcb-render0:arm64 (1.15-1) ... 167s Selecting previously unselected package libxcb-shm0:arm64. 167s Preparing to unpack .../44-libxcb-shm0_1.15-1_arm64.deb ... 167s Unpacking libxcb-shm0:arm64 (1.15-1) ... 167s Selecting previously unselected package libxrender1:arm64. 167s Preparing to unpack .../45-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 167s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 167s Selecting previously unselected package libcairo2:arm64. 167s Preparing to unpack .../46-libcairo2_1.18.0-1_arm64.deb ... 167s Unpacking libcairo2:arm64 (1.18.0-1) ... 167s Selecting previously unselected package libltdl7:arm64. 167s Preparing to unpack .../47-libltdl7_2.4.7-7_arm64.deb ... 167s Unpacking libltdl7:arm64 (2.4.7-7) ... 167s Selecting previously unselected package fontconfig. 167s Preparing to unpack .../48-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 167s Unpacking fontconfig (2.15.0-1ubuntu1) ... 167s Selecting previously unselected package libgraphite2-3:arm64. 167s Preparing to unpack .../49-libgraphite2-3_1.3.14-2_arm64.deb ... 167s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 167s Selecting previously unselected package libharfbuzz0b:arm64. 167s Preparing to unpack .../50-libharfbuzz0b_8.3.0-2_arm64.deb ... 167s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 167s Selecting previously unselected package libthai-data. 167s Preparing to unpack .../51-libthai-data_0.1.29-2_all.deb ... 167s Unpacking libthai-data (0.1.29-2) ... 168s Selecting previously unselected package libdatrie1:arm64. 168s Preparing to unpack .../52-libdatrie1_0.2.13-3_arm64.deb ... 168s Unpacking libdatrie1:arm64 (0.2.13-3) ... 168s Selecting previously unselected package libthai0:arm64. 168s Preparing to unpack .../53-libthai0_0.1.29-2_arm64.deb ... 168s Unpacking libthai0:arm64 (0.1.29-2) ... 168s Selecting previously unselected package libpango-1.0-0:arm64. 168s Preparing to unpack .../54-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 168s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 168s Selecting previously unselected package libpangoft2-1.0-0:arm64. 168s Preparing to unpack .../55-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 168s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 168s Selecting previously unselected package libpangocairo-1.0-0:arm64. 168s Preparing to unpack .../56-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 168s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 168s Selecting previously unselected package libpathplan4:arm64. 168s Preparing to unpack .../57-libpathplan4_2.42.2-8build1_arm64.deb ... 168s Unpacking libpathplan4:arm64 (2.42.2-8build1) ... 168s Selecting previously unselected package libgvc6. 168s Preparing to unpack .../58-libgvc6_2.42.2-8build1_arm64.deb ... 168s Unpacking libgvc6 (2.42.2-8build1) ... 168s Selecting previously unselected package libgvpr2:arm64. 168s Preparing to unpack .../59-libgvpr2_2.42.2-8build1_arm64.deb ... 168s Unpacking libgvpr2:arm64 (2.42.2-8build1) ... 168s Selecting previously unselected package liblab-gamut1:arm64. 168s Preparing to unpack .../60-liblab-gamut1_2.42.2-8build1_arm64.deb ... 168s Unpacking liblab-gamut1:arm64 (2.42.2-8build1) ... 168s Selecting previously unselected package x11-common. 168s Preparing to unpack .../61-x11-common_1%3a7.7+23ubuntu2_all.deb ... 168s Unpacking x11-common (1:7.7+23ubuntu2) ... 168s Selecting previously unselected package libice6:arm64. 168s Preparing to unpack .../62-libice6_2%3a1.0.10-1build2_arm64.deb ... 168s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 168s Selecting previously unselected package libsm6:arm64. 168s Preparing to unpack .../63-libsm6_2%3a1.2.3-1build2_arm64.deb ... 168s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 168s Selecting previously unselected package libxt6:arm64. 168s Preparing to unpack .../64-libxt6_1%3a1.2.1-1.1_arm64.deb ... 168s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 168s Selecting previously unselected package libxmu6:arm64. 168s Preparing to unpack .../65-libxmu6_2%3a1.1.3-3_arm64.deb ... 168s Unpacking libxmu6:arm64 (2:1.1.3-3) ... 168s Selecting previously unselected package libxaw7:arm64. 168s Preparing to unpack .../66-libxaw7_2%3a1.0.14-1_arm64.deb ... 168s Unpacking libxaw7:arm64 (2:1.0.14-1) ... 168s Selecting previously unselected package graphviz. 168s Preparing to unpack .../67-graphviz_2.42.2-8build1_arm64.deb ... 168s Unpacking graphviz (2.42.2-8build1) ... 169s Selecting previously unselected package python3-pydot. 169s Preparing to unpack .../68-python3-pydot_1.4.2-2_all.deb ... 169s Unpacking python3-pydot (1.4.2-2) ... 169s Selecting previously unselected package python3-shellescape. 169s Preparing to unpack .../69-python3-shellescape_3.4.1-5_all.deb ... 169s Unpacking python3-shellescape (3.4.1-5) ... 169s Selecting previously unselected package python3-spython. 169s Preparing to unpack .../70-python3-spython_0.3.13-2_all.deb ... 169s Unpacking python3-spython (0.3.13-2) ... 169s Selecting previously unselected package python3-arcp. 169s Preparing to unpack .../71-python3-arcp_0.2.1-6_all.deb ... 169s Unpacking python3-arcp (0.2.1-6) ... 169s Selecting previously unselected package python3-lib2to3. 169s Preparing to unpack .../72-python3-lib2to3_3.11.5-1_all.deb ... 169s Unpacking python3-lib2to3 (3.11.5-1) ... 169s Selecting previously unselected package python3-distutils. 169s Preparing to unpack .../73-python3-distutils_3.11.5-1_all.deb ... 169s Unpacking python3-distutils (3.11.5-1) ... 169s Selecting previously unselected package python3-setuptools. 169s Preparing to unpack .../74-python3-setuptools_68.1.2-2_all.deb ... 169s Unpacking python3-setuptools (68.1.2-2) ... 169s Selecting previously unselected package cwltool. 169s Preparing to unpack .../75-cwltool_3.1.20240112164112-2_all.deb ... 169s Unpacking cwltool (3.1.20240112164112-2) ... 169s Selecting previously unselected package libgomp1:arm64. 169s Preparing to unpack .../76-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 169s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 169s Selecting previously unselected package libc-ares2:arm64. 169s Preparing to unpack .../77-libc-ares2_1.27.0-1_arm64.deb ... 169s Unpacking libc-ares2:arm64 (1.27.0-1) ... 169s Selecting previously unselected package node-xtend. 169s Preparing to unpack .../78-node-xtend_4.0.2-3_all.deb ... 169s Unpacking node-xtend (4.0.2-3) ... 169s Selecting previously unselected package nodejs. 169s Preparing to unpack .../79-nodejs_18.19.1+dfsg-2ubuntu4_arm64.deb ... 169s Unpacking nodejs (18.19.1+dfsg-2ubuntu4) ... 169s Selecting previously unselected package node-acorn. 169s Preparing to unpack .../80-node-acorn_8.8.1+ds+~cs25.17.7-2_all.deb ... 169s Unpacking node-acorn (8.8.1+ds+~cs25.17.7-2) ... 169s Selecting previously unselected package node-cjs-module-lexer. 169s Preparing to unpack .../81-node-cjs-module-lexer_1.2.3+dfsg-1_all.deb ... 169s Unpacking node-cjs-module-lexer (1.2.3+dfsg-1) ... 169s Selecting previously unselected package node-busboy. 169s Preparing to unpack .../82-node-busboy_1.6.0+~cs2.6.0-2_all.deb ... 169s Unpacking node-busboy (1.6.0+~cs2.6.0-2) ... 169s Selecting previously unselected package node-undici. 170s Preparing to unpack .../83-node-undici_5.26.3+dfsg1+~cs23.10.12-2_all.deb ... 170s Unpacking node-undici (5.26.3+dfsg1+~cs23.10.12-2) ... 170s Selecting previously unselected package libnode108:arm64. 170s Preparing to unpack .../84-libnode108_18.19.1+dfsg-2ubuntu4_arm64.deb ... 170s Unpacking libnode108:arm64 (18.19.1+dfsg-2ubuntu4) ... 170s Selecting previously unselected package libyaml-cpp0.8:arm64. 170s Preparing to unpack .../85-libyaml-cpp0.8_0.8.0+dfsg-6_arm64.deb ... 170s Unpacking libyaml-cpp0.8:arm64 (0.8.0+dfsg-6) ... 170s Selecting previously unselected package seqan-raptor. 170s Preparing to unpack .../86-seqan-raptor_3.0.1+ds-5_arm64.deb ... 170s Unpacking seqan-raptor (3.0.1+ds-5) ... 170s Selecting previously unselected package seqan-raptor-doc. 170s Preparing to unpack .../87-seqan-raptor-doc_3.0.1+ds-5_all.deb ... 170s Unpacking seqan-raptor-doc (3.0.1+ds-5) ... 170s Selecting previously unselected package autopkgtest-satdep. 170s Preparing to unpack .../88-1-autopkgtest-satdep.deb ... 170s Unpacking autopkgtest-satdep (0) ... 170s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 170s Setting up python3-arcp (0.2.1-6) ... 170s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 170s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 170s Setting up python3-filelock (3.13.1-1) ... 171s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 171s Setting up libxpm4:arm64 (1:3.5.17-1) ... 171s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 171s Setting up libdatrie1:arm64 (0.2.13-3) ... 171s Setting up libxcb-render0:arm64 (1.15-1) ... 171s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 171s Setting up python3-mypy-extensions (1.0.0-1) ... 171s Setting up libyaml-cpp0.8:arm64 (0.8.0+dfsg-6) ... 171s Setting up liblab-gamut1:arm64 (2.42.2-8build1) ... 171s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8-1) ... 171s Setting up x11-common (1:7.7+23ubuntu2) ... 171s Setting up libdeflate0:arm64 (1.19-1) ... 171s Setting up node-cjs-module-lexer (1.2.3+dfsg-1) ... 171s Setting up libxcb-shm0:arm64 (1.15-1) ... 171s Setting up libc-ares2:arm64 (1.27.0-1) ... 171s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 171s Setting up python3-networkx (2.8.8-1ubuntu1) ... 172s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 172s "graph [edge [ source u'u\4200' target u'u\4200' ] " 172s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 172s + "node [ id u'u\4200' label b ] ]" 172s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 172s Setting up python3-psutil (5.9.8-1) ... 172s Setting up libgts-0.7-5:arm64 (0.7.6+darcs121130-5) ... 172s Setting up python3-isodate (0.6.1-2) ... 173s Setting up python3-packaging (23.2-1) ... 173s Setting up python3-humanfriendly (10.0-3) ... 173s Setting up python3-spython (0.3.13-2) ... 174s Setting up libpathplan4:arm64 (2.42.2-8build1) ... 174s Setting up libann0 (1.1.2+doc-9) ... 174s Setting up fonts-dejavu-mono (2.37-8) ... 174s Setting up fonts-dejavu-core (2.37-8) ... 174s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 174s Setting up libltdl7:arm64 (2.4.7-7) ... 174s Setting up libwebp7:arm64 (1.3.2-0.4) ... 174s Setting up python3-ruamel.yaml (0.17.21-1) ... 174s Setting up python3-rdflib (6.1.1-3) ... 174s /usr/lib/python3/dist-packages/rdflib/extras/external_graph_libs.py:75: SyntaxWarning: invalid escape sequence '\*' 174s """Converts the given graph into a networkx.MultiDiGraph. 174s /usr/lib/python3/dist-packages/rdflib/extras/external_graph_libs.py:132: SyntaxWarning: invalid escape sequence '\*' 174s """Converts the given graph into a networkx.DiGraph. 174s /usr/lib/python3/dist-packages/rdflib/extras/external_graph_libs.py:195: SyntaxWarning: invalid escape sequence '\*' 174s """Converts the given graph into a networkx.Graph. 175s Setting up libxslt1.1:arm64 (1.1.35-1) ... 175s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 175s Setting up libthai-data (0.1.29-2) ... 175s Setting up python3-dateutil (2.8.2-3) ... 175s Setting up python3-msgpack (1.0.3-3build1) ... 175s Setting up libcdt5:arm64 (2.42.2-8build1) ... 175s Setting up libcgraph6:arm64 (2.42.2-8build1) ... 175s Setting up python3-cachecontrol (0.14.0-1) ... 175s Setting up python3-shellescape (3.4.1-5) ... 175s Setting up node-xtend (4.0.2-3) ... 175s Setting up seqan-raptor (3.0.1+ds-5) ... 175s Setting up python3-argcomplete (3.1.4-1) ... 175s Setting up python3-lib2to3 (3.11.5-1) ... 176s Setting up python3-coloredlogs (15.0.1-1) ... 176s Setting up seqan-raptor-doc (3.0.1+ds-5) ... 176s Setting up python3-mistune (3.0.2-1) ... 176s Setting up libjs-bootstrap (3.4.1+dfsg-3) ... 176s Setting up node-busboy (1.6.0+~cs2.6.0-2) ... 176s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 176s Setting up python3-distutils (3.11.5-1) ... 176s python3.12: can't get files for byte-compilation 176s Setting up libice6:arm64 (2:1.0.10-1build2) ... 176s Setting up python3-setuptools (68.1.2-2) ... 176s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 176s Setting up python3-schema-salad (8.5.20240102191335-1) ... 177s Setting up libthai0:arm64 (0.1.29-2) ... 177s Setting up cwl-upgrader (1.2.11-1) ... 177s Setting up libgvpr2:arm64 (2.42.2-8build1) ... 177s Setting up node-undici (5.26.3+dfsg1+~cs23.10.12-2) ... 177s Setting up python3-lxml:arm64 (5.1.0-1) ... 177s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 177s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 177s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 177s Setting up fontconfig (2.15.0-1ubuntu1) ... 179s Regenerating fonts cache... done. 179s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 179s Setting up python3-cwl-utils (0.32-1) ... 180s Setting up libcairo2:arm64 (1.18.0-1) ... 180s Setting up python3-prov (2.0.0-2) ... 180s Setting up libgd3:arm64 (2.3.3-9ubuntu1) ... 180s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 180s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 180s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 180s Setting up libxmu6:arm64 (2:1.1.3-3) ... 180s Setting up libxaw7:arm64 (2:1.0.14-1) ... 180s Setting up libgvc6 (2.42.2-8build1) ... 180s Setting up graphviz (2.42.2-8build1) ... 180s Setting up python3-pydot (1.4.2-2) ... 180s Setting up cwltool (3.1.20240112164112-2) ... 181s Setting up libnode108:arm64 (18.19.1+dfsg-2ubuntu4) ... 181s Setting up nodejs (18.19.1+dfsg-2ubuntu4) ... 181s update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode 181s Setting up node-acorn (8.8.1+ds+~cs25.17.7-2) ... 181s Setting up autopkgtest-satdep (0) ... 181s Processing triggers for libc-bin (2.39-0ubuntu2) ... 181s Processing triggers for man-db (2.12.0-3) ... 187s (Reading database ... 80694 files and directories currently installed.) 187s Removing autopkgtest-satdep (0) ... 188s autopkgtest [07:19:53]: test cwl: [----------------------- 189s INFO /usr/bin/cwltool 3.1.20240112164112 189s INFO Resolved '/usr/share/commonwl/raptor-build.cwl' to 'file:///usr/share/commonwl/raptor-build.cwl' 191s INFO [job raptor-build.cwl] /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/zfwejuz8$ raptor \ 191s build \ 191s --input \ 191s input_bins_filepaths.txt \ 191s --output \ 191s 0_bins_window_19.index 191s ============= Timings ============= 191s Wall clock time [s]: 0.01 191s Peak memory usage [MiB]: 72.3 191s Determine IBF size [s]: 0.00 191s Index allocation [s]: 0.00 191s User bin I/O avg per thread [s]: 0.00 191s User bin I/O sum [s]: 0.00 191s Fill IBF avg per thread [s]: 0.00 191s Fill IBF sum [s]: 0.00 191s Store index [s]: 0.00 191s INFO [job raptor-build.cwl] completed success 191s INFO Final process status is success 192s "checksum": "sha1$098169f476fb949b0d08f2d1e05881049819b811", 192s INFO /usr/bin/cwltool 3.1.20240112164112 192s INFO Resolved '/usr/share/commonwl/raptor-build.cwl' to 'file:///usr/share/commonwl/raptor-build.cwl' 194s INFO [job raptor-build.cwl] /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/tyr35o31$ raptor \ 194s build \ 194s --input \ 194s input_bins_filepaths.txt \ 194s --output \ 194s 0_bins_window_19.index 194s ============= Timings ============= 194s Wall clock time [s]: 0.01 194s Peak memory usage [MiB]: 72.7 194s Determine IBF size [s]: 0.00 194s Index allocation [s]: 0.00 194s User bin I/O avg per thread [s]: 0.00 194s User bin I/O sum [s]: 0.00 194s Fill IBF avg per thread [s]: 0.00 194s Fill IBF sum [s]: 0.00 194s Store index [s]: 0.00 194s INFO [job raptor-build.cwl] completed success 194s INFO Final process status is success 194s "checksum": "sha1$64a4328eb3dab99bf6ecd38f84f4ae45fd01a4dd", 195s autopkgtest [07:20:00]: test cwl: -----------------------] 195s cwl PASS 195s autopkgtest [07:20:00]: test cwl: - - - - - - - - - - results - - - - - - - - - - 196s autopkgtest [07:20:01]: test run-unit-test: preparing testbed 280s autopkgtest [07:21:25]: testbed dpkg architecture: arm64 280s autopkgtest [07:21:25]: testbed apt version: 2.7.12 280s autopkgtest [07:21:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 280s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 280s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 281s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [482 kB] 281s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 281s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 281s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [652 kB] 281s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 281s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 281s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 281s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4029 kB] 281s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 281s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.4 kB] 281s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 283s Fetched 9149 kB in 2s (5221 kB/s) 283s Reading package lists... 286s Reading package lists... 286s Building dependency tree... 286s Reading state information... 286s Calculating upgrade... 287s The following packages will be REMOVED: 287s libssl3 287s The following NEW packages will be installed: 287s libssl3t64 287s The following packages will be upgraded: 287s openssl 287s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 287s Need to get 2753 kB of archives. 287s After this operation, 72.7 kB of additional disk space will be used. 287s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 287s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 288s Fetched 2753 kB in 1s (4143 kB/s) 288s (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 ... 74758 files and directories currently installed.) 288s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 288s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 288s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 288s wget depends on libssl3 (>= 3.0.0). 288s u-boot-tools depends on libssl3 (>= 3.0.0). 288s tnftp depends on libssl3 (>= 3.0.0). 288s tcpdump depends on libssl3 (>= 3.0.0). 288s systemd-resolved depends on libssl3 (>= 3.0.0). 288s systemd depends on libssl3 (>= 3.0.0). 288s sudo depends on libssl3 (>= 3.0.0). 288s sbsigntool depends on libssl3 (>= 3.0.0). 288s rsync depends on libssl3 (>= 3.0.0). 288s python3-cryptography depends on libssl3 (>= 3.0.0). 288s openssh-server depends on libssl3 (>= 3.0.10). 288s openssh-client depends on libssl3 (>= 3.0.10). 288s mtd-utils depends on libssl3 (>= 3.0.0). 288s mokutil depends on libssl3 (>= 3.0.0). 288s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 288s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 288s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 288s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 288s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 288s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 288s libnvme1 depends on libssl3 (>= 3.0.0). 288s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 288s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 288s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 288s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 288s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 288s kmod depends on libssl3 (>= 3.0.0). 288s dhcpcd-base depends on libssl3 (>= 3.0.0). 288s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 288s 288s (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 ... 74758 files and directories currently installed.) 288s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 288s Selecting previously unselected package libssl3t64:arm64. 288s (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 ... 74747 files and directories currently installed.) 288s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 288s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 288s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 288s Setting up openssl (3.0.13-0ubuntu1) ... 288s Processing triggers for man-db (2.12.0-3) ... 289s Processing triggers for libc-bin (2.39-0ubuntu2) ... 289s Reading package lists... 290s Building dependency tree... 290s Reading state information... 290s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 291s sh: Attempting to set up Debian/Ubuntu apt sources automatically 291s sh: Distribution appears to be Ubuntu 291s Reading package lists... 292s Building dependency tree... 292s Reading state information... 292s eatmydata is already the newest version (131-1). 292s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 292s Reading package lists... 292s Building dependency tree... 292s Reading state information... 293s dbus is already the newest version (1.14.10-4ubuntu1). 293s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 294s rng-tools-debian is already the newest version (2.4). 294s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 294s The following packages will be REMOVED: 294s cloud-init* python3-configobj* python3-debconf* 295s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 295s After this operation, 3252 kB disk space will be freed. 295s (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 ... 74760 files and directories currently installed.) 295s Removing cloud-init (24.1.1-0ubuntu1) ... 295s Removing python3-configobj (5.0.8-3) ... 295s Removing python3-debconf (1.5.86) ... 295s Processing triggers for man-db (2.12.0-3) ... 296s (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 ... 74371 files and directories currently installed.) 296s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 296s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 296s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 296s invoke-rc.d: policy-rc.d denied execution of try-restart. 296s Reading package lists... 297s Building dependency tree... 297s Reading state information... 297s linux-generic is already the newest version (6.8.0-11.11+1). 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 298s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 298s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 298s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 299s Reading package lists... 300s Reading package lists... 300s Building dependency tree... 300s Reading state information... 300s Calculating upgrade... 300s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 301s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 302s autopkgtest [07:21:47]: rebooting testbed after setup commands that affected boot 472s Reading package lists... 472s Building dependency tree... 472s Reading state information... 472s Starting pkgProblemResolver with broken count: 0 472s Starting 2 pkgProblemResolver with broken count: 0 473s Done 473s The following additional packages will be installed: 473s cmake cmake-data cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 473s g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 473s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu googletest libasan8 473s libatomic1 libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcereal-dev 473s libcrypt-dev libgcc-13-dev libgomp1 libgtest-dev libhwasan0 libisl23 libitm1 473s libjsoncpp25 liblsan0 libmpc3 libnsl-dev libpkgconf3 librhash0 libseqan3-dev 473s libsimde-dev libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 libxxhash-dev 473s libyaml-cpp-dev libyaml-cpp0.8 linux-libc-dev pkg-config pkgconf pkgconf-bin 473s rapidjson-dev rpcsvc-proto seqan-raptor seqan-raptor-doc zlib1g-dev 473s Suggested packages: 473s cmake-doc cmake-format elpa-cmake-mode ninja-build cpp-doc gcc-13-locales 473s cpp-13-doc gcc-13-doc gcc-multilib manpages-dev autoconf automake libtool 473s flex bison gdb gcc-doc gdb-aarch64-linux-gnu glibc-doc libstdc++-13-doc 473s rapidjson-doc cwl-runner 473s Recommended packages: 473s bzip2-doc manpages manpages-dev libc-devtools 473s The following NEW packages will be installed: 473s autopkgtest-satdep cmake cmake-data cpp cpp-13 cpp-13-aarch64-linux-gnu 473s cpp-aarch64-linux-gnu g++ g++-13 g++-13-aarch64-linux-gnu 473s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 473s gcc-aarch64-linux-gnu googletest libasan8 libatomic1 libbz2-dev libc-dev-bin 473s libc6-dev libcc1-0 libcereal-dev libcrypt-dev libgcc-13-dev libgomp1 473s libgtest-dev libhwasan0 libisl23 libitm1 libjsoncpp25 liblsan0 libmpc3 473s libnsl-dev libpkgconf3 librhash0 libseqan3-dev libsimde-dev libstdc++-13-dev 473s libtirpc-dev libtsan2 libubsan1 libxxhash-dev libyaml-cpp-dev libyaml-cpp0.8 473s linux-libc-dev pkg-config pkgconf pkgconf-bin rapidjson-dev rpcsvc-proto 473s seqan-raptor seqan-raptor-doc zlib1g-dev 473s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 473s Need to get 79.8 MB/79.8 MB of archives. 473s After this operation, 297 MB of additional disk space will be used. 473s Get:1 /tmp/autopkgtest.fy7WQs/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [780 B] 473s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libjsoncpp25 arm64 1.9.5-6 [76.0 kB] 474s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 librhash0 arm64 1.4.3-3 [125 kB] 474s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 cmake-data all 3.28.3-1 [2155 kB] 474s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 cmake arm64 3.28.3-1 [10.3 MB] 474s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 474s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 474s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 474s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 474s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 474s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 474s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 474s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 474s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 474s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 474s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 474s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 475s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 475s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 475s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 475s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 475s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 475s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 475s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 475s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 475s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 475s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 475s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 475s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] 475s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 475s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 475s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 475s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 475s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 476s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 476s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 476s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 476s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 googletest all 1.14.0-1 [521 kB] 476s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 476s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 rapidjson-dev all 1.1.0+dfsg2-7.1 [96.7 kB] 476s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 libcereal-dev arm64 1.3.2+dfsg-5 [222 kB] 476s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 libgtest-dev arm64 1.14.0-1 [266 kB] 476s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 476s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 476s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 libseqan3-dev all 3.3.0+ds-1 [748 kB] 476s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 libsimde-dev all 0.7.2-6 [261 kB] 476s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash-dev arm64 0.8.2-2 [80.3 kB] 476s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libyaml-cpp0.8 arm64 0.8.0+dfsg-6 [112 kB] 476s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libyaml-cpp-dev arm64 0.8.0+dfsg-6 [189 kB] 476s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 476s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 476s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 476s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 seqan-raptor arm64 3.0.1+ds-5 [648 kB] 476s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 seqan-raptor-doc all 3.0.1+ds-5 [1247 kB] 477s Fetched 79.8 MB in 3s (28.8 MB/s) 477s Selecting previously unselected package libjsoncpp25:arm64. 477s (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 ... 74316 files and directories currently installed.) 477s Preparing to unpack .../00-libjsoncpp25_1.9.5-6_arm64.deb ... 477s Unpacking libjsoncpp25:arm64 (1.9.5-6) ... 477s Selecting previously unselected package librhash0:arm64. 477s Preparing to unpack .../01-librhash0_1.4.3-3_arm64.deb ... 477s Unpacking librhash0:arm64 (1.4.3-3) ... 477s Selecting previously unselected package cmake-data. 477s Preparing to unpack .../02-cmake-data_3.28.3-1_all.deb ... 477s Unpacking cmake-data (3.28.3-1) ... 477s Selecting previously unselected package cmake. 477s Preparing to unpack .../03-cmake_3.28.3-1_arm64.deb ... 477s Unpacking cmake (3.28.3-1) ... 477s Selecting previously unselected package libisl23:arm64. 477s Preparing to unpack .../04-libisl23_0.26-3_arm64.deb ... 477s Unpacking libisl23:arm64 (0.26-3) ... 477s Selecting previously unselected package libmpc3:arm64. 477s Preparing to unpack .../05-libmpc3_1.3.1-1_arm64.deb ... 477s Unpacking libmpc3:arm64 (1.3.1-1) ... 478s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 478s Preparing to unpack .../06-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 478s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 478s Selecting previously unselected package cpp-13. 478s Preparing to unpack .../07-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 478s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 478s Selecting previously unselected package cpp-aarch64-linux-gnu. 478s Preparing to unpack .../08-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 478s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 478s Selecting previously unselected package cpp. 478s Preparing to unpack .../09-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 478s Unpacking cpp (4:13.2.0-7ubuntu1) ... 478s Selecting previously unselected package libcc1-0:arm64. 478s Preparing to unpack .../10-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libgomp1:arm64. 478s Preparing to unpack .../11-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libitm1:arm64. 478s Preparing to unpack .../12-libitm1_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libatomic1:arm64. 478s Preparing to unpack .../13-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libasan8:arm64. 478s Preparing to unpack .../14-libasan8_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package liblsan0:arm64. 478s Preparing to unpack .../15-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libtsan2:arm64. 478s Preparing to unpack .../16-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libubsan1:arm64. 478s Preparing to unpack .../17-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libhwasan0:arm64. 478s Preparing to unpack .../18-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 478s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 478s Selecting previously unselected package libgcc-13-dev:arm64. 478s Preparing to unpack .../19-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 478s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 479s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 479s Preparing to unpack .../20-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 479s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 479s Selecting previously unselected package gcc-13. 479s Preparing to unpack .../21-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 479s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 479s Selecting previously unselected package gcc-aarch64-linux-gnu. 479s Preparing to unpack .../22-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 479s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 479s Selecting previously unselected package gcc. 479s Preparing to unpack .../23-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 479s Unpacking gcc (4:13.2.0-7ubuntu1) ... 479s Selecting previously unselected package libc-dev-bin. 479s Preparing to unpack .../24-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 479s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 479s Selecting previously unselected package linux-libc-dev:arm64. 479s Preparing to unpack .../25-linux-libc-dev_6.8.0-11.11_arm64.deb ... 479s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 479s Selecting previously unselected package libcrypt-dev:arm64. 479s Preparing to unpack .../26-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 479s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 479s Selecting previously unselected package libtirpc-dev:arm64. 479s Preparing to unpack .../27-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ... 479s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 479s Selecting previously unselected package libnsl-dev:arm64. 480s Preparing to unpack .../28-libnsl-dev_1.3.0-3_arm64.deb ... 480s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 480s Selecting previously unselected package rpcsvc-proto. 480s Preparing to unpack .../29-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 480s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 480s Selecting previously unselected package libc6-dev:arm64. 480s Preparing to unpack .../30-libc6-dev_2.39-0ubuntu2_arm64.deb ... 480s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 480s Selecting previously unselected package libstdc++-13-dev:arm64. 480s Preparing to unpack .../31-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 480s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 480s Selecting previously unselected package g++-13-aarch64-linux-gnu. 480s Preparing to unpack .../32-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 480s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 480s Selecting previously unselected package g++-13. 480s Preparing to unpack .../33-g++-13_13.2.0-17ubuntu2_arm64.deb ... 480s Unpacking g++-13 (13.2.0-17ubuntu2) ... 480s Selecting previously unselected package g++-aarch64-linux-gnu. 480s Preparing to unpack .../34-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 480s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 480s Selecting previously unselected package g++. 480s Preparing to unpack .../35-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 480s Unpacking g++ (4:13.2.0-7ubuntu1) ... 480s Selecting previously unselected package googletest. 480s Preparing to unpack .../36-googletest_1.14.0-1_all.deb ... 480s Unpacking googletest (1.14.0-1) ... 480s Selecting previously unselected package libbz2-dev:arm64. 480s Preparing to unpack .../37-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 480s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 480s Selecting previously unselected package rapidjson-dev. 480s Preparing to unpack .../38-rapidjson-dev_1.1.0+dfsg2-7.1_all.deb ... 480s Unpacking rapidjson-dev (1.1.0+dfsg2-7.1) ... 481s Selecting previously unselected package libcereal-dev. 481s Preparing to unpack .../39-libcereal-dev_1.3.2+dfsg-5_arm64.deb ... 481s Unpacking libcereal-dev (1.3.2+dfsg-5) ... 481s Selecting previously unselected package libgtest-dev:arm64. 481s Preparing to unpack .../40-libgtest-dev_1.14.0-1_arm64.deb ... 481s Unpacking libgtest-dev:arm64 (1.14.0-1) ... 481s Selecting previously unselected package libpkgconf3:arm64. 481s Preparing to unpack .../41-libpkgconf3_1.8.1-2_arm64.deb ... 481s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 481s Selecting previously unselected package zlib1g-dev:arm64. 481s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 481s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 481s Selecting previously unselected package libseqan3-dev. 481s Preparing to unpack .../43-libseqan3-dev_3.3.0+ds-1_all.deb ... 481s Unpacking libseqan3-dev (3.3.0+ds-1) ... 481s Selecting previously unselected package libsimde-dev. 481s Preparing to unpack .../44-libsimde-dev_0.7.2-6_all.deb ... 481s Unpacking libsimde-dev (0.7.2-6) ... 481s Selecting previously unselected package libxxhash-dev:arm64. 481s Preparing to unpack .../45-libxxhash-dev_0.8.2-2_arm64.deb ... 481s Unpacking libxxhash-dev:arm64 (0.8.2-2) ... 481s Selecting previously unselected package libyaml-cpp0.8:arm64. 481s Preparing to unpack .../46-libyaml-cpp0.8_0.8.0+dfsg-6_arm64.deb ... 481s Unpacking libyaml-cpp0.8:arm64 (0.8.0+dfsg-6) ... 481s Selecting previously unselected package libyaml-cpp-dev:arm64. 481s Preparing to unpack .../47-libyaml-cpp-dev_0.8.0+dfsg-6_arm64.deb ... 481s Unpacking libyaml-cpp-dev:arm64 (0.8.0+dfsg-6) ... 481s Selecting previously unselected package pkgconf-bin. 481s Preparing to unpack .../48-pkgconf-bin_1.8.1-2_arm64.deb ... 481s Unpacking pkgconf-bin (1.8.1-2) ... 481s Selecting previously unselected package pkgconf:arm64. 481s Preparing to unpack .../49-pkgconf_1.8.1-2_arm64.deb ... 481s Unpacking pkgconf:arm64 (1.8.1-2) ... 481s Selecting previously unselected package pkg-config:arm64. 481s Preparing to unpack .../50-pkg-config_1.8.1-2_arm64.deb ... 481s Unpacking pkg-config:arm64 (1.8.1-2) ... 481s Selecting previously unselected package seqan-raptor. 481s Preparing to unpack .../51-seqan-raptor_3.0.1+ds-5_arm64.deb ... 481s Unpacking seqan-raptor (3.0.1+ds-5) ... 481s Selecting previously unselected package seqan-raptor-doc. 481s Preparing to unpack .../52-seqan-raptor-doc_3.0.1+ds-5_all.deb ... 481s Unpacking seqan-raptor-doc (3.0.1+ds-5) ... 481s Selecting previously unselected package autopkgtest-satdep. 481s Preparing to unpack .../53-2-autopkgtest-satdep.deb ... 481s Unpacking autopkgtest-satdep (0) ... 481s Setting up libsimde-dev (0.7.2-6) ... 481s Setting up libyaml-cpp0.8:arm64 (0.8.0+dfsg-6) ... 481s Setting up libyaml-cpp-dev:arm64 (0.8.0+dfsg-6) ... 481s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 481s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 481s Setting up googletest (1.14.0-1) ... 481s Setting up rapidjson-dev (1.1.0+dfsg2-7.1) ... 481s Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 481s Setting up libpkgconf3:arm64 (1.8.1-2) ... 481s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 481s Setting up libmpc3:arm64 (1.3.1-1) ... 481s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 481s Setting up libjsoncpp25:arm64 (1.9.5-6) ... 481s Setting up pkgconf-bin (1.8.1-2) ... 481s Setting up libxxhash-dev:arm64 (0.8.2-2) ... 481s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 481s Setting up libnsl-dev:arm64 (1.3.0-3) ... 481s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 481s Setting up librhash0:arm64 (1.4.3-3) ... 481s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 481s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 481s Setting up cmake-data (3.28.3-1) ... 481s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 481s Setting up libisl23:arm64 (0.26-3) ... 481s Setting up seqan-raptor (3.0.1+ds-5) ... 481s Setting up libc-dev-bin (2.39-0ubuntu2) ... 481s Setting up seqan-raptor-doc (3.0.1+ds-5) ... 481s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 481s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 481s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 481s Setting up libgtest-dev:arm64 (1.14.0-1) ... 481s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 481s Setting up libcereal-dev (1.3.2+dfsg-5) ... 481s Setting up pkgconf:arm64 (1.8.1-2) ... 481s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 481s Setting up pkg-config:arm64 (1.8.1-2) ... 481s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 481s Setting up cmake (3.28.3-1) ... 481s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 481s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 481s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 481s Setting up cpp-13 (13.2.0-17ubuntu2) ... 481s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 481s Setting up gcc-13 (13.2.0-17ubuntu2) ... 481s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 481s Setting up cpp (4:13.2.0-7ubuntu1) ... 481s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 481s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 481s Setting up g++-13 (13.2.0-17ubuntu2) ... 481s Setting up libseqan3-dev (3.3.0+ds-1) ... 481s Setting up gcc (4:13.2.0-7ubuntu1) ... 481s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 481s Setting up g++ (4:13.2.0-7ubuntu1) ... 481s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 481s Setting up autopkgtest-satdep (0) ... 481s Processing triggers for man-db (2.12.0-3) ... 482s Processing triggers for libc-bin (2.39-0ubuntu2) ... 486s (Reading database ... 82726 files and directories currently installed.) 486s Removing autopkgtest-satdep (0) ... 488s autopkgtest [07:24:53]: test run-unit-test: [----------------------- 488s + pkg=seqan-raptor 488s + export LC_ALL=C.UTF-8 488s + LC_ALL=C.UTF-8 488s + '[' /tmp/autopkgtest.fy7WQs/autopkgtest_tmp = '' ']' 488s + 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.fy7WQs/autopkgtest_tmp 488s + export 'CXXFLAGS=-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/sharg-parser/include/ -I/tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/' 488s + CXXFLAGS='-I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/sharg-parser/include/ -I/tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/' 488s + cd /tmp/autopkgtest.fy7WQs/autopkgtest_tmp 488s + patch -p1 489s patching file test/raptor-test.cmake 489s + cd /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/test/unit 489s + cmake -DRAPTOR_SUBMODULES_DIR=/tmp/autopkgtest.fy7WQs/autopkgtest_tmp/test/unit/../../lib -DRAPTOR_NATIVE_BUILD=OFF . 489s -- The CXX compiler identification is GNU 13.2.0 489s -- The C compiler identification is GNU 13.2.0 489s -- Detecting CXX compiler ABI info 489s -- Detecting CXX compiler ABI info - done 489s -- Check for working CXX compiler: /usr/bin/c++ - skipped 489s -- Detecting CXX compile features 489s -- Detecting CXX compile features - done 489s -- Detecting C compiler ABI info 490s -- Detecting C compiler ABI info - done 490s -- Check for working C compiler: /usr/bin/cc - skipped 490s -- Detecting C compile features 490s -- Detecting C compile features - done 490s -- Finding RAPTOR and checking requirements: 490s -- RAPTOR include dir found: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include 490s -- Detected as running from a repository checkout… 490s -- …adding submodule include: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/chopper/include 490s -- …adding submodule include: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/robin-hood-hashing/src/include 490s -- …adding submodule include: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/sharg-parser/include 490s -- …adding submodule include: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/sharg-parser/test/include 490s -- …adding submodule include: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include 490s -- C++ Standard-20 support: via -std=c++20 490s -- OpenMP Support: via -fopenmp 490s -- SIMD-OpenMP Support: via -fopenmp-simd 491s -- Suppressing GCC 4 warnings: via -Wno-psabi 491s -- Optimize build: disabled 491s -- Link Time Optimization: enabled 491s -- Binary-stripping: via -s 491s -- Thread support: builtin 491s -- Optional dependency: ZLIB-1.3 found 491s -- Optional dependency: BZip2-1.0.8 found 491s -- Optional dependency: libexecinfo found 491s -- Found Raptor: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include 491s -- Finding program ccache 491s -- Finding program ccache - Failed 494s -- You can run `make` to build the application. 494s -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") 494s -- Checking for module 'libxxhash' 494s -- Found libxxhash, version 0.8.2 494s -- Test dependency: Google Test 1.14.0 found. 494s -- Configuring done (5.8s) 495s -- Generating done (0.1s) 495s -- Build files have been written to: /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/test/unit 495s + make 495s [ 1%] Building CXX object src/upgrade/CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o 515s [ 2%] Linking CXX static library ../../lib/libraptor_upgrade.a 515s [ 2%] Built target raptor_upgrade 515s [ 2%] Built target xxhash_project 515s [ 3%] Building CXX object _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o 524s [ 5%] Linking CXX static library ../../../lib/libchopper_layout_lib.a 524s [ 5%] Built target chopper_layout_lib 524s [ 6%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/parse_chopper_pack_line.cpp.o 525s [ 7%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o 549s [ 8%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o 557s [ 10%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o 569s [ 11%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o 584s [ 12%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o 606s [ 13%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o 636s [ 15%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o 661s [ 16%] Linking CXX static library ../../lib/libraptor_argument_parsing.a 662s [ 16%] Built target raptor_argument_parsing 662s [ 17%] Building CXX object src/prepare/CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o 670s [ 18%] Linking CXX static library ../../lib/libraptor_prepare.a 670s [ 18%] Built target raptor_prepare 670s [ 20%] Building CXX object src/build/CMakeFiles/raptor_build.dir/build_ibf.cpp.o 682s [ 21%] Building CXX object src/build/CMakeFiles/raptor_build.dir/max_count_per_partition.cpp.o 690s [ 22%] Building CXX object src/build/CMakeFiles/raptor_build.dir/raptor_build.cpp.o 694s [ 24%] Linking CXX static library ../../lib/libraptor_build.a 694s [ 24%] Built target raptor_build 694s [ 25%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/bin_size_in_bits.cpp.o 696s [ 26%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/chopper_build.cpp.o 697s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 697s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 697s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/chopper_build.cpp:13: 697s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 697s 20 | : public T, public std::iterator { 697s | ^~~~~~~~ 697s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 697s from /usr/include/c++/13/vector:62, 697s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 697s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 697s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 697s 127 | struct _GLIBCXX17_DEPRECATED iterator 697s | ^~~~~~~~ 700s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/create_ibfs_from_chopper_pack.hpp:16, 700s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/chopper_build.cpp:16: 700s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 700s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 700s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 700s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 700s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 700s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 700s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 700s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 700s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 700s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 704s [ 27%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/compute_kmers.cpp.o 712s [ 29%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/construct_ibf.cpp.o 713s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 713s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 713s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/construct_ibf.cpp:13: 713s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 713s 20 | : public T, public std::iterator { 713s | ^~~~~~~~ 713s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 713s from /usr/include/c++/13/vector:62, 713s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 713s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 713s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 713s 127 | struct _GLIBCXX17_DEPRECATED iterator 713s | ^~~~~~~~ 716s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/construct_ibf.hpp:18, 716s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/construct_ibf.cpp:16: 716s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 716s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 716s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 716s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 716s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 716s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 716s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 716s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 716s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 716s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 717s [ 30%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/create_ibfs_from_chopper_pack.cpp.o 718s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 718s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 718s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/create_ibfs_from_chopper_pack.cpp:13: 718s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 718s 20 | : public T, public std::iterator { 718s | ^~~~~~~~ 718s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 718s from /usr/include/c++/13/vector:62, 718s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 718s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 718s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 718s 127 | struct _GLIBCXX17_DEPRECATED iterator 718s | ^~~~~~~~ 721s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/create_ibfs_from_chopper_pack.hpp:16, 721s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/create_ibfs_from_chopper_pack.cpp:15: 721s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 721s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 721s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 721s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 721s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 721s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 721s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 721s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 721s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 721s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 723s [ 31%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/hierarchical_build.cpp.o 724s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 724s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 724s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/hierarchical_build.cpp:13: 724s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 724s 20 | : public T, public std::iterator { 724s | ^~~~~~~~ 724s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 724s from /usr/include/c++/13/vector:62, 724s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 724s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 724s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 724s 127 | struct _GLIBCXX17_DEPRECATED iterator 724s | ^~~~~~~~ 726s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/construct_ibf.hpp:18, 726s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/hierarchical_build.cpp:16: 726s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 726s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 726s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 726s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 726s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 726s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 726s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 726s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 726s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 726s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 728s [ 32%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/insert_into_ibf.cpp.o 738s [ 34%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/loop_over_children.cpp.o 739s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 739s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 739s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/loop_over_children.cpp:13: 739s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 739s 20 | : public T, public std::iterator { 739s | ^~~~~~~~ 739s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 739s from /usr/include/c++/13/vector:62, 739s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 739s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 739s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 739s 127 | struct _GLIBCXX17_DEPRECATED iterator 739s | ^~~~~~~~ 742s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/hierarchical_build.hpp:18, 742s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/loop_over_children.cpp:17: 742s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 742s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 742s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 742s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 742s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 742s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 742s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 742s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 742s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 742s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 744s [ 35%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_header.cpp.o 745s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 745s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 745s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/parse_chopper_pack_header.cpp:17: 745s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 745s 20 | : public T, public std::iterator { 745s | ^~~~~~~~ 745s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 745s from /usr/include/c++/13/algorithm:60, 745s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/parse_chopper_pack_header.cpp:13: 745s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 745s 127 | struct _GLIBCXX17_DEPRECATED iterator 745s | ^~~~~~~~ 746s [ 36%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_line.cpp.o 746s [ 37%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/read_chopper_pack_file.cpp.o 747s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 747s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 747s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/read_chopper_pack_file.cpp:13: 747s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 747s 20 | : public T, public std::iterator { 747s | ^~~~~~~~ 747s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 747s from /usr/include/c++/13/vector:62, 747s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 747s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 747s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 747s 127 | struct _GLIBCXX17_DEPRECATED iterator 747s | ^~~~~~~~ 750s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/read_chopper_pack_file.hpp:17, 750s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/read_chopper_pack_file.cpp:17: 750s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 750s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 750s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 750s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 750s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 750s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 750s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 750s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 750s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 750s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 752s [ 39%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/update_parent_kmers.cpp.o 754s [ 40%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/update_user_bins.cpp.o 755s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30, 755s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:28, 755s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/update_user_bins.cpp:13: 755s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 755s 20 | : public T, public std::iterator { 755s | ^~~~~~~~ 755s In file included from /usr/include/c++/13/bits/stl_algobase.h:65, 755s from /usr/include/c++/13/vector:62, 755s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/core.h:45, 755s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/lib/submodules/lemon/include/lemon/list_graph.h:26: 755s /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 755s 127 | struct _GLIBCXX17_DEPRECATED iterator 755s | ^~~~~~~~ 757s In file included from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/update_user_bins.hpp:15, 757s from /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/src/build/hibf/update_user_bins.cpp:15: 757s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 757s 27 | alignas(std::hardware_destructive_interference_size) std::atomic ibf_number{}; 757s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 757s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags 757s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define 757s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 256 bytes 757s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=256’, or disable this warning with ‘-Wno-interference-size’ 757s /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size] 757s 28 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; 757s | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 758s [ 41%] Linking CXX static library ../../../lib/libraptor_build_hibf.a 758s [ 41%] Built target raptor_build_hibf 758s [ 43%] Building CXX object src/layout/CMakeFiles/raptor_layout.dir/raptor_layout.cpp.o 783s [ 44%] Linking CXX static library ../../lib/libraptor_layout.a 783s [ 44%] Built target raptor_layout 783s [ 45%] Building CXX object src/search/CMakeFiles/raptor_search.dir/raptor_search.cpp.o 785s [ 46%] Building CXX object src/search/CMakeFiles/raptor_search.dir/search_hibf.cpp.o 799s [ 48%] Building CXX object src/search/CMakeFiles/raptor_search.dir/search_ibf.cpp.o 812s [ 49%] Building CXX object src/search/CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o 826s [ 50%] Linking CXX static library ../../lib/libraptor_search.a 826s [ 50%] Built target raptor_search 826s [ 51%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/multiple_error_model.cpp.o 827s [ 53%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/one_error_model.cpp.o 827s [ 54%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/one_indirect_error_model.cpp.o 830s [ 55%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/pascal_row.cpp.o 830s [ 56%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/precompute_correction.cpp.o 832s [ 58%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/precompute_threshold.cpp.o 834s [ 59%] Linking CXX static library ../../lib/libraptor_threshold.a 834s [ 59%] Built target raptor_threshold 834s [ 60%] Building CXX object src/CMakeFiles/raptor.dir/raptor.cpp.o 852s [ 62%] Linking CXX executable ../bin/raptor 870s [ 62%] Built target raptor 870s [ 63%] Building CXX object _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/chopper.cpp.o 920s [ 64%] Linking CXX executable ../../../bin/chopper 920s [ 64%] Built target chopper 920s [ 65%] Building CXX object api/CMakeFiles/issue_142.dir/issue_142.cpp.o 922s [ 67%] Linking CXX executable issue_142 923s [ 67%] Built target issue_142 923s [ 68%] Building CXX object api/CMakeFiles/memory_usage.dir/memory_usage.cpp.o 925s [ 69%] Linking CXX executable memory_usage 926s [ 69%] Built target memory_usage 926s [ 70%] Building CXX object api/CMakeFiles/validate_shape.dir/validate_shape.cpp.o 947s [ 72%] Linking CXX executable validate_shape 953s [ 72%] Built target validate_shape 953s [ 73%] Building CXX object cli/argument_parsing/CMakeFiles/options_test.dir/options_test.cpp.o 959s [ 74%] Linking CXX executable options_test 961s [ 74%] Built target options_test 961s [ 75%] Building CXX object cli/build/CMakeFiles/build_hibf_chopper_test.dir/build_hibf_chopper_test.cpp.o 967s [ 77%] Linking CXX executable build_hibf_chopper_test 969s [ 77%] Built target build_hibf_chopper_test 969s [ 78%] Building CXX object cli/build/CMakeFiles/build_hibf_test.dir/build_hibf_test.cpp.o 978s [ 79%] Linking CXX executable build_hibf_test 981s [ 79%] Built target build_hibf_test 981s [ 81%] Building CXX object cli/build/CMakeFiles/build_ibf_compressed_test.dir/build_ibf_compressed_test.cpp.o 990s [ 82%] Linking CXX executable build_ibf_compressed_test 993s [ 82%] Built target build_ibf_compressed_test 993s [ 83%] Building CXX object cli/build/CMakeFiles/build_ibf_partitioned_test.dir/build_ibf_partitioned_test.cpp.o 1000s [ 84%] Linking CXX executable build_ibf_partitioned_test 1002s [ 84%] Built target build_ibf_partitioned_test 1002s [ 86%] Building CXX object cli/build/CMakeFiles/build_ibf_test.dir/build_ibf_test.cpp.o 1010s [ 87%] Linking CXX executable build_ibf_test 1012s [ 87%] Built target build_ibf_test 1012s [ 88%] Building CXX object cli/search/CMakeFiles/search_hibf_test.dir/search_hibf_test.cpp.o 1018s [ 89%] Linking CXX executable search_hibf_test 1021s [ 89%] Built target search_hibf_test 1021s [ 91%] Building CXX object cli/search/CMakeFiles/search_hibf_preprocessing_test.dir/search_hibf_preprocessing_test.cpp.o 1029s [ 92%] Linking CXX executable search_hibf_preprocessing_test 1031s [ 92%] Built target search_hibf_preprocessing_test 1031s [ 93%] Building CXX object cli/search/CMakeFiles/search_ibf_preprocessing_test.dir/search_ibf_preprocessing_test.cpp.o 1040s [ 94%] Linking CXX executable search_ibf_preprocessing_test 1043s [ 94%] Built target search_ibf_preprocessing_test 1043s [ 96%] Building CXX object cli/search/CMakeFiles/search_ibf_test.dir/search_ibf_test.cpp.o 1049s [ 97%] Linking CXX executable search_ibf_test 1051s [ 97%] Built target search_ibf_test 1051s [ 98%] Building CXX object cli/upgrade/CMakeFiles/upgrade_test.dir/upgrade_test.cpp.o 1059s [100%] Linking CXX executable upgrade_test 1061s [100%] Built target upgrade_test 1061s + find . -name raptor -delete 1061s + ctest . 1061s Test project /tmp/autopkgtest.fy7WQs/autopkgtest_tmp/test/unit 1061s Start 1: api/issue_142 1061s 1/14 Test #1: api/issue_142 ............................... Passed 0.17 sec 1061s Start 2: api/memory_usage 1061s 2/14 Test #2: api/memory_usage ............................ Passed 0.09 sec 1061s Start 3: api/validate_shape 1061s 3/14 Test #3: api/validate_shape .......................... Passed 0.18 sec 1061s Start 4: cli/argument_parsing/options_test 1062s 4/14 Test #4: cli/argument_parsing/options_test ........... Passed 0.49 sec 1062s Start 5: cli/build/build_hibf_chopper_test 1062s 5/14 Test #5: cli/build/build_hibf_chopper_test ........... Passed 0.17 sec 1062s Start 6: cli/build/build_hibf_test 1063s 6/14 Test #6: cli/build/build_hibf_test ................... Passed 0.54 sec 1063s Start 7: cli/build/build_ibf_compressed_test 1063s 7/14 Test #7: cli/build/build_ibf_compressed_test ......... Passed 0.76 sec 1063s Start 8: cli/build/build_ibf_partitioned_test 1065s 8/14 Test #8: cli/build/build_ibf_partitioned_test ........ Passed 1.62 sec 1065s Start 9: cli/build/build_ibf_test 1066s 9/14 Test #9: cli/build/build_ibf_test .................... Passed 0.56 sec 1066s Start 10: cli/search/search_hibf_test 1066s 10/14 Test #10: cli/search/search_hibf_test ................. Passed 0.54 sec 1066s Start 11: cli/search/search_hibf_preprocessing_test 1068s 11/14 Test #11: cli/search/search_hibf_preprocessing_test ... Passed 1.73 sec 1068s Start 12: cli/search/search_ibf_preprocessing_test 1070s 12/14 Test #12: cli/search/search_ibf_preprocessing_test .... Passed 1.93 sec 1070s Start 13: cli/search/search_ibf_test 1071s 13/14 Test #13: cli/search/search_ibf_test .................. Passed 0.80 sec 1071s Start 14: cli/upgrade/upgrade_test 1072s 14/14 Test #14: cli/upgrade/upgrade_test .................... Passed 0.85 sec 1072s 1072s 100% tests passed, 0 tests failed out of 14 1072s 1072s Total Test time (real) = 10.45 sec 1072s + find . -name raptor 1073s autopkgtest [07:34:38]: test run-unit-test: -----------------------] 1073s autopkgtest [07:34:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1073s run-unit-test PASS 1074s autopkgtest [07:34:39]: @@@@@@@@@@@@@@@@@@@@ summary 1074s cwl PASS 1074s run-unit-test PASS 1085s Creating nova instance adt-noble-arm64-seqan-raptor-20240317-071645-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240317.img (UUID e1706a76-a641-4f6f-90fe-65f00771b7d2)... 1085s Creating nova instance adt-noble-arm64-seqan-raptor-20240317-071645-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240317.img (UUID e1706a76-a641-4f6f-90fe-65f00771b7d2)...