0s autopkgtest [18:01:27]: starting date and time: 2024-03-24 18:01:27+0000 0s autopkgtest [18:01:27]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:01:27]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a8p7c781/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade srst2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-5.secgroup --name adt-noble-arm64-srst2-20240324-174620-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://us.ports.ubuntu.com/ubuntu-ports/ 93s autopkgtest [18:03:00]: testbed dpkg architecture: arm64 93s autopkgtest [18:03:00]: testbed apt version: 2.7.12 93s autopkgtest [18:03:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 94s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 94s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 94s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 94s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 94s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 94s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 94s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 94s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 94s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 95s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 97s Fetched 9851 kB in 2s (5752 kB/s) 97s Reading package lists... 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 102s The following packages will be REMOVED: 102s libssl3 102s The following NEW packages will be installed: 102s libssl3t64 102s The following packages have been kept back: 102s curl 102s The following packages will be upgraded: 102s openssl 102s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 102s Need to get 2777 kB of archives. 102s After this operation, 139 kB of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 103s Fetched 2777 kB in 1s (4073 kB/s) 103s (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 ... 75911 files and directories currently installed.) 103s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 103s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 103s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 103s wget depends on libssl3 (>= 3.0.0). 103s u-boot-tools depends on libssl3 (>= 3.0.0). 103s tnftp depends on libssl3 (>= 3.0.0). 103s tcpdump depends on libssl3 (>= 3.0.0). 103s systemd-resolved depends on libssl3 (>= 3.0.0). 103s systemd depends on libssl3 (>= 3.0.0). 103s sudo depends on libssl3 (>= 3.0.0). 103s sbsigntool depends on libssl3 (>= 3.0.0). 103s rsync depends on libssl3 (>= 3.0.0). 103s python3-cryptography depends on libssl3 (>= 3.0.0). 103s openssh-server depends on libssl3 (>= 3.0.10). 103s openssh-client depends on libssl3 (>= 3.0.10). 103s mtd-utils depends on libssl3 (>= 3.0.0). 103s mokutil depends on libssl3 (>= 3.0.0). 103s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 103s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 103s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 103s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 103s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 103s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 103s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 103s libnvme1 depends on libssl3 (>= 3.0.0). 103s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 103s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 103s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 103s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 103s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 103s kmod depends on libssl3 (>= 3.0.0). 103s dhcpcd-base depends on libssl3 (>= 3.0.0). 103s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 103s 103s (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 ... 75911 files and directories currently installed.) 103s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 103s Selecting previously unselected package libssl3t64:arm64. 103s (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 ... 75900 files and directories currently installed.) 103s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 103s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 103s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 103s Setting up openssl (3.0.13-0ubuntu2) ... 103s Processing triggers for man-db (2.12.0-3) ... 104s Processing triggers for libc-bin (2.39-0ubuntu6) ... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 105s sh: Attempting to set up Debian/Ubuntu apt sources automatically 105s sh: Distribution appears to be Ubuntu 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s eatmydata is already the newest version (131-1). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s dbus is already the newest version (1.14.10-4ubuntu1). 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 rng-tools-debian is already the newest version (2.4). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s The following packages will be REMOVED: 109s cloud-init* python3-configobj* python3-debconf* 109s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 109s After this operation, 3256 kB disk space will be freed. 109s (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 ... 75913 files and directories currently installed.) 109s Removing cloud-init (24.1.2-0ubuntu1) ... 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 ... 75524 files and directories currently installed.) 110s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 110s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 110s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 110s invoke-rc.d: policy-rc.d denied execution of try-restart. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s linux-generic is already the newest version (6.8.0-11.11+1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 112s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 113s Reading package lists... 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [18:03:22]: rebooting testbed after setup commands that affected boot 263s autopkgtest [18:05:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 265s autopkgtest [18:05:52]: @@@@@@@@@@@@@@@@@@@@ apt-source srst2 267s Get:1 http://ftpmaster.internal/ubuntu noble/universe srst2 0.2.0-11 (dsc) [2144 B] 267s Get:2 http://ftpmaster.internal/ubuntu noble/universe srst2 0.2.0-11 (tar) [1380 kB] 267s Get:3 http://ftpmaster.internal/ubuntu noble/universe srst2 0.2.0-11 (diff) [17.9 kB] 267s gpgv: Signature made Thu Jan 18 20:18:47 2024 UTC 267s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 267s gpgv: issuer "tille@debian.org" 267s gpgv: Can't check signature: No public key 267s dpkg-source: warning: cannot verify inline signature for ./srst2_0.2.0-11.dsc: no acceptable signature found 267s autopkgtest [18:05:54]: testing package srst2 version 0.2.0-11 268s autopkgtest [18:05:55]: build not needed 269s autopkgtest [18:05:56]: test run-unit-test: preparing testbed 274s Reading package lists... 274s Building dependency tree... 274s Reading state information... 274s Starting pkgProblemResolver with broken count: 0 274s Starting 2 pkgProblemResolver with broken count: 0 274s Done 275s The following additional packages will be installed: 275s bowtie2 cd-hit fontconfig-config fonts-dejavu-core fonts-dejavu-extra 275s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 275s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 275s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 275s libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 275s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 275s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-biopython 275s python3-cairo python3-decorator python3-freetype python3-mock python3-numpy 275s python3-pil python3-reportlab python3-rlpycairo python3-scipy samtools 275s sgml-base srst2 w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 275s xml-core 275s Suggested packages: 275s bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 275s liblcms2-utils python3-tk bwa clustalo clustalw dialign dssp emboss fasttree 275s mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib 275s python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise 275s python-mock-doc gcc gfortran python3-dev python3-pytest python-pil-doc 275s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 275s rl-renderpm python-scipy-doc cwltool sgml-base-doc debhelper 275s Recommended packages: 275s python-biopython-doc ncbi-blast+ python3-olefile g++ | c++-compiler 275s python3-rpy2 275s The following NEW packages will be installed: 275s autopkgtest-satdep bowtie2 cd-hit fontconfig-config fonts-dejavu-core 275s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 275s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 275s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 275s libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 275s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 275s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-biopython 275s python3-cairo python3-decorator python3-freetype python3-mock python3-numpy 275s python3-pil python3-reportlab python3-rlpycairo python3-scipy samtools 275s sgml-base srst2 w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 275s xml-core 275s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 275s Need to get 50.2 MB/50.2 MB of archives. 275s After this operation, 200 MB of additional disk space will be used. 275s Get:1 /tmp/autopkgtest.qlpJ1E/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 275s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 275s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 275s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 cd-hit arm64 4.8.1-4 [522 kB] 275s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 275s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 276s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 276s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 276s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 276s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 276s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 276s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 276s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 276s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 276s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 276s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 276s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 276s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 276s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 276s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 276s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 276s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 276s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 276s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 276s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 276s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 276s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 276s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 276s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 276s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 276s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 276s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 276s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 276s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 276s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 276s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 276s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 276s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 276s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 276s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 276s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 277s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 277s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 277s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 277s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 277s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 277s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 277s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 277s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 277s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 277s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 277s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 277s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie2 arm64 2.5.2-1 [1261 kB] 277s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 277s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 srst2 arm64 0.2.0-11 [61.8 kB] 277s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mock all 5.1.0-1 [64.1 kB] 278s Fetched 50.2 MB in 2s (22.0 MB/s) 278s Selecting previously unselected package sgml-base. 278s (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 ... 75469 files and directories currently installed.) 278s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 278s Unpacking sgml-base (1.31) ... 278s Selecting previously unselected package libgomp1:arm64. 278s Preparing to unpack .../01-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 278s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 278s Selecting previously unselected package cd-hit. 278s Preparing to unpack .../02-cd-hit_4.8.1-4_arm64.deb ... 278s Unpacking cd-hit (4.8.1-4) ... 278s Selecting previously unselected package fonts-dejavu-mono. 278s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 278s Unpacking fonts-dejavu-mono (2.37-8) ... 278s Selecting previously unselected package fonts-dejavu-core. 278s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 278s Unpacking fonts-dejavu-core (2.37-8) ... 278s Selecting previously unselected package libfontenc1:arm64. 278s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1_arm64.deb ... 278s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 278s Selecting previously unselected package x11-common. 278s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu2_all.deb ... 278s Unpacking x11-common (1:7.7+23ubuntu2) ... 278s Selecting previously unselected package xfonts-encodings. 278s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 278s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 278s Selecting previously unselected package xfonts-utils. 278s Preparing to unpack .../08-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 278s Unpacking xfonts-utils (1:7.7+6build2) ... 278s Selecting previously unselected package fonts-urw-base35. 278s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 278s Unpacking fonts-urw-base35 (20200910-8) ... 278s Selecting previously unselected package fontconfig-config. 278s Preparing to unpack .../10-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 278s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 278s Selecting previously unselected package fonts-dejavu-extra. 278s Preparing to unpack .../11-fonts-dejavu-extra_2.37-8_all.deb ... 278s Unpacking fonts-dejavu-extra (2.37-8) ... 278s Selecting previously unselected package libblas3:arm64. 278s Preparing to unpack .../12-libblas3_3.12.0-3_arm64.deb ... 278s Unpacking libblas3:arm64 (3.12.0-3) ... 278s Selecting previously unselected package libfontconfig1:arm64. 278s Preparing to unpack .../13-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 278s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 278s Selecting previously unselected package libpixman-1-0:arm64. 278s Preparing to unpack .../14-libpixman-1-0_0.42.2-1_arm64.deb ... 278s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 278s Selecting previously unselected package libxcb-render0:arm64. 278s Preparing to unpack .../15-libxcb-render0_1.15-1_arm64.deb ... 278s Unpacking libxcb-render0:arm64 (1.15-1) ... 278s Selecting previously unselected package libxcb-shm0:arm64. 278s Preparing to unpack .../16-libxcb-shm0_1.15-1_arm64.deb ... 278s Unpacking libxcb-shm0:arm64 (1.15-1) ... 278s Selecting previously unselected package libxrender1:arm64. 278s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 278s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 278s Selecting previously unselected package libcairo2:arm64. 278s Preparing to unpack .../18-libcairo2_1.18.0-1_arm64.deb ... 278s Unpacking libcairo2:arm64 (1.18.0-1) ... 278s Selecting previously unselected package libdeflate0:arm64. 278s Preparing to unpack .../19-libdeflate0_1.19-1_arm64.deb ... 278s Unpacking libdeflate0:arm64 (1.19-1) ... 279s Selecting previously unselected package libgfortran5:arm64. 279s Preparing to unpack .../20-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 279s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 279s Selecting previously unselected package libgraphite2-3:arm64. 279s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_arm64.deb ... 279s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 279s Selecting previously unselected package libharfbuzz0b:arm64. 279s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_arm64.deb ... 279s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 279s Selecting previously unselected package libhtscodecs2:arm64. 279s Preparing to unpack .../23-libhtscodecs2_1.6.0-1_arm64.deb ... 279s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 279s Selecting previously unselected package libhts3:arm64. 279s Preparing to unpack .../24-libhts3_1.18+ds-1_arm64.deb ... 279s Unpacking libhts3:arm64 (1.18+ds-1) ... 279s Selecting previously unselected package libimagequant0:arm64. 279s Preparing to unpack .../25-libimagequant0_2.18.0-1_arm64.deb ... 279s Unpacking libimagequant0:arm64 (2.18.0-1) ... 279s Selecting previously unselected package libjpeg-turbo8:arm64. 279s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 279s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 279s Selecting previously unselected package libjpeg8:arm64. 279s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_arm64.deb ... 279s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 279s Selecting previously unselected package liblapack3:arm64. 279s Preparing to unpack .../28-liblapack3_3.12.0-3_arm64.deb ... 279s Unpacking liblapack3:arm64 (3.12.0-3) ... 279s Selecting previously unselected package liblbfgsb0:arm64. 279s Preparing to unpack .../29-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 279s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 279s Selecting previously unselected package liblcms2-2:arm64. 279s Preparing to unpack .../30-liblcms2-2_2.14-2_arm64.deb ... 279s Unpacking liblcms2-2:arm64 (2.14-2) ... 279s Selecting previously unselected package liblerc4:arm64. 279s Preparing to unpack .../31-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 279s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 279s Selecting previously unselected package libraqm0:arm64. 279s Preparing to unpack .../32-libraqm0_0.10.1-1_arm64.deb ... 279s Unpacking libraqm0:arm64 (0.10.1-1) ... 279s Selecting previously unselected package libsharpyuv0:arm64. 279s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_arm64.deb ... 279s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 279s Selecting previously unselected package libjbig0:arm64. 279s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 279s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 279s Selecting previously unselected package libwebp7:arm64. 279s Preparing to unpack .../35-libwebp7_1.3.2-0.4_arm64.deb ... 279s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 279s Selecting previously unselected package libtiff6:arm64. 279s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 279s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 279s Selecting previously unselected package libwebpdemux2:arm64. 279s Preparing to unpack .../37-libwebpdemux2_1.3.2-0.4_arm64.deb ... 279s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 279s Selecting previously unselected package libwebpmux3:arm64. 279s Preparing to unpack .../38-libwebpmux3_1.3.2-0.4_arm64.deb ... 279s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 279s Selecting previously unselected package python3-numpy. 279s Preparing to unpack .../39-python3-numpy_1%3a1.24.2-2_arm64.deb ... 279s Unpacking python3-numpy (1:1.24.2-2) ... 279s Selecting previously unselected package libopenjp2-7:arm64. 279s Preparing to unpack .../40-libopenjp2-7_2.5.0-2_arm64.deb ... 279s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 279s Selecting previously unselected package python3-pil:arm64. 279s Preparing to unpack .../41-python3-pil_10.2.0-1_arm64.deb ... 279s Unpacking python3-pil:arm64 (10.2.0-1) ... 279s Selecting previously unselected package python3-cairo. 279s Preparing to unpack .../42-python3-cairo_1.25.1-2_arm64.deb ... 279s Unpacking python3-cairo (1.25.1-2) ... 279s Selecting previously unselected package python3-freetype. 279s Preparing to unpack .../43-python3-freetype_2.4.0-1_all.deb ... 279s Unpacking python3-freetype (2.4.0-1) ... 279s Selecting previously unselected package python3-rlpycairo. 279s Preparing to unpack .../44-python3-rlpycairo_0.3.0-3_all.deb ... 279s Unpacking python3-rlpycairo (0.3.0-3) ... 279s Selecting previously unselected package python3-reportlab. 279s Preparing to unpack .../45-python3-reportlab_4.1.0-1_all.deb ... 279s Unpacking python3-reportlab (4.1.0-1) ... 279s Selecting previously unselected package xml-core. 279s Preparing to unpack .../46-xml-core_0.19_all.deb ... 279s Unpacking xml-core (0.19) ... 279s Selecting previously unselected package w3c-sgml-lib. 279s Preparing to unpack .../47-w3c-sgml-lib_1.3-3_all.deb ... 279s Unpacking w3c-sgml-lib (1.3-3) ... 279s Selecting previously unselected package python3-biopython. 280s Preparing to unpack .../48-python3-biopython_1.81+dfsg-3_arm64.deb ... 280s Unpacking python3-biopython (1.81+dfsg-3) ... 280s Selecting previously unselected package python3-decorator. 280s Preparing to unpack .../49-python3-decorator_5.1.1-5_all.deb ... 280s Unpacking python3-decorator (5.1.1-5) ... 280s Selecting previously unselected package samtools. 280s Preparing to unpack .../50-samtools_1.19.2-1_arm64.deb ... 280s Unpacking samtools (1.19.2-1) ... 280s Selecting previously unselected package bowtie2. 280s Preparing to unpack .../51-bowtie2_2.5.2-1_arm64.deb ... 280s Unpacking bowtie2 (2.5.2-1) ... 280s Selecting previously unselected package python3-scipy. 280s Preparing to unpack .../52-python3-scipy_1.11.4-6_arm64.deb ... 280s Unpacking python3-scipy (1.11.4-6) ... 280s Selecting previously unselected package srst2. 280s Preparing to unpack .../53-srst2_0.2.0-11_arm64.deb ... 280s Unpacking srst2 (0.2.0-11) ... 280s Selecting previously unselected package python3-mock. 280s Preparing to unpack .../54-python3-mock_5.1.0-1_all.deb ... 280s Unpacking python3-mock (5.1.0-1) ... 280s Selecting previously unselected package autopkgtest-satdep. 280s Preparing to unpack .../55-1-autopkgtest-satdep.deb ... 280s Unpacking autopkgtest-satdep (0) ... 281s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 281s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 281s Setting up liblcms2-2:arm64 (2.14-2) ... 281s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 281s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 281s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 281s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 281s Setting up libxcb-render0:arm64 (1.15-1) ... 281s Setting up x11-common (1:7.7+23ubuntu2) ... 281s Setting up libdeflate0:arm64 (1.19-1) ... 281s Setting up libxcb-shm0:arm64 (1.15-1) ... 281s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 281s Setting up python3-freetype (2.4.0-1) ... 281s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 281s Setting up bowtie2 (2.5.2-1) ... 281s Setting up python3-mock (5.1.0-1) ... 281s Setting up python3-decorator (5.1.1-5) ... 281s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 281s Setting up libblas3:arm64 (3.12.0-3) ... 281s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 281s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 281s Setting up libimagequant0:arm64 (2.18.0-1) ... 281s Setting up fonts-dejavu-mono (2.37-8) ... 281s Setting up fonts-dejavu-core (2.37-8) ... 281s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 281s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 281s Setting up libwebp7:arm64 (1.3.2-0.4) ... 281s Setting up fonts-dejavu-extra (2.37-8) ... 281s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 281s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 281s Setting up sgml-base (1.31) ... 281s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 281s Setting up cd-hit (4.8.1-4) ... 281s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 281s Setting up liblapack3:arm64 (3.12.0-3) ... 281s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 281s Setting up libhts3:arm64 (1.18+ds-1) ... 281s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 282s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 282s Setting up xfonts-utils (1:7.7+6build2) ... 282s Setting up samtools (1.19.2-1) ... 282s Setting up libraqm0:arm64 (0.10.1-1) ... 282s Setting up python3-numpy (1:1.24.2-2) ... 283s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 283s Setting up xml-core (0.19) ... 283s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 283s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 283s Setting up python3-scipy (1.11.4-6) ... 286s Setting up fonts-urw-base35 (20200910-8) ... 286s Setting up libcairo2:arm64 (1.18.0-1) ... 286s Setting up python3-pil:arm64 (10.2.0-1) ... 287s Setting up python3-cairo (1.25.1-2) ... 287s Setting up python3-rlpycairo (0.3.0-3) ... 287s Setting up python3-reportlab (4.1.0-1) ... 287s Processing triggers for libc-bin (2.39-0ubuntu6) ... 288s Processing triggers for man-db (2.12.0-3) ... 288s Processing triggers for sgml-base (1.31) ... 288s Setting up w3c-sgml-lib (1.3-3) ... 311s Setting up python3-biopython (1.81+dfsg-3) ... 312s Setting up srst2 (0.2.0-11) ... 312s /usr/share/srst2/database_clustering/VFDB_cdhit_to_csv.py:53: SyntaxWarning: invalid escape sequence '\(' 312s in_brackets = re.findall('\((.*?)\)', full_name) 312s /usr/share/srst2/database_clustering/align_plot_tree_min3.py:28: SyntaxWarning: invalid escape sequence '\.' 312s r(''' 312s /usr/share/srst2/getmlst.py:181: SyntaxWarning: invalid escape sequence '\d' 312s m = re.match('>(.*)([_-])(\d*)',head).groups() 312s /usr/share/srst2/srst2.py:90: SyntaxWarning: invalid escape sequence '\-' 312s parser.add_argument('--other', type=str, help='Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".', required=False) 312s /usr/share/srst2/srst2.py:99: SyntaxWarning: invalid escape sequence '\-' 312s parser.add_argument('--samtools_args', type=str, help='Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").', required=False) 312s /usr/share/srst2/srst2.py:241: SyntaxWarning: invalid escape sequence '\d' 312s m = re.search("NM:i:(\d+)\s",line) 312s Setting up autopkgtest-satdep (0) ... 316s (Reading database ... 80481 files and directories currently installed.) 316s Removing autopkgtest-satdep (0) ... 317s autopkgtest [18:06:43]: test run-unit-test: [----------------------- 317s ........... 317s ---------------------------------------------------------------------- 317s Ran 11 tests in 0.018s 317s 317s OK 317s ................. 317s ---------------------------------------------------------------------- 317s Ran 17 tests in 0.045s 317s 317s OK 318s autopkgtest [18:06:45]: test run-unit-test: -----------------------] 318s autopkgtest [18:06:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 318s run-unit-test PASS 319s autopkgtest [18:06:46]: @@@@@@@@@@@@@@@@@@@@ summary 319s run-unit-test PASS 331s Creating nova instance adt-noble-arm64-srst2-20240324-174620-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...