0s autopkgtest [18:38:14]: starting date and time: 2025-03-15 18:38:14+0000 0s autopkgtest [18:38:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:38:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j6vdh153/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade reapr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-19.secgroup --name adt-plucky-s390x-reapr-20250315-183814-juju-7f2275-prod-proposed-migration-environment-2-ce5fe76d-b24c-4f48-8342-2141e64d8ac9 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 154s autopkgtest [18:40:48]: testbed dpkg architecture: s390x 154s autopkgtest [18:40:48]: testbed apt version: 2.9.33 154s autopkgtest [18:40:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s autopkgtest [18:40:49]: testbed release detected to be: None 155s autopkgtest [18:40:49]: updating testbed package index (apt update) 156s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 156s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 156s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 156s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 156s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 157s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 157s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 157s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 157s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 157s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 157s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 157s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 157s Fetched 1073 kB in 2s (608 kB/s) 158s Reading package lists... 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s Calculating upgrade... 159s Calculating upgrade... 159s The following packages were automatically installed and are no longer required: 159s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 159s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 159s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 159s linux-tools-6.11.0-8-generic 159s Use 'sudo apt autoremove' to remove them. 159s The following packages will be upgraded: 159s pinentry-curses python3-jinja2 strace 159s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 652 kB of archives. 159s After this operation, 27.6 kB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 160s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 160s Fetched 652 kB in 1s (604 kB/s) 160s (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 ... 81428 files and directories currently installed.) 160s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 160s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 160s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 160s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 160s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 160s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 161s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 161s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 161s Setting up strace (6.13+ds-1ubuntu1) ... 161s Processing triggers for man-db (2.13.0-1) ... 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Solving dependencies... 162s The following packages will be REMOVED: 162s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 162s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 162s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 162s linux-tools-6.11.0-8-generic* 162s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 162s After this operation, 167 MB disk space will be freed. 162s (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 ... 81428 files and directories currently installed.) 162s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 162s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 162s Removing libpython3.12t64:s390x (3.12.9-1) ... 162s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 162s Removing libnsl2:s390x (1.3.0-3build3) ... 162s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 162s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 162s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 163s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 163s Processing triggers for libc-bin (2.41-1ubuntu1) ... 163s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56328 files and directories currently installed.) 163s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 163s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 163s autopkgtest [18:40:57]: upgrading testbed (apt dist-upgrade and autopurge) 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 164s Entering ResolveByKeep 164s 164s Calculating upgrade... 164s The following packages will be upgraded: 164s libc-bin libc-dev-bin libc6 libc6-dev locales 164s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 9512 kB of archives. 164s After this operation, 8192 B of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 166s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 166s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 170s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 170s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 175s Preconfiguring packages ... 175s Fetched 9512 kB in 11s (884 kB/s) 175s (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 ... 56326 files and directories currently installed.) 175s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 175s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 175s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 175s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 175s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 175s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 175s Setting up libc6:s390x (2.41-1ubuntu2) ... 175s (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 ... 56326 files and directories currently installed.) 175s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 175s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 175s Setting up libc-bin (2.41-1ubuntu2) ... 175s (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 ... 56326 files and directories currently installed.) 175s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 175s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 176s Setting up locales (2.41-1ubuntu2) ... 176s Generating locales (this might take a while)... 177s en_US.UTF-8... done 177s Generation complete. 177s Setting up libc-dev-bin (2.41-1ubuntu2) ... 177s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 177s Processing triggers for man-db (2.13.0-1) ... 177s Processing triggers for systemd (257.3-1ubuntu3) ... 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 179s Solving dependencies... 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s autopkgtest [18:41:13]: rebooting testbed after setup commands that affected boot 198s autopkgtest [18:41:32]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 200s autopkgtest [18:41:34]: @@@@@@@@@@@@@@@@@@@@ apt-source reapr 202s Get:1 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (dsc) [2160 B] 202s Get:2 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (tar) [74.6 kB] 202s Get:3 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (diff) [320 kB] 202s gpgv: Signature made Sat Dec 21 22:15:37 2024 UTC 202s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 202s gpgv: issuer "tille@debian.org" 202s gpgv: Can't check signature: No public key 202s dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-7.dsc: no acceptable signature found 202s autopkgtest [18:41:36]: testing package reapr version 1.0.18+dfsg-7 203s autopkgtest [18:41:37]: build not needed 203s autopkgtest [18:41:37]: test test-example: preparing testbed 204s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Starting pkgProblemResolver with broken count: 0 204s Starting 2 pkgProblemResolver with broken count: 0 204s Done 204s The following NEW packages will be installed: 204s bamtools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 204s libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 libdeflate0 204s libfile-copy-link-perl libfontconfig1 libfreetype6 libgfortran5 libgomp1 204s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libjbig0 204s libjpeg-turbo8 libjpeg8 libjsoncpp26 liblapack3 libpango-1.0-0 204s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 204s libsharpyuv0 libsm6 libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6 204s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 204s libxt6t64 r-base r-base-core r-cran-boot r-cran-class r-cran-cluster 204s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass 204s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart 204s r-cran-spatial r-cran-survival r-recommended reapr samtools smalt snpomatic 204s tabix unzip x11-common xdg-utils zip 204s 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. 204s Need to get 66.2 MB of archives. 204s After this operation, 121 MB of additional disk space will be used. 204s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-6build1 [142 kB] 205s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libjsoncpp26 s390x 1.9.6-3 [80.8 kB] 205s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x bamtools s390x 2.5.2+dfsg-6build1 [174 kB] 205s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 205s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 206s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 206s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 207s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 207s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 207s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libbambamc0 s390x 0.0.50-6build1 [45.3 kB] 207s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 207s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 207s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 207s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 207s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 207s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 208s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 208s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 208s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x libfile-copy-link-perl all 0.200-1 [12.8 kB] 208s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 209s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 209s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 209s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 209s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 210s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 210s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 210s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 210s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 210s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 210s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 214s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 214s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 214s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 214s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 214s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 214s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 214s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 214s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 214s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 214s Get:40 http://ftpmaster.internal/ubuntu plucky/universe s390x libtabixpp0t64 s390x 1.1.2-2.1build1 [10.6 kB] 214s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 215s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 215s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 215s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 216s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 216s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 216s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 217s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 217s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 217s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 217s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 217s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 251s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-boot all 1.3-31-1 [635 kB] 251s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cluster s390x 2.1.8-1 [577 kB] 252s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-foreign s390x 0.8.88-1 [249 kB] 252s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB] 253s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-kernsmooth s390x 2.23-26-1 [94.7 kB] 253s Get:58 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB] 255s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB] 258s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-3-1 [4449 kB] 262s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 266s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-survival s390x 3.8-3-1 [8250 kB] 274s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rpart s390x 4.1.24-1 [672 kB] 275s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-class s390x 7.3-23-1 [92.0 kB] 275s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nnet s390x 7.3-20-1 [116 kB] 275s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-spatial s390x 7.3-18-1 [136 kB] 275s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-codetools all 0.2-20-1 [90.5 kB] 275s Get:68 http://ftpmaster.internal/ubuntu plucky/universe s390x r-recommended all 4.4.3-1 [2630 B] 275s Get:69 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base all 4.4.3-1 [9290 B] 275s Get:70 http://ftpmaster.internal/ubuntu plucky/universe s390x samtools s390x 1.21-1 [633 kB] 276s Get:71 http://ftpmaster.internal/ubuntu plucky/universe s390x smalt s390x 0.7.6-13 [109 kB] 276s Get:72 http://ftpmaster.internal/ubuntu plucky/universe s390x snpomatic s390x 1.0-7 [92.2 kB] 276s Get:73 http://ftpmaster.internal/ubuntu plucky/universe s390x tabix s390x 1.21+ds-1 [546 kB] 277s Get:74 http://ftpmaster.internal/ubuntu plucky/universe s390x reapr s390x 1.0.18+dfsg-7 [224 kB] 277s Preconfiguring packages ... 277s Fetched 66.2 MB in 1min 13s (909 kB/s) 277s Selecting previously unselected package libbamtools2.5.2:s390x. 277s (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 ... 56326 files and directories currently installed.) 277s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-6build1_s390x.deb ... 277s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-6build1) ... 277s Selecting previously unselected package libjsoncpp26:s390x. 277s Preparing to unpack .../01-libjsoncpp26_1.9.6-3_s390x.deb ... 277s Unpacking libjsoncpp26:s390x (1.9.6-3) ... 277s Selecting previously unselected package bamtools. 277s Preparing to unpack .../02-bamtools_2.5.2+dfsg-6build1_s390x.deb ... 277s Unpacking bamtools (2.5.2+dfsg-6build1) ... 277s Selecting previously unselected package libfreetype6:s390x. 277s Preparing to unpack .../03-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 277s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 277s Selecting previously unselected package fonts-dejavu-mono. 277s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 277s Unpacking fonts-dejavu-mono (2.37-8) ... 277s Selecting previously unselected package fonts-dejavu-core. 277s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 277s Unpacking fonts-dejavu-core (2.37-8) ... 277s Selecting previously unselected package fontconfig-config. 277s Preparing to unpack .../06-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 278s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 278s Selecting previously unselected package libfontconfig1:s390x. 278s Preparing to unpack .../07-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 278s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 278s Selecting previously unselected package fontconfig. 278s Preparing to unpack .../08-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 278s Unpacking fontconfig (2.15.0-2ubuntu1) ... 278s Selecting previously unselected package libbambamc0:s390x. 278s Preparing to unpack .../09-libbambamc0_0.0.50-6build1_s390x.deb ... 278s Unpacking libbambamc0:s390x (0.0.50-6build1) ... 278s Selecting previously unselected package libblas3:s390x. 278s Preparing to unpack .../10-libblas3_3.12.1-2_s390x.deb ... 278s Unpacking libblas3:s390x (3.12.1-2) ... 278s Selecting previously unselected package libpixman-1-0:s390x. 278s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_s390x.deb ... 278s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 278s Selecting previously unselected package libxcb-render0:s390x. 278s Preparing to unpack .../12-libxcb-render0_1.17.0-2_s390x.deb ... 278s Unpacking libxcb-render0:s390x (1.17.0-2) ... 278s Selecting previously unselected package libxcb-shm0:s390x. 278s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_s390x.deb ... 278s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 278s Selecting previously unselected package libxrender1:s390x. 278s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 278s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 278s Selecting previously unselected package libcairo2:s390x. 278s Preparing to unpack .../15-libcairo2_1.18.2-2_s390x.deb ... 278s Unpacking libcairo2:s390x (1.18.2-2) ... 278s Selecting previously unselected package libdatrie1:s390x. 278s Preparing to unpack .../16-libdatrie1_0.2.13-3build1_s390x.deb ... 278s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 278s Selecting previously unselected package libdeflate0:s390x. 278s Preparing to unpack .../17-libdeflate0_1.23-1_s390x.deb ... 278s Unpacking libdeflate0:s390x (1.23-1) ... 278s Selecting previously unselected package libfile-copy-link-perl. 278s Preparing to unpack .../18-libfile-copy-link-perl_0.200-1_all.deb ... 278s Unpacking libfile-copy-link-perl (0.200-1) ... 278s Selecting previously unselected package libgfortran5:s390x. 278s Preparing to unpack .../19-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 278s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 278s Selecting previously unselected package libgomp1:s390x. 278s Preparing to unpack .../20-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 278s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 278s Selecting previously unselected package libgraphite2-3:s390x. 278s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 278s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 278s Selecting previously unselected package libharfbuzz0b:s390x. 278s Preparing to unpack .../22-libharfbuzz0b_10.2.0-1_s390x.deb ... 278s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 278s Selecting previously unselected package libhtscodecs2:s390x. 278s Preparing to unpack .../23-libhtscodecs2_1.6.1-2_s390x.deb ... 278s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 278s Selecting previously unselected package libhts3t64:s390x. 278s Preparing to unpack .../24-libhts3t64_1.21+ds-1_s390x.deb ... 278s Unpacking libhts3t64:s390x (1.21+ds-1) ... 278s Selecting previously unselected package x11-common. 278s Preparing to unpack .../25-x11-common_1%3a7.7+23ubuntu3_all.deb ... 278s Unpacking x11-common (1:7.7+23ubuntu3) ... 278s Selecting previously unselected package libice6:s390x. 278s Preparing to unpack .../26-libice6_2%3a1.1.1-1_s390x.deb ... 278s Unpacking libice6:s390x (2:1.1.1-1) ... 278s Selecting previously unselected package libjpeg-turbo8:s390x. 278s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 278s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 278s Selecting previously unselected package libjpeg8:s390x. 278s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_s390x.deb ... 278s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 278s Selecting previously unselected package liblapack3:s390x. 278s Preparing to unpack .../29-liblapack3_3.12.1-2_s390x.deb ... 278s Unpacking liblapack3:s390x (3.12.1-2) ... 278s Selecting previously unselected package libthai-data. 278s Preparing to unpack .../30-libthai-data_0.1.29-2build1_all.deb ... 278s Unpacking libthai-data (0.1.29-2build1) ... 278s Selecting previously unselected package libthai0:s390x. 278s Preparing to unpack .../31-libthai0_0.1.29-2build1_s390x.deb ... 278s Unpacking libthai0:s390x (0.1.29-2build1) ... 278s Selecting previously unselected package libpango-1.0-0:s390x. 278s Preparing to unpack .../32-libpango-1.0-0_1.56.2-1_s390x.deb ... 278s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 278s Selecting previously unselected package libpangoft2-1.0-0:s390x. 278s Preparing to unpack .../33-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 278s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 278s Selecting previously unselected package libpangocairo-1.0-0:s390x. 278s Preparing to unpack .../34-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 278s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 278s Selecting previously unselected package libpaper2:s390x. 278s Preparing to unpack .../35-libpaper2_2.2.5-0.3_s390x.deb ... 278s Unpacking libpaper2:s390x (2.2.5-0.3) ... 278s Selecting previously unselected package libpaper-utils. 278s Preparing to unpack .../36-libpaper-utils_2.2.5-0.3_s390x.deb ... 278s Unpacking libpaper-utils (2.2.5-0.3) ... 278s Selecting previously unselected package libsharpyuv0:s390x. 278s Preparing to unpack .../37-libsharpyuv0_1.5.0-0.1_s390x.deb ... 278s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 278s Selecting previously unselected package libsm6:s390x. 278s Preparing to unpack .../38-libsm6_2%3a1.2.4-1_s390x.deb ... 278s Unpacking libsm6:s390x (2:1.2.4-1) ... 278s Selecting previously unselected package libtabixpp0t64:s390x. 278s Preparing to unpack .../39-libtabixpp0t64_1.1.2-2.1build1_s390x.deb ... 278s Unpacking libtabixpp0t64:s390x (1.1.2-2.1build1) ... 278s Selecting previously unselected package libtcl8.6:s390x. 278s Preparing to unpack .../40-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 278s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 278s Selecting previously unselected package libjbig0:s390x. 278s Preparing to unpack .../41-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 278s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 278s Selecting previously unselected package libwebp7:s390x. 278s Preparing to unpack .../42-libwebp7_1.5.0-0.1_s390x.deb ... 278s Unpacking libwebp7:s390x (1.5.0-0.1) ... 278s Selecting previously unselected package libtiff6:s390x. 278s Preparing to unpack .../43-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 278s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 278s Selecting previously unselected package libxft2:s390x. 278s Preparing to unpack .../44-libxft2_2.3.6-1build1_s390x.deb ... 278s Unpacking libxft2:s390x (2.3.6-1build1) ... 278s Selecting previously unselected package libxss1:s390x. 278s Preparing to unpack .../45-libxss1_1%3a1.2.3-1build3_s390x.deb ... 278s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 278s Selecting previously unselected package libtk8.6:s390x. 278s Preparing to unpack .../46-libtk8.6_8.6.16-1_s390x.deb ... 278s Unpacking libtk8.6:s390x (8.6.16-1) ... 278s Selecting previously unselected package libxt6t64:s390x. 278s Preparing to unpack .../47-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 278s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 278s Selecting previously unselected package zip. 278s Preparing to unpack .../48-zip_3.0-14ubuntu2_s390x.deb ... 278s Unpacking zip (3.0-14ubuntu2) ... 278s Selecting previously unselected package unzip. 278s Preparing to unpack .../49-unzip_6.0-28ubuntu6_s390x.deb ... 278s Unpacking unzip (6.0-28ubuntu6) ... 278s Selecting previously unselected package xdg-utils. 278s Preparing to unpack .../50-xdg-utils_1.2.1-2ubuntu1_all.deb ... 278s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 278s Selecting previously unselected package r-base-core. 278s Preparing to unpack .../51-r-base-core_4.4.3-1_s390x.deb ... 278s Unpacking r-base-core (4.4.3-1) ... 278s Selecting previously unselected package r-cran-boot. 278s Preparing to unpack .../52-r-cran-boot_1.3-31-1_all.deb ... 278s Unpacking r-cran-boot (1.3-31-1) ... 278s Selecting previously unselected package r-cran-cluster. 278s Preparing to unpack .../53-r-cran-cluster_2.1.8-1_s390x.deb ... 278s Unpacking r-cran-cluster (2.1.8-1) ... 278s Selecting previously unselected package r-cran-foreign. 278s Preparing to unpack .../54-r-cran-foreign_0.8.88-1_s390x.deb ... 278s Unpacking r-cran-foreign (0.8.88-1) ... 278s Selecting previously unselected package r-cran-mass. 278s Preparing to unpack .../55-r-cran-mass_7.3-64-1_s390x.deb ... 278s Unpacking r-cran-mass (7.3-64-1) ... 278s Selecting previously unselected package r-cran-kernsmooth. 278s Preparing to unpack .../56-r-cran-kernsmooth_2.23-26-1_s390x.deb ... 278s Unpacking r-cran-kernsmooth (2.23-26-1) ... 278s Selecting previously unselected package r-cran-lattice. 278s Preparing to unpack .../57-r-cran-lattice_0.22-6-1_s390x.deb ... 278s Unpacking r-cran-lattice (0.22-6-1) ... 279s Selecting previously unselected package r-cran-nlme. 279s Preparing to unpack .../58-r-cran-nlme_3.1.167-1_s390x.deb ... 279s Unpacking r-cran-nlme (3.1.167-1) ... 279s Selecting previously unselected package r-cran-matrix. 279s Preparing to unpack .../59-r-cran-matrix_1.7-3-1_s390x.deb ... 279s Unpacking r-cran-matrix (1.7-3-1) ... 279s Selecting previously unselected package r-cran-mgcv. 279s Preparing to unpack .../60-r-cran-mgcv_1.9-1-1_s390x.deb ... 279s Unpacking r-cran-mgcv (1.9-1-1) ... 279s Selecting previously unselected package r-cran-survival. 279s Preparing to unpack .../61-r-cran-survival_3.8-3-1_s390x.deb ... 279s Unpacking r-cran-survival (3.8-3-1) ... 279s Selecting previously unselected package r-cran-rpart. 279s Preparing to unpack .../62-r-cran-rpart_4.1.24-1_s390x.deb ... 279s Unpacking r-cran-rpart (4.1.24-1) ... 279s Selecting previously unselected package r-cran-class. 279s Preparing to unpack .../63-r-cran-class_7.3-23-1_s390x.deb ... 279s Unpacking r-cran-class (7.3-23-1) ... 279s Selecting previously unselected package r-cran-nnet. 279s Preparing to unpack .../64-r-cran-nnet_7.3-20-1_s390x.deb ... 279s Unpacking r-cran-nnet (7.3-20-1) ... 279s Selecting previously unselected package r-cran-spatial. 279s Preparing to unpack .../65-r-cran-spatial_7.3-18-1_s390x.deb ... 279s Unpacking r-cran-spatial (7.3-18-1) ... 279s Selecting previously unselected package r-cran-codetools. 279s Preparing to unpack .../66-r-cran-codetools_0.2-20-1_all.deb ... 279s Unpacking r-cran-codetools (0.2-20-1) ... 279s Selecting previously unselected package r-recommended. 279s Preparing to unpack .../67-r-recommended_4.4.3-1_all.deb ... 279s Unpacking r-recommended (4.4.3-1) ... 279s Selecting previously unselected package r-base. 279s Preparing to unpack .../68-r-base_4.4.3-1_all.deb ... 279s Unpacking r-base (4.4.3-1) ... 279s Selecting previously unselected package samtools. 279s Preparing to unpack .../69-samtools_1.21-1_s390x.deb ... 279s Unpacking samtools (1.21-1) ... 279s Selecting previously unselected package smalt. 279s Preparing to unpack .../70-smalt_0.7.6-13_s390x.deb ... 279s Unpacking smalt (0.7.6-13) ... 279s Selecting previously unselected package snpomatic. 279s Preparing to unpack .../71-snpomatic_1.0-7_s390x.deb ... 279s Unpacking snpomatic (1.0-7) ... 279s Selecting previously unselected package tabix. 279s Preparing to unpack .../72-tabix_1.21+ds-1_s390x.deb ... 279s Unpacking tabix (1.21+ds-1) ... 279s Selecting previously unselected package reapr. 279s Preparing to unpack .../73-reapr_1.0.18+dfsg-7_s390x.deb ... 279s Unpacking reapr (1.0.18+dfsg-7) ... 279s Setting up libhtscodecs2:s390x (1.6.1-2) ... 279s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 279s Setting up libpixman-1-0:s390x (0.44.0-3) ... 279s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 279s Setting up libfile-copy-link-perl (0.200-1) ... 279s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 279s Setting up libdatrie1:s390x (0.2.13-3build1) ... 279s Setting up libxcb-render0:s390x (1.17.0-2) ... 279s Setting up unzip (6.0-28ubuntu6) ... 279s Setting up x11-common (1:7.7+23ubuntu3) ... 279s Setting up libdeflate0:s390x (1.23-1) ... 279s Setting up libxcb-shm0:s390x (1.17.0-2) ... 279s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 279s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 279s Setting up zip (3.0-14ubuntu2) ... 279s Setting up libblas3:s390x (3.12.1-2) ... 279s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 279s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 279s Setting up libjsoncpp26:s390x (1.9.6-3) ... 279s Setting up libbambamc0:s390x (0.0.50-6build1) ... 279s Setting up fonts-dejavu-mono (2.37-8) ... 279s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 279s Setting up fonts-dejavu-core (2.37-8) ... 279s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 279s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-6build1) ... 279s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 279s Setting up libwebp7:s390x (1.5.0-0.1) ... 279s Setting up bamtools (2.5.2+dfsg-6build1) ... 279s Setting up snpomatic (1.0-7) ... 279s Setting up libhts3t64:s390x (1.21+ds-1) ... 279s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 279s Setting up libthai-data (0.1.29-2build1) ... 279s Setting up libxss1:s390x (1:1.2.3-1build3) ... 279s Setting up libpaper2:s390x (2.2.5-0.3) ... 279s Setting up tabix (1.21+ds-1) ... 279s Setting up xdg-utils (1.2.1-2ubuntu1) ... 279s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 279s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 279s Setting up smalt (0.7.6-13) ... 279s Setting up libice6:s390x (2:1.1.1-1) ... 279s Setting up liblapack3:s390x (3.12.1-2) ... 279s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 279s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 279s Setting up libpaper-utils (2.2.5-0.3) ... 279s Setting up samtools (1.21-1) ... 279s Setting up libthai0:s390x (0.1.29-2build1) ... 279s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 279s Setting up libtabixpp0t64:s390x (1.1.2-2.1build1) ... 279s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 279s Setting up libsm6:s390x (2:1.2.4-1) ... 279s Setting up fontconfig (2.15.0-2ubuntu1) ... 281s Regenerating fonts cache... done. 281s Setting up libxft2:s390x (2.3.6-1build1) ... 281s Setting up libtk8.6:s390x (8.6.16-1) ... 281s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 281s Setting up libcairo2:s390x (1.18.2-2) ... 281s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 281s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 281s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 281s Setting up r-base-core (4.4.3-1) ... 281s Creating config file /etc/R/Renviron with new version 281s Setting up r-cran-lattice (0.22-6-1) ... 281s Setting up r-cran-nlme (3.1.167-1) ... 281s Setting up r-cran-cluster (2.1.8-1) ... 281s Setting up r-cran-nnet (7.3-20-1) ... 281s Setting up r-cran-codetools (0.2-20-1) ... 281s Setting up r-cran-boot (1.3-31-1) ... 281s Setting up r-cran-spatial (7.3-18-1) ... 281s Setting up r-cran-mass (7.3-64-1) ... 281s Setting up r-cran-foreign (0.8.88-1) ... 281s Setting up r-cran-matrix (1.7-3-1) ... 281s Setting up r-cran-kernsmooth (2.23-26-1) ... 281s Setting up r-cran-mgcv (1.9-1-1) ... 281s Setting up r-cran-class (7.3-23-1) ... 281s Setting up r-cran-survival (3.8-3-1) ... 281s Setting up r-cran-rpart (4.1.24-1) ... 281s Setting up r-recommended (4.4.3-1) ... 281s Setting up r-base (4.4.3-1) ... 281s Setting up reapr (1.0.18+dfsg-7) ... 281s Processing triggers for man-db (2.13.0-1) ... 282s Processing triggers for install-info (7.1.1-1) ... 282s Processing triggers for libc-bin (2.41-1ubuntu2) ... 283s autopkgtest [18:42:57]: test test-example: [----------------------- 283s [wgsim] seed = 42 283s [wgsim_core] calculating the total length of the reference sequence... 283s [wgsim_core] 1 sequences, total length: 1000111 284s foo 1384 T K + 284s foo 4961 T W + 284s foo 5885 - T - 284s foo 9598 A C - 284s foo 10177 G R + 284s foo 11305 G K + 284s foo 11592 G R + 284s foo 13931 T - - 284s foo 15907 C A - 284s foo 17264 G K + 284s foo 17780 A - - 284s foo 18711 A W + 284s foo 19249 T W + 284s foo 19522 C S + 284s foo 23053 T K + 284s foo 23681 A R + 284s foo 23730 C S + 284s foo 24075 G S + 284s foo 24555 G C - 284s foo 26775 G K + 284s foo 26896 C M + 284s foo 27253 G K + 284s foo 28210 T Y + 284s foo 28224 A W + 284s foo 28377 - G + 284s foo 29035 G K + 284s foo 29898 C M + 284s foo 30274 A R + 284s foo 30542 G K + 284s foo 31566 A C - 284s foo 32252 - A - 284s foo 33303 T K + 284s foo 33390 - G + 284s foo 34073 A R + 284s foo 34171 G R + 284s foo 34718 T Y + 284s foo 34801 - C + 284s foo 35204 T W + 284s foo 35342 G S + 284s foo 35489 G T - 284s foo 36153 A M + 284s foo 36273 C S + 284s foo 37356 G T - 284s foo 37596 C S + 284s foo 39308 T - - 284s foo 40333 C G - 284s foo 42295 T K + 284s foo 42372 T Y + 284s foo 44433 C G - 284s foo 44630 - AG + 284s foo 44902 T C - 284s foo 47156 C A - 284s foo 48210 C M + 284s foo 48390 A R + 284s foo 49652 C M + 284s foo 52739 T Y + 284s foo 52858 A M + 284s foo 54737 A G - 284s foo 55306 C T - 284s foo 55434 C T - 284s foo 59204 A W + 284s foo 59300 G C - 284s foo 59335 T Y + 284s foo 59444 T - - 284s foo 59531 C S + 284s foo 59766 C Y + 284s foo 61950 C S + 284s foo 62887 G S + 284s foo 63390 A G - 284s foo 64365 G K + 284s foo 64703 C S + 284s foo 64932 C Y + 284s foo 68383 - CG + 284s foo 68464 A W + 284s foo 68727 A W + 284s foo 69080 A M + 284s foo 72071 T C - 284s foo 72720 - G - 284s foo 73354 C T - 284s foo 73637 G T - 284s foo 74741 A M + 284s foo 75101 C T - 284s foo 75207 T K + 284s foo 76400 T Y + 284s foo 76780 A C - 284s foo 77172 A W + 284s foo 78385 C Y + 284s foo 80705 C M + 284s foo 82440 A R + 284s foo 83021 G K + 284s foo 83116 A - - 284s foo 83846 T K + 284s foo 84633 G S + 284s foo 85891 G S + 284s foo 87759 A C - 284s foo 87778 T W + 284s foo 88581 T K + 284s foo 88606 T Y + 284s foo 88880 A G - 284s foo 89945 G C - 284s foo 90728 T K + 284s foo 91798 G R + 284s foo 95957 G C - 284s foo 96173 T W + 284s foo 96665 A M + 284s foo 98019 - G + 284s foo 98131 A M + 284s foo 98669 A R + 284s foo 98719 G T - 284s foo 99062 A W + 284s foo 99590 A T - 284s foo 100532 - TC + 284s foo 103015 A W + 284s foo 103172 G S + 284s foo 103609 G R + 284s foo 106549 T Y + 284s foo 108808 C Y + 284s foo 109191 G C - 284s foo 111686 C G - 284s foo 113436 C A - 284s foo 113763 A W + 284s foo 115671 C T - 284s foo 117460 - A - 284s foo 118193 G - - 284s foo 118585 T K + 284s foo 121219 A M + 284s foo 121876 T K + 284s foo 122071 T A - 284s foo 124918 C G - 284s foo 125300 G S + 284s foo 125967 C S + 284s foo 127443 G S + 284s foo 127565 C Y + 284s foo 128700 C A - 284s foo 129912 G A - 284s foo 130847 T W + 284s foo 131677 G S + 284s foo 132189 T C - 284s foo 135878 CGGC - - 284s foo 136825 T K + 284s foo 138881 TGT - - 284s foo 139288 A W + 284s foo 141054 A W + 284s foo 141055 - T + 284s foo 141101 C S + 284s foo 141404 A R + 284s foo 142698 T C - 284s foo 143990 C A - 284s foo 144167 T Y + 284s foo 144814 C Y + 284s foo 146381 T Y + 284s foo 146393 C A - 284s foo 146510 A C - 284s foo 147182 A W + 284s foo 148783 T C - 284s foo 149068 G S + 284s foo 150208 T K + 284s foo 151554 T W + 284s foo 151709 C G - 284s foo 153072 G R + 284s foo 153307 T Y + 284s foo 154050 G S + 284s foo 154415 C S + 284s foo 154594 G R + 284s foo 155839 G T - 284s foo 156106 G A - 284s foo 159356 T W + 284s foo 159926 A W + 284s foo 160303 T K + 284s foo 161323 C Y + 284s foo 161904 G S + 284s foo 162533 - ACC - 284s foo 164738 C G - 284s foo 165413 A R + 284s foo 166944 C M + 284s foo 167464 T Y + 284s foo 168420 T C - 284s foo 168579 A M + 284s foo 168787 T W + 284s foo 168959 A T - 284s foo 169884 G S + 284s foo 170032 G T - 284s foo 172058 G K + 284s foo 174942 A R + 284s foo 175014 G K + 284s foo 178406 G A - 284s foo 179028 - A + 284s foo 182394 C M + 284s foo 182735 T Y + 284s foo 183384 T K + 284s foo 183893 - AT - 284s foo 185360 G A - 284s foo 185538 - G - 284s foo 187948 G S + 284s foo 188120 T G - 284s foo 188179 T W + 284s foo 188316 T Y + 284s foo 189963 - G + 284s foo 190093 C Y + 284s foo 192220 C M + 284s foo 192368 A W + 284s foo 192782 T K + 284s foo 193307 A R + 284s foo 193501 G K + 284s foo 194276 G S + 284s foo 194930 C S + 284s foo 196728 A W + 284s foo 197559 G C - 284s foo 198467 T W + 284s foo 199042 C Y + 284s foo 199259 AA - - 284s foo 199687 TT - - 284s foo 200287 C A - 284s foo 200678 A R + 284s foo 201208 C T - 284s foo 201882 A - - 284s foo 204456 T K + 284s foo 206327 G R + 284s foo 207311 G T - 284s foo 209184 G A - 284s foo 209279 C Y + 284s foo 211459 C Y + 284s foo 213807 T Y + 284s foo 213846 T Y + 284s foo 214635 A G - 284s foo 214884 C A - 284s foo 216244 A M + 284s foo 216652 A M + 284s foo 216745 T - - 284s foo 216909 A T - 284s foo 217579 A G - 284s foo 217895 C Y + 284s foo 218870 G K + 284s foo 223098 T A - 284s foo 223283 - C + 284s foo 223666 C A - 284s foo 224011 - C + 284s foo 225681 C S + 284s foo 227345 T C - 284s foo 228778 T G - 284s foo 229926 C - - 284s foo 230778 T K + 284s foo 230939 CG - - 284s foo 231988 CT - - 284s foo 234593 T W + 284s foo 235496 C S + 284s foo 235705 G K + 284s foo 235758 A G - 284s foo 236852 T C - 284s foo 238790 A M + 284s foo 238865 T K + 284s foo 239329 A M + 284s foo 239576 - C + 284s foo 243058 G S + 284s foo 244147 T - - 284s foo 244462 C G - 284s foo 245443 - A + 284s foo 246544 C Y + 284s foo 246744 T W + 284s foo 247473 C M + 284s foo 248129 C T - 284s foo 249060 A C - 284s foo 249515 G T - 284s foo 250138 G S + 284s foo 250567 C A - 284s foo 254381 G R + 284s foo 257864 C M + 284s foo 257879 C Y + 284s foo 259859 A M + 284s foo 260643 C S + 284s foo 261681 C G - 284s foo 262645 T Y + 284s foo 263279 A R + 284s foo 263575 A - - 284s foo 264587 - TA + 284s foo 264689 T K + 284s foo 265758 G K + 284s foo 266272 A M + 284s foo 268550 C M + 284s foo 269986 G S + 284s foo 270321 AC - - 284s foo 273346 C S + 284s foo 275367 C A - 284s foo 277334 C G - 284s foo 277629 G T - 284s foo 278431 C Y + 284s foo 281456 T Y + 284s foo 281556 T G - 284s foo 281737 G K + 284s foo 282290 AC - - 284s foo 282851 - C - 284s foo 284405 A C - 284s foo 288751 A C - 284s foo 290501 TAAA - - 284s foo 291315 A W + 284s foo 291368 C - - 284s foo 292154 A C - 284s foo 292385 C M + 284s foo 292555 G K + 284s foo 297709 G C - 284s foo 298183 A W + 284s foo 298228 T W + 284s foo 299902 T G - 284s foo 302575 A T - 284s foo 304823 G R + 284s foo 305308 T Y + 284s foo 305487 G S + 284s foo 305697 G T - 284s foo 306098 C G - 284s foo 306882 T Y + 284s foo 308201 A M + 284s foo 308833 A T - 284s foo 312033 A - - 284s foo 312895 C G - 284s foo 313889 C - - 284s foo 315109 A R + 284s foo 316083 C - - 284s foo 316466 A R + 284s foo 318040 G C - 284s foo 319446 T C - 284s foo 320236 C S + 284s foo 320652 A - - 284s foo 320716 T K + 284s foo 323644 A - - 284s foo 325359 G T - 284s foo 329476 - CA + 284s foo 329706 T G - 284s foo 330181 T Y + 284s foo 330703 C Y + 284s foo 331315 G S + 284s foo 332351 C A - 284s foo 333408 A R + 284s foo 333468 C S + 284s foo 336247 A G - 284s foo 336586 A M + 284s foo 337364 G K + 284s foo 337686 A T - 284s foo 338043 A - - 284s foo 338292 C G - 284s foo 338962 A C - 284s foo 339353 G K + 284s foo 340647 - A + 284s foo 341705 G R + 284s foo 344283 C M + 284s foo 345898 - AG - 284s foo 347959 T - - 284s foo 349162 C M + 284s foo 352072 T Y + 284s foo 354614 C Y + 284s foo 359304 T - - 284s foo 359312 - G + 284s foo 360972 C S + 284s foo 363857 C Y + 284s foo 366226 A C - 284s foo 367259 C M + 284s foo 372502 T Y + 284s foo 372747 A M + 284s foo 375140 C S + 284s foo 376298 T W + 284s foo 376313 C - - 284s foo 376760 T W + 284s foo 378494 A W + 284s foo 381137 T G - 284s foo 381186 A R + 284s foo 381701 A G - 284s foo 382614 A W + 284s foo 382761 C T - 284s foo 382854 T C - 284s foo 383201 C T - 284s foo 385104 G S + 284s foo 385233 - A + 284s foo 386138 C T - 284s foo 386316 A W + 284s foo 387072 A R + 284s foo 387642 - A + 284s foo 388232 T C - 284s foo 388890 GGG - - 284s foo 390508 C S + 284s foo 390625 C M + 284s foo 391921 C G - 284s foo 395256 G T - 284s foo 395542 G S + 284s foo 397015 A - - 284s foo 397516 C Y + 284s foo 397528 GC - - 284s foo 398152 C T - 284s foo 399802 A W + 284s foo 400972 T K + 284s foo 401419 - T + 284s foo 401477 T W + 284s foo 402437 A M + 284s foo 402722 G R + 284s foo 403452 C M + 284s foo 404234 - A + 284s foo 405344 A W + 284s foo 407040 G S + 284s foo 408483 G R + 284s foo 408586 A C - 284s foo 408721 A R + 284s foo 409494 A M + 284s foo 410078 A G - 284s foo 411170 C A - 284s foo 415342 T Y + 284s foo 416265 C G - 284s foo 417740 C A - 284s foo 418622 C S + 284s foo 420232 A W + 284s foo 420288 T Y + 284s foo 420908 A W + 284s foo 421109 T A - 284s foo 421357 A R + 284s foo 422799 G A - 284s foo 424383 C S + 284s foo 424871 - GCA + 284s foo 427273 T A - 284s foo 429822 C M + 284s foo 429846 T W + 284s foo 432015 A G - 284s foo 432414 G K + 284s foo 433606 C Y + 284s foo 433831 T Y + 284s foo 437721 - A - 284s foo 438402 G - - 284s foo 438799 A T - 284s foo 439422 C M + 284s foo 440734 C A - 284s foo 441840 T G - 284s foo 442021 - C + 284s foo 445021 T A - 284s foo 445591 G A - 284s foo 446138 T W + 284s foo 447757 A W + 284s foo 449156 T - - 284s foo 449161 G K + 284s foo 450114 A W + 284s foo 450688 A W + 284s foo 454421 C G - 284s foo 454718 T Y + 284s foo 455675 TC - - 284s foo 461721 G R + 284s foo 462526 G S + 284s foo 467296 G A - 284s foo 467510 G K + 284s foo 468267 T K + 284s foo 469118 G R + 284s foo 469830 C Y + 284s foo 471073 G T - 284s foo 472056 G A - 284s foo 472773 - A + 284s foo 473046 G R + 284s foo 473188 G A - 284s foo 473742 C - - 284s foo 474789 T A - 284s foo 477763 G R + 284s foo 478246 T W + 284s foo 478975 T G - 284s foo 479038 A R + 284s foo 480275 T Y + 284s foo 480317 G A - 284s foo 481512 T K + 284s foo 482069 G S + 284s foo 482534 A R + 284s foo 483760 C Y + 284s foo 485281 T W + 284s foo 486255 T C - 284s foo 487038 T K + 284s foo 487225 T A - 284s foo 488012 C Y + 284s foo 488795 T C - 284s foo 490241 A R + 284s foo 492595 - CGG + 284s foo 493224 C A - 284s foo 494284 A T - 284s foo 495990 - T - 284s foo 497306 A R + 284s foo 497403 T Y + 284s foo 499569 C Y + 284s foo 499651 T K + 284s foo 503139 T C - 284s foo 504660 A R + 284s foo 508679 C - - 284s foo 513643 G K + 284s foo 515668 CC - - 284s foo 515836 G R + 284s foo 516488 C S + 284s foo 517602 G R + 284s foo 517962 G K + 284s foo 517975 T K + 284s foo 519144 A T - 284s foo 520068 T K + 284s foo 520926 A W + 284s foo 521562 C S + 284s foo 522076 CG - - 284s foo 522838 T Y + 284s foo 523513 - C + 284s foo 523907 - TA + 284s foo 526271 T A - 284s foo 526533 AC - - 284s foo 526767 C Y + 284s foo 528217 C Y + 284s foo 531924 G S + 284s foo 532333 - TT + 284s foo 533132 C M + 284s foo 534689 A T - 284s foo 534779 A W + 284s foo 535594 C A - 284s foo 535795 G R + 284s foo 538368 A R + 284s foo 540879 G K + 284s foo 542530 A - - 284s foo 543620 G R + 284s foo 544733 - C - 284s foo 546300 - TT + 284s foo 548196 A T - 284s foo 548878 C M + 284s foo 548885 G R + 284s foo 549459 T K + 284s foo 550908 A G - 284s foo 551170 A - - 284s foo 553130 T Y + 284s foo 555293 T G - 284s foo 556198 G R + 284s foo 556355 A T - 284s foo 557688 G K + 284s foo 558415 G C - 284s foo 558461 - G + 284s foo 559287 T Y + 284s foo 559465 C M + 284s foo 560184 T W + 284s foo 560252 T W + 284s foo 562579 A M + 284s foo 562961 G A - 284s foo 566986 C A - 284s foo 568134 C A - 284s foo 569698 T C - 284s foo 570180 T K + 284s foo 570451 TG - - 284s foo 570832 - A - 284s foo 571589 A W + 284s foo 572208 C M + 284s foo 572871 C S + 284s foo 574334 G - - 284s foo 575673 T Y + 284s foo 576797 G S + 284s foo 578486 - C - 284s foo 578494 C S + 284s foo 579257 G A - 284s foo 580103 G T - 284s foo 580872 A W + 284s foo 580925 G S + 284s foo 580950 G C - 284s foo 581637 T Y + 284s foo 581654 A G - 284s foo 582538 A T - 284s foo 582691 C M + 284s foo 582938 A W + 284s foo 583104 T K + 284s foo 584763 T W + 284s foo 585723 T W + 284s foo 588253 T Y + 284s foo 588972 T C - 284s foo 589438 - C - 284s foo 591131 C Y + 284s foo 591950 G R + 284s foo 592194 T G - 284s foo 592310 G S + 284s foo 593892 G A - 284s foo 598556 A - - 284s foo 601660 G S + 284s foo 602112 G T - 284s foo 602412 T Y + 284s foo 607282 - C + 284s foo 607394 A M + 284s foo 608438 A T - 284s foo 609255 A W + 284s foo 609365 - T + 284s foo 611161 G K + 284s foo 612224 C G - 284s foo 614493 G R + 284s foo 614601 G A - 284s foo 614607 C Y + 284s foo 619507 C M + 284s foo 619798 T C - 284s foo 621872 C T - 284s foo 622375 C Y + 284s foo 623208 - G - 284s foo 624366 C A - 284s foo 625320 - ACA - 284s foo 626664 - G + 284s foo 627140 T C - 284s foo 627353 G T - 284s foo 628714 T Y + 284s foo 628744 A - - 284s foo 629152 A G - 284s foo 630110 T G - 284s foo 631744 G K + 284s foo 632763 C S + 284s foo 634419 G - - 284s foo 634459 A G - 284s foo 634571 G A - 284s foo 635366 - A + 284s foo 635604 G T - 284s foo 637057 T C - 284s foo 637525 A T - 284s foo 638412 A R + 284s foo 640547 A W + 284s foo 641514 T K + 284s foo 642219 A R + 284s foo 642427 A G - 284s foo 642612 A R + 284s foo 643553 T W + 284s foo 647316 - T + 284s foo 647598 C - - 284s foo 651093 G A - 284s foo 651718 G R + 284s foo 652235 A G - 284s foo 652579 A C - 284s foo 653355 A W + 284s foo 655174 C M + 284s foo 655487 A M + 284s foo 656849 G S + 284s foo 661081 T K + 284s foo 661134 G C - 284s foo 661935 A W + 284s foo 662010 A M + 284s foo 662040 G R + 284s foo 663030 A W + 284s foo 663268 - C + 284s foo 664991 T - - 284s foo 665489 T K + 284s foo 665555 C M + 284s foo 665965 C Y + 284s foo 668725 A C - 284s foo 668834 - G - 284s foo 668873 C S + 284s foo 669654 T W + 284s foo 671041 G S + 284s foo 671485 T W + 284s foo 671690 C M + 284s foo 673022 G R + 284s foo 674137 - T + 284s foo 674782 A C - 284s foo 676373 G T - 284s foo 676793 T C - 284s foo 677409 G S + 284s foo 677536 - AA - 284s foo 677620 G K + 284s foo 677686 C Y + 284s foo 678327 G S + 284s foo 678704 G S + 284s foo 678771 A C - 284s foo 678866 C T - 284s foo 679960 A W + 284s foo 680447 - C + 284s foo 682102 C T - 284s foo 685497 T A - 284s foo 686884 G S + 284s foo 687324 ACA - - 284s foo 687684 - AC + 284s foo 687823 T C - 284s foo 688590 G K + 284s foo 690802 C M + 284s foo 691388 T C - 284s foo 691403 T G - 284s foo 691790 G A - 284s foo 692973 C A - 284s foo 694058 G S + 284s foo 694550 G R + 284s foo 694968 T W + 284s foo 695898 A T - 284s foo 696721 C S + 284s foo 696787 C S + 284s foo 696935 A M + 284s foo 698024 - C + 284s foo 699813 A - - 284s foo 700179 G R + 284s foo 701421 A M + 284s foo 701989 T A - 284s foo 702862 C A - 284s foo 707020 G A - 284s foo 708420 A - - 284s foo 708669 C G - 284s foo 710521 T W + 284s foo 711801 G C - 284s foo 711913 T G - 284s foo 715830 C M + 284s foo 717664 TC - - 284s foo 718845 A W + 284s foo 719069 T Y + 284s foo 719565 A W + 284s foo 721136 T K + 284s foo 726116 T K + 284s foo 727809 T K + 284s foo 728864 G K + 284s foo 728918 G A - 284s foo 730296 - T + 284s foo 731988 C Y + 284s foo 734658 A M + 284s foo 734715 A W + 284s foo 736618 C G - 284s foo 737257 T Y + 284s foo 740864 C A - 284s foo 741640 G - - 284s foo 741859 - TA - 284s foo 742011 T K + 284s foo 742237 A R + 284s foo 742960 G K + 284s foo 743731 G R + 284s foo 743971 A W + 284s foo 744635 T K + 284s foo 746430 C G - 284s foo 746489 - GC - 284s foo 746881 C M + 284s foo 756997 TC - - 284s foo 757776 A M + 284s foo 759870 A T - 284s foo 760224 G K + 284s foo 760799 G C - 284s foo 761692 T C - 284s foo 762569 G S + 284s foo 763140 A G - 284s foo 763842 - T - 284s foo 764192 A M + 284s foo 764334 G A - 284s foo 764889 - AAT + 284s foo 766464 G S + 284s foo 768226 G A - 284s foo 770272 T G - 284s foo 771145 C Y + 284s foo 772209 T A - 284s foo 773672 T K + 284s foo 773932 G C - 284s foo 774658 C S + 284s foo 775969 A M + 284s foo 776816 T G - 284s foo 777591 C Y + 284s foo 777891 A M + 284s foo 778164 C M + 284s foo 778219 T W + 284s foo 779260 G T - 284s foo 779465 A W + 284s foo 779779 G S + 284s foo 780033 G K + 284s foo 783243 C M + 284s foo 783860 A R + 284s foo 788345 A M + 284s foo 789554 G - - 284s foo 790025 G K + 284s foo 791454 T K + 284s foo 792009 C A - 284s foo 792872 C G - 284s foo 794616 T W + 284s foo 795031 G R + 284s foo 796919 C M + 284s foo 797020 G S + 284s foo 797042 G C - 284s foo 797149 G A - 284s foo 797177 A C - 284s foo 799076 G C - 284s foo 799580 G S + 284s foo 800356 A R + 284s foo 802297 G T - 284s foo 802309 T Y + 284s foo 802343 - C + 284s foo 802769 A W + 284s foo 803104 C G - 284s foo 805819 C Y + 284s foo 805972 T Y + 284s foo 807503 T K + 284s foo 807950 C M + 284s foo 807994 - A - 284s foo 809167 A G - 284s foo 809658 A W + 284s foo 810152 A M + 284s foo 811506 G R + 284s foo 813494 A M + 284s foo 814035 G T - 284s foo 814476 A W + 284s foo 819399 T K + 284s foo 820171 T W + 284s foo 820445 G C - 284s foo 822178 C G - 284s foo 822504 C T - 284s foo 823378 C M + 284s foo 823591 CG - - 284s foo 824229 C M + 284s foo 824579 C T - 284s foo 824858 C M + 284s foo 826101 T K + 284s foo 827593 C G - 284s foo 827794 T Y + 284s foo 828228 A M + 284s foo 828367 T K + 284s foo 828788 C M + 284s foo 829002 C Y + 284s foo 830345 C M + 284s foo 831018 C A - 284s foo 831459 T K + 284s foo 832413 A T - 284s foo 832782 T Y + 284s foo 832908 T Y + 284s foo 833130 T - - 284s foo 833142 G S + 284s foo 833241 G A - 284s foo 836727 A T - 284s foo 836829 G S + 284s foo 838452 T G - 284s foo 838543 A T - 284s foo 838605 C M + 284s foo 838954 G C - 284s foo 841829 G K + 284s foo 842324 - TC + 284s foo 842996 - C + 284s foo 844390 C A - 284s foo 844793 A C - 284s foo 844925 C A - 284s foo 845082 G C - 284s foo 846202 G R + 284s foo 846707 A G - 284s foo 848713 G A - 284s foo 849372 C S + 284s foo 849742 G A - 284s foo 850499 C - - 284s foo 850927 GT - - 284s foo 851084 - G + 284s foo 852247 A R + 284s foo 852972 C A - 284s foo 854808 T W + 284s foo 855956 G K + 284s foo 856225 G A - 284s foo 856582 T K + 284s foo 857351 C M + 284s foo 857504 AC - - 284s foo 858324 A T - 284s foo 858858 T C - 284s foo 859488 T Y + 284s foo 862441 T Y + 284s foo 863827 C Y + 284s foo 864165 C A - 284s foo 865997 C M + 284s foo 866370 G S + 284s foo 867653 G S + 284s foo 867722 C Y + 284s foo 868696 C M + 284s foo 869005 T W + 284s foo 869791 T Y + 284s foo 875339 C Y + 284s foo 875347 C M + 284s foo 875584 T G - 284s foo 876780 C T - 284s foo 878368 A C - 284s foo 878916 - CAG + 284s foo 879005 A R + 284s foo 880112 G T - 284s foo 881021 - T - 284s foo 881175 T W + 284s foo 882168 - GGG + 284s foo 882223 - G - 284s foo 883033 TG - - 284s foo 883381 C G - 284s foo 884378 C - - 284s foo 885075 A M + 284s foo 885190 A W + 284s foo 885568 A W + 284s foo 885827 T Y + 284s foo 887610 TG - - 284s foo 889139 G R + 284s foo 890978 T - - 284s foo 891500 C Y + 284s foo 892257 G C - 284s foo 892642 G R + 284s foo 892644 T W + 284s foo 892757 C A - 284s foo 893222 T - - 284s foo 893348 T W + 284s foo 894161 - C - 284s foo 894447 A G - 284s foo 894614 A W + 284s foo 897817 T W + 284s foo 899408 C S + 284s foo 902450 A T - 284s foo 902970 AT - - 284s foo 905836 G K + 284s foo 906524 GA - - 284s foo 907484 A W + 284s foo 907537 C M + 284s foo 908515 G R + 284s foo 908642 C T - 284s foo 911145 T C - 284s foo 912220 T Y + 284s foo 912682 C Y + 284s foo 914260 C S + 284s foo 914757 T Y + 284s foo 916413 G C - 284s foo 916783 T G - 284s foo 917033 G C - 284s foo 917218 A - - 284s foo 918225 G - - 284s foo 918459 A - - 284s foo 918732 A M + 284s foo 919640 TC - - 284s foo 920824 T W + 284s foo 920836 G C - 284s foo 924560 G R + 284s foo 924659 GA - - 284s foo 925868 T A - 284s foo 928254 T G - 284s foo 928369 - A - 284s foo 928641 - AG + 284s foo 929857 C M + 284s foo 930211 T W + 284s foo 930935 C T - 284s foo 931986 A M + 284s foo 932852 G T - 284s foo 933965 T A - 284s foo 935564 A W + 284s foo 936034 T Y + 284s foo 936221 AC - - 284s foo 936670 C S + 284s foo 936704 T A - 284s foo 936786 T W + 284s foo 939218 C S + 284s foo 939312 A W + 284s foo 939467 A W + 284s foo 939934 C S + 284s foo 941603 C Y + 284s foo 942910 A W + 284s foo 944654 T Y + 284s foo 945301 A C - 284s foo 945770 C T - 284s foo 946078 G S + 284s foo 948833 G K + 284s foo 948999 A W + 284s foo 949193 A R + 284s foo 950276 C M + 284s foo 950414 A W + 284s foo 951285 G C - 284s foo 953158 G R + 284s foo 953287 A W + 284s foo 954150 C G - 284s foo 954258 G - - 284s foo 955396 CC - - 284s foo 956490 - AC + 284s foo 958129 A R + 284s foo 959027 T A - 284s foo 959964 A W + 284s foo 962042 A G - 284s foo 962742 C G - 284s foo 963306 T W + 284s foo 963422 G K + 284s foo 964082 G S + 284s foo 965561 C S + 284s foo 966531 T K + 284s foo 967324 T W + 284s foo 968419 - C - 284s foo 969054 G - - 284s foo 969158 G S + 284s foo 972658 C M + 284s foo 974266 T W + 284s foo 974629 G K + 284s foo 975034 A R + 284s foo 975636 T W + 284s foo 977078 - A - 284s foo 978321 G T - 284s foo 978595 C G - 284s foo 979090 C M + 284s foo 983855 TA - - 284s foo 985725 T A - 284s foo 988497 C Y + 284s foo 990171 C M + 284s foo 990804 - CA - 284s foo 990941 T W + 284s foo 991797 A W + 284s foo 992469 A M + 284s foo 994610 C Y + 284s foo 998107 - T + 284s foo 999725 G R + 284s [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.2556.smaltmap.smalt_index foo1.fasta 284s # Command line: smalt index -k 13 -s 2 out.bam.tmp.2556.smaltmap.smalt_index foo1.fasta 284s # Reading sequences ... 284s # Writing sequence set ... 284s # Setting up hash index with collisions ... 284s # word length = 13 bases, skip step = 2 bases ... 284s # number of bits for key = 18 with 0 perfect bits 284s # Counting keys ... 284s # Counting k-tuples ... 284s # Allocating k-tuple arrays ... 284s # Counting k-tuple occurrences ... 284s # Setting the k-tuple positions in index ... 284s # Hash table is set up. 284s # =-=-=-=-= Hash Index Stats =-=-=-=-= 284s # Hash index with collisions. 284s # Word length: 13 bases 284s # Skip step: 2 bases 284s # Number of hash keys: 262144 284s # Number of word positions: 499970 284s # Number of different words: 498076 284s # Maximum number of words per key: 11 284s # Number of keys without words: 39377 284s # =-=-= End of Hash Index Stats =-=-= 284s # Writing table to file ... 284s [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.2556.smaltmap.smalt_sample out.bam.tmp.2556.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 284s # smalt: Total elapsed wall clock time: 0 seconds 284s # Command line: smalt sample -u 1000 -o out.bam.tmp.2556.smaltmap.smalt_sample out.bam.tmp.2556.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 284s # Opening read files ... 284s # Reading reference sequences ... 284s # Reading hash table ... 284s # =-=-=-=-= Hash Index Stats =-=-=-=-= 284s # Hash index with collisions. 284s # Word length: 13 bases 284s # Skip step: 2 bases 284s # Number of hash keys: 262144 284s # Number of word positions: 499970 284s # Number of different words: 498076 284s # Maximum number of words per key: 11 284s # Number of keys without words: 39377 284s # =-=-= End of Hash Index Stats =-=-= 284s # Check of read pairs ok ... 284s # Mate names match ... 284s # Sampling insert size distribution ... 287s # Processed 9999 read pairs. 287s # smalt: Time spent setting up hash index:0 seconds 287s # smalt: Time spent mapping reads:3 seconds 287s # smalt: Total elapsed wall clock time: 3 seconds 287s [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2556.smaltmap.smalt_sample -f samsoft out.bam.tmp.2556.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.2556.smaltmap.raw.bam 287s # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2556.smaltmap.smalt_sample -f samsoft out.bam.tmp.2556.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 287s # Reading distribution of insert sizes from file ... 287s # Sampled histogram 287s # Smoothed histogram 287s # Opening read files ... 287s # Reading reference sequences ... 287s # Reading hash table ... 287s # =-=-=-=-= Hash Index Stats =-=-=-=-= 287s # Hash index with collisions. 287s # Word length: 13 bases 287s # Skip step: 2 bases 287s # Number of hash keys: 262144 287s # Number of word positions: 499970 287s # Number of different words: 498076 287s # Maximum number of words per key: 11 287s # Number of keys without words: 39377 287s # =-=-= End of Hash Index Stats =-=-= 287s # Processing query reads ... 301s # Processed 10000 read pairs. 301s # smalt: Time spent setting up hash index:0 seconds 301s # smalt: Time spent mapping reads:14 seconds 301s # smalt: Total elapsed wall clock time: 14 seconds 301s [REAPR smaltmap] Running: samtools sort out.bam.tmp.2556.smaltmap.raw.bam -O bam -o out.bam.tmp.2556.smaltmap.raw.bam.sort.bam 301s [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.2556.smaltmap.raw.bam.sort.bam out.bam.tmp.2556.smaltmap.rmdup.bam 301s [bam_rmdup_core] processing reference foo... 302s [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' 302s [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.2556.smaltmap.header 302s [REAPR smaltmap] Running: samtools view -H out.bam.tmp.2556.smaltmap.rmdup.bam >> out.bam.tmp.2556.smaltmap.header 302s [REAPR smaltmap] Running: samtools reheader out.bam.tmp.2556.smaltmap.header out.bam.tmp.2556.smaltmap.rmdup.bam > out.bam 302s [REAPR smaltmap] Running: samtools index out.bam 302s [REAPR smaltmap] Running: rm out.bam.tmp.2556.smaltmap.* 302s Running reapr version 1.0.18 pipeline: 302s reapr foo1.fasta out.bam result 302s [REAPR pipeline] Running facheck 302s [REAPR pipeline] Running preprocess 303s [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases 303s [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases 303s [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases 303s [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases 304s [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation 308s [REAPR pipeline] Running stats 321s [REAPR pipeline] Running fcdrate 323s [REAPR pipeline] Running score 326s [REAPR pipeline] Running break 326s [REAPR pipeline] Running summary 327s autopkgtest [18:43:41]: test test-example: -----------------------] 327s test-example PASS 327s autopkgtest [18:43:41]: test test-example: - - - - - - - - - - results - - - - - - - - - - 328s autopkgtest [18:43:42]: @@@@@@@@@@@@@@@@@@@@ summary 328s test-example PASS 345s nova [W] Using flock in prodstack6-s390x 345s Creating nova instance adt-plucky-s390x-reapr-20250315-183814-juju-7f2275-prod-proposed-migration-environment-2-ce5fe76d-b24c-4f48-8342-2141e64d8ac9 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 345s nova [W] Timed out waiting for 9a3e6789-b5de-4233-bb5f-9040914d715f to get deleted.