0s autopkgtest [16:10:13]: starting date and time: 2025-03-15 16:10:13+0000 0s autopkgtest [16:10:13]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:10:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x24dbuz6/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-10.secgroup --name adt-plucky-arm64-reapr-20250315-161013-juju-7f2275-prod-proposed-migration-environment-2-68c94139-5575-491b-8c30-b3a9c5505f28 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 200s autopkgtest [16:13:33]: testbed dpkg architecture: arm64 200s autopkgtest [16:13:33]: testbed apt version: 2.9.33 200s autopkgtest [16:13:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 201s autopkgtest [16:13:34]: testbed release detected to be: None 201s autopkgtest [16:13:34]: updating testbed package index (apt update) 202s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 202s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 202s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 202s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 202s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 203s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 203s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 203s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 203s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 203s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 203s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 203s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 203s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 203s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 204s Fetched 1078 kB in 2s (626 kB/s) 204s Reading package lists... 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 206s Calculating upgrade... 206s Calculating upgrade... 207s The following packages will be upgraded: 207s pinentry-curses python3-jinja2 strace 207s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 207s Need to get 647 kB of archives. 207s After this operation, 11.3 kB of additional disk space will be used. 207s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 208s Fetched 647 kB in 1s (518 kB/s) 209s (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 ... 117701 files and directories currently installed.) 209s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 209s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 209s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 209s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 209s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 209s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 209s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 209s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 209s Setting up strace (6.13+ds-1ubuntu1) ... 209s Processing triggers for man-db (2.13.0-1) ... 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s Solving dependencies... 211s The following packages will be REMOVED: 211s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 211s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 211s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 211s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 211s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 211s After this operation, 267 MB disk space will be freed. 211s (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 ... 117701 files and directories currently installed.) 211s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 211s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 211s Removing libpython3.12t64:arm64 (3.12.9-1) ... 211s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 212s Removing libnsl2:arm64 (1.3.0-3build3) ... 212s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 212s Removing libunwind8:arm64 (1.6.2-3.1) ... 212s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 212s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 214s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 214s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 214s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 214s /etc/kernel/postrm.d/initramfs-tools: 214s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 215s /etc/kernel/postrm.d/zz-flash-kernel: 215s flash-kernel: Kernel 6.11.0-8-generic has been removed. 215s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 215s /etc/kernel/postrm.d/zz-update-grub: 215s Sourcing file `/etc/default/grub' 215s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 215s Generating grub configuration file ... 215s Found linux image: /boot/vmlinuz-6.14.0-10-generic 215s Found initrd image: /boot/initrd.img-6.14.0-10-generic 216s Warning: os-prober will not be executed to detect other bootable partitions. 216s Systems on them will not be added to the GRUB boot configuration. 216s Check GRUB_DISABLE_OS_PROBER documentation entry. 216s Adding boot menu entry for UEFI Firmware Settings ... 216s done 216s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 216s Processing triggers for libc-bin (2.41-1ubuntu1) ... 216s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81650 files and directories currently installed.) 216s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 216s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 217s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 217s autopkgtest [16:13:50]: upgrading testbed (apt dist-upgrade and autopurge) 217s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 218s Starting 2 pkgProblemResolver with broken count: 0 218s Done 219s Entering ResolveByKeep 219s 220s Calculating upgrade... 220s The following packages will be upgraded: 220s libc-bin libc-dev-bin libc6 libc6-dev locales 220s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 220s Need to get 9530 kB of archives. 220s After this operation, 0 B of additional disk space will be used. 220s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 223s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 226s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 226s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 231s Preconfiguring packages ... 231s Fetched 9530 kB in 11s (894 kB/s) 231s (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 ... 81647 files and directories currently installed.) 231s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 231s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 231s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 231s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 231s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 232s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 232s Setting up libc6:arm64 (2.41-1ubuntu2) ... 232s (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 ... 81647 files and directories currently installed.) 232s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 232s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 232s Setting up libc-bin (2.41-1ubuntu2) ... 232s (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 ... 81647 files and directories currently installed.) 232s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 232s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 232s Setting up locales (2.41-1ubuntu2) ... 233s Generating locales (this might take a while)... 235s en_US.UTF-8... done 235s Generation complete. 235s Setting up libc-dev-bin (2.41-1ubuntu2) ... 235s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 235s Processing triggers for man-db (2.13.0-1) ... 236s Processing triggers for systemd (257.3-1ubuntu3) ... 237s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s Starting pkgProblemResolver with broken count: 0 238s Starting 2 pkgProblemResolver with broken count: 0 238s Done 238s Solving dependencies... 239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 239s autopkgtest [16:14:12]: rebooting testbed after setup commands that affected boot 262s autopkgtest [16:14:35]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 265s autopkgtest [16:14:38]: @@@@@@@@@@@@@@@@@@@@ apt-source reapr 268s Get:1 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (dsc) [2160 B] 268s Get:2 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (tar) [74.6 kB] 268s Get:3 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (diff) [320 kB] 268s gpgv: Signature made Sat Dec 21 22:15:37 2024 UTC 268s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 268s gpgv: issuer "tille@debian.org" 268s gpgv: Can't check signature: No public key 268s dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-7.dsc: no acceptable signature found 268s autopkgtest [16:14:41]: testing package reapr version 1.0.18+dfsg-7 269s autopkgtest [16:14:42]: build not needed 269s autopkgtest [16:14:42]: test test-example: preparing testbed 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 270s Starting pkgProblemResolver with broken count: 0 270s Starting 2 pkgProblemResolver with broken count: 0 270s Done 271s The following NEW packages will be installed: 271s bamtools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 271s libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 libdeflate0 271s libfile-copy-link-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 271s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 271s libjpeg8 libjsoncpp26 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 271s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 271s libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 271s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base 271s r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools 271s r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix 271s r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial 271s r-cran-survival r-recommended reapr samtools smalt snpomatic tabix unzip 271s x11-common xdg-utils zip 271s 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. 271s Need to get 63.7 MB of archives. 271s After this operation, 120 MB of additional disk space will be used. 271s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-6build1 [132 kB] 271s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libjsoncpp26 arm64 1.9.6-3 [78.7 kB] 271s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 bamtools arm64 2.5.2+dfsg-6build1 [159 kB] 271s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 272s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 273s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 273s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 273s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 273s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbambamc0 arm64 0.0.50-6build1 [38.4 kB] 273s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 273s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 274s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 274s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 274s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 274s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 274s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 274s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 274s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfile-copy-link-perl all 0.200-1 [12.8 kB] 274s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 275s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 275s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 275s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 275s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 275s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 276s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 276s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 276s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 276s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 276s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 279s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 279s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 279s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 279s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 279s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 279s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 279s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 279s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 279s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 279s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 279s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtabixpp0t64 arm64 1.1.2-2.1build1 [10.0 kB] 279s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 280s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 280s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 281s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 281s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 281s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 281s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 282s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 282s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 282s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 282s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 282s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 314s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-boot all 1.3-31-1 [635 kB] 315s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cluster arm64 2.1.8-1 [568 kB] 315s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-foreign arm64 0.8.88-1 [243 kB] 316s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 317s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-kernsmooth arm64 2.23-26-1 [93.3 kB] 317s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 319s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 322s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 326s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 330s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 339s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 340s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-class arm64 7.3-23-1 [90.5 kB] 340s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 340s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 341s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-codetools all 0.2-20-1 [90.5 kB] 341s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-recommended all 4.4.3-1 [2630 B] 341s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base all 4.4.3-1 [9290 B] 341s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 342s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 smalt arm64 0.7.6-13 [95.2 kB] 342s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 snpomatic arm64 1.0-7 [78.4 kB] 342s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 tabix arm64 1.21+ds-1 [527 kB] 342s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 reapr arm64 1.0.18+dfsg-7 [186 kB] 343s Preconfiguring packages ... 343s Fetched 63.7 MB in 1min 12s (888 kB/s) 343s Selecting previously unselected package libbamtools2.5.2:arm64. 343s (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 ... 81647 files and directories currently installed.) 343s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-6build1_arm64.deb ... 343s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-6build1) ... 343s Selecting previously unselected package libjsoncpp26:arm64. 343s Preparing to unpack .../01-libjsoncpp26_1.9.6-3_arm64.deb ... 343s Unpacking libjsoncpp26:arm64 (1.9.6-3) ... 343s Selecting previously unselected package bamtools. 343s Preparing to unpack .../02-bamtools_2.5.2+dfsg-6build1_arm64.deb ... 343s Unpacking bamtools (2.5.2+dfsg-6build1) ... 343s Selecting previously unselected package fonts-dejavu-mono. 343s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 343s Unpacking fonts-dejavu-mono (2.37-8) ... 343s Selecting previously unselected package fonts-dejavu-core. 343s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 343s Unpacking fonts-dejavu-core (2.37-8) ... 343s Selecting previously unselected package fontconfig-config. 343s Preparing to unpack .../05-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 344s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 344s Selecting previously unselected package libfontconfig1:arm64. 344s Preparing to unpack .../06-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 344s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 344s Selecting previously unselected package fontconfig. 344s Preparing to unpack .../07-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 344s Unpacking fontconfig (2.15.0-2ubuntu1) ... 344s Selecting previously unselected package libbambamc0:arm64. 344s Preparing to unpack .../08-libbambamc0_0.0.50-6build1_arm64.deb ... 344s Unpacking libbambamc0:arm64 (0.0.50-6build1) ... 344s Selecting previously unselected package libblas3:arm64. 344s Preparing to unpack .../09-libblas3_3.12.1-2_arm64.deb ... 344s Unpacking libblas3:arm64 (3.12.1-2) ... 344s Selecting previously unselected package libpixman-1-0:arm64. 344s Preparing to unpack .../10-libpixman-1-0_0.44.0-3_arm64.deb ... 344s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 344s Selecting previously unselected package libxcb-render0:arm64. 344s Preparing to unpack .../11-libxcb-render0_1.17.0-2_arm64.deb ... 344s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 344s Selecting previously unselected package libxcb-shm0:arm64. 344s Preparing to unpack .../12-libxcb-shm0_1.17.0-2_arm64.deb ... 344s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 344s Selecting previously unselected package libxrender1:arm64. 344s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 344s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 344s Selecting previously unselected package libcairo2:arm64. 344s Preparing to unpack .../14-libcairo2_1.18.2-2_arm64.deb ... 344s Unpacking libcairo2:arm64 (1.18.2-2) ... 344s Selecting previously unselected package libdatrie1:arm64. 344s Preparing to unpack .../15-libdatrie1_0.2.13-3build1_arm64.deb ... 344s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 344s Selecting previously unselected package libdeflate0:arm64. 344s Preparing to unpack .../16-libdeflate0_1.23-1_arm64.deb ... 344s Unpacking libdeflate0:arm64 (1.23-1) ... 344s Selecting previously unselected package libfile-copy-link-perl. 344s Preparing to unpack .../17-libfile-copy-link-perl_0.200-1_all.deb ... 344s Unpacking libfile-copy-link-perl (0.200-1) ... 344s Selecting previously unselected package libgfortran5:arm64. 344s Preparing to unpack .../18-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 344s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 344s Selecting previously unselected package libgomp1:arm64. 344s Preparing to unpack .../19-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 344s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 344s Selecting previously unselected package libgraphite2-3:arm64. 344s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 344s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 344s Selecting previously unselected package libharfbuzz0b:arm64. 344s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_arm64.deb ... 344s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 344s Selecting previously unselected package libhtscodecs2:arm64. 344s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_arm64.deb ... 344s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 344s Selecting previously unselected package libhts3t64:arm64. 344s Preparing to unpack .../23-libhts3t64_1.21+ds-1_arm64.deb ... 344s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 344s Selecting previously unselected package x11-common. 344s Preparing to unpack .../24-x11-common_1%3a7.7+23ubuntu3_all.deb ... 344s Unpacking x11-common (1:7.7+23ubuntu3) ... 344s Selecting previously unselected package libice6:arm64. 344s Preparing to unpack .../25-libice6_2%3a1.1.1-1_arm64.deb ... 344s Unpacking libice6:arm64 (2:1.1.1-1) ... 344s Selecting previously unselected package libjpeg-turbo8:arm64. 345s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 345s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 345s Selecting previously unselected package libjpeg8:arm64. 345s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_arm64.deb ... 345s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 345s Selecting previously unselected package liblapack3:arm64. 345s Preparing to unpack .../28-liblapack3_3.12.1-2_arm64.deb ... 345s Unpacking liblapack3:arm64 (3.12.1-2) ... 345s Selecting previously unselected package liblerc4:arm64. 345s Preparing to unpack .../29-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 345s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 345s Selecting previously unselected package libthai-data. 345s Preparing to unpack .../30-libthai-data_0.1.29-2build1_all.deb ... 345s Unpacking libthai-data (0.1.29-2build1) ... 345s Selecting previously unselected package libthai0:arm64. 345s Preparing to unpack .../31-libthai0_0.1.29-2build1_arm64.deb ... 345s Unpacking libthai0:arm64 (0.1.29-2build1) ... 345s Selecting previously unselected package libpango-1.0-0:arm64. 345s Preparing to unpack .../32-libpango-1.0-0_1.56.2-1_arm64.deb ... 345s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ... 345s Selecting previously unselected package libpangoft2-1.0-0:arm64. 345s Preparing to unpack .../33-libpangoft2-1.0-0_1.56.2-1_arm64.deb ... 345s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ... 345s Selecting previously unselected package libpangocairo-1.0-0:arm64. 345s Preparing to unpack .../34-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 345s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 345s Selecting previously unselected package libpaper2:arm64. 345s Preparing to unpack .../35-libpaper2_2.2.5-0.3_arm64.deb ... 345s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 345s Selecting previously unselected package libpaper-utils. 345s Preparing to unpack .../36-libpaper-utils_2.2.5-0.3_arm64.deb ... 345s Unpacking libpaper-utils (2.2.5-0.3) ... 345s Selecting previously unselected package libsharpyuv0:arm64. 345s Preparing to unpack .../37-libsharpyuv0_1.5.0-0.1_arm64.deb ... 345s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 345s Selecting previously unselected package libsm6:arm64. 345s Preparing to unpack .../38-libsm6_2%3a1.2.4-1_arm64.deb ... 345s Unpacking libsm6:arm64 (2:1.2.4-1) ... 345s Selecting previously unselected package libtabixpp0t64:arm64. 345s Preparing to unpack .../39-libtabixpp0t64_1.1.2-2.1build1_arm64.deb ... 345s Unpacking libtabixpp0t64:arm64 (1.1.2-2.1build1) ... 345s Selecting previously unselected package libtcl8.6:arm64. 345s Preparing to unpack .../40-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 345s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 345s Selecting previously unselected package libjbig0:arm64. 345s Preparing to unpack .../41-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 345s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 345s Selecting previously unselected package libwebp7:arm64. 345s Preparing to unpack .../42-libwebp7_1.5.0-0.1_arm64.deb ... 345s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 345s Selecting previously unselected package libtiff6:arm64. 345s Preparing to unpack .../43-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 345s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 345s Selecting previously unselected package libxft2:arm64. 345s Preparing to unpack .../44-libxft2_2.3.6-1build1_arm64.deb ... 345s Unpacking libxft2:arm64 (2.3.6-1build1) ... 345s Selecting previously unselected package libxss1:arm64. 345s Preparing to unpack .../45-libxss1_1%3a1.2.3-1build3_arm64.deb ... 345s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 345s Selecting previously unselected package libtk8.6:arm64. 345s Preparing to unpack .../46-libtk8.6_8.6.16-1_arm64.deb ... 345s Unpacking libtk8.6:arm64 (8.6.16-1) ... 345s Selecting previously unselected package libxt6t64:arm64. 345s Preparing to unpack .../47-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 345s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 345s Selecting previously unselected package zip. 345s Preparing to unpack .../48-zip_3.0-14ubuntu2_arm64.deb ... 345s Unpacking zip (3.0-14ubuntu2) ... 345s Selecting previously unselected package unzip. 345s Preparing to unpack .../49-unzip_6.0-28ubuntu6_arm64.deb ... 345s Unpacking unzip (6.0-28ubuntu6) ... 345s Selecting previously unselected package xdg-utils. 345s Preparing to unpack .../50-xdg-utils_1.2.1-2ubuntu1_all.deb ... 345s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 346s Selecting previously unselected package r-base-core. 346s Preparing to unpack .../51-r-base-core_4.4.3-1_arm64.deb ... 346s Unpacking r-base-core (4.4.3-1) ... 346s Selecting previously unselected package r-cran-boot. 346s Preparing to unpack .../52-r-cran-boot_1.3-31-1_all.deb ... 346s Unpacking r-cran-boot (1.3-31-1) ... 346s Selecting previously unselected package r-cran-cluster. 346s Preparing to unpack .../53-r-cran-cluster_2.1.8-1_arm64.deb ... 346s Unpacking r-cran-cluster (2.1.8-1) ... 346s Selecting previously unselected package r-cran-foreign. 346s Preparing to unpack .../54-r-cran-foreign_0.8.88-1_arm64.deb ... 346s Unpacking r-cran-foreign (0.8.88-1) ... 346s Selecting previously unselected package r-cran-mass. 346s Preparing to unpack .../55-r-cran-mass_7.3-64-1_arm64.deb ... 346s Unpacking r-cran-mass (7.3-64-1) ... 346s Selecting previously unselected package r-cran-kernsmooth. 346s Preparing to unpack .../56-r-cran-kernsmooth_2.23-26-1_arm64.deb ... 346s Unpacking r-cran-kernsmooth (2.23-26-1) ... 346s Selecting previously unselected package r-cran-lattice. 346s Preparing to unpack .../57-r-cran-lattice_0.22-6-1_arm64.deb ... 346s Unpacking r-cran-lattice (0.22-6-1) ... 346s Selecting previously unselected package r-cran-nlme. 346s Preparing to unpack .../58-r-cran-nlme_3.1.167-1_arm64.deb ... 346s Unpacking r-cran-nlme (3.1.167-1) ... 346s Selecting previously unselected package r-cran-matrix. 346s Preparing to unpack .../59-r-cran-matrix_1.7-3-1_arm64.deb ... 346s Unpacking r-cran-matrix (1.7-3-1) ... 346s Selecting previously unselected package r-cran-mgcv. 346s Preparing to unpack .../60-r-cran-mgcv_1.9-1-1_arm64.deb ... 346s Unpacking r-cran-mgcv (1.9-1-1) ... 346s Selecting previously unselected package r-cran-survival. 346s Preparing to unpack .../61-r-cran-survival_3.8-3-1_arm64.deb ... 346s Unpacking r-cran-survival (3.8-3-1) ... 346s Selecting previously unselected package r-cran-rpart. 346s Preparing to unpack .../62-r-cran-rpart_4.1.24-1_arm64.deb ... 346s Unpacking r-cran-rpart (4.1.24-1) ... 346s Selecting previously unselected package r-cran-class. 346s Preparing to unpack .../63-r-cran-class_7.3-23-1_arm64.deb ... 346s Unpacking r-cran-class (7.3-23-1) ... 346s Selecting previously unselected package r-cran-nnet. 347s Preparing to unpack .../64-r-cran-nnet_7.3-20-1_arm64.deb ... 347s Unpacking r-cran-nnet (7.3-20-1) ... 347s Selecting previously unselected package r-cran-spatial. 347s Preparing to unpack .../65-r-cran-spatial_7.3-18-1_arm64.deb ... 347s Unpacking r-cran-spatial (7.3-18-1) ... 347s Selecting previously unselected package r-cran-codetools. 347s Preparing to unpack .../66-r-cran-codetools_0.2-20-1_all.deb ... 347s Unpacking r-cran-codetools (0.2-20-1) ... 347s Selecting previously unselected package r-recommended. 347s Preparing to unpack .../67-r-recommended_4.4.3-1_all.deb ... 347s Unpacking r-recommended (4.4.3-1) ... 347s Selecting previously unselected package r-base. 347s Preparing to unpack .../68-r-base_4.4.3-1_all.deb ... 347s Unpacking r-base (4.4.3-1) ... 347s Selecting previously unselected package samtools. 347s Preparing to unpack .../69-samtools_1.21-1_arm64.deb ... 347s Unpacking samtools (1.21-1) ... 347s Selecting previously unselected package smalt. 347s Preparing to unpack .../70-smalt_0.7.6-13_arm64.deb ... 347s Unpacking smalt (0.7.6-13) ... 347s Selecting previously unselected package snpomatic. 347s Preparing to unpack .../71-snpomatic_1.0-7_arm64.deb ... 347s Unpacking snpomatic (1.0-7) ... 347s Selecting previously unselected package tabix. 347s Preparing to unpack .../72-tabix_1.21+ds-1_arm64.deb ... 347s Unpacking tabix (1.21+ds-1) ... 347s Selecting previously unselected package reapr. 347s Preparing to unpack .../73-reapr_1.0.18+dfsg-7_arm64.deb ... 347s Unpacking reapr (1.0.18+dfsg-7) ... 347s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 347s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 347s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 347s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 347s Setting up libfile-copy-link-perl (0.200-1) ... 347s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 347s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 347s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 347s Setting up libxcb-render0:arm64 (1.17.0-2) ... 347s Setting up unzip (6.0-28ubuntu6) ... 347s Setting up x11-common (1:7.7+23ubuntu3) ... 347s Setting up libdeflate0:arm64 (1.23-1) ... 347s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 347s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 347s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 347s Setting up zip (3.0-14ubuntu2) ... 347s Setting up libblas3:arm64 (3.12.1-2) ... 347s 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 347s Setting up libjsoncpp26:arm64 (1.9.6-3) ... 347s Setting up libbambamc0:arm64 (0.0.50-6build1) ... 347s Setting up fonts-dejavu-mono (2.37-8) ... 347s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 347s Setting up fonts-dejavu-core (2.37-8) ... 347s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 347s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-6build1) ... 347s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 347s Setting up libwebp7:arm64 (1.5.0-0.1) ... 347s Setting up bamtools (2.5.2+dfsg-6build1) ... 347s Setting up snpomatic (1.0-7) ... 347s Setting up libhts3t64:arm64 (1.21+ds-1) ... 347s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 347s Setting up libthai-data (0.1.29-2build1) ... 347s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 347s Setting up libpaper2:arm64 (2.2.5-0.3) ... 347s Setting up tabix (1.21+ds-1) ... 347s Setting up xdg-utils (1.2.1-2ubuntu1) ... 347s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 347s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 347s Setting up smalt (0.7.6-13) ... 347s Setting up libice6:arm64 (2:1.1.1-1) ... 347s Setting up liblapack3:arm64 (3.12.1-2) ... 347s 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 347s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 348s Setting up libpaper-utils (2.2.5-0.3) ... 348s Setting up samtools (1.21-1) ... 348s Setting up libthai0:arm64 (0.1.29-2build1) ... 348s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 348s Setting up libtabixpp0t64:arm64 (1.1.2-2.1build1) ... 348s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 348s Setting up libsm6:arm64 (2:1.2.4-1) ... 348s Setting up fontconfig (2.15.0-2ubuntu1) ... 350s Regenerating fonts cache... done. 350s Setting up libxft2:arm64 (2.3.6-1build1) ... 350s Setting up libtk8.6:arm64 (8.6.16-1) ... 350s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 350s Setting up libcairo2:arm64 (1.18.2-2) ... 350s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 350s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 350s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 350s Setting up r-base-core (4.4.3-1) ... 350s Creating config file /etc/R/Renviron with new version 350s Setting up r-cran-lattice (0.22-6-1) ... 350s Setting up r-cran-nlme (3.1.167-1) ... 350s Setting up r-cran-cluster (2.1.8-1) ... 350s Setting up r-cran-nnet (7.3-20-1) ... 350s Setting up r-cran-codetools (0.2-20-1) ... 350s Setting up r-cran-boot (1.3-31-1) ... 350s Setting up r-cran-spatial (7.3-18-1) ... 350s Setting up r-cran-mass (7.3-64-1) ... 350s Setting up r-cran-foreign (0.8.88-1) ... 350s Setting up r-cran-matrix (1.7-3-1) ... 350s Setting up r-cran-kernsmooth (2.23-26-1) ... 350s Setting up r-cran-mgcv (1.9-1-1) ... 350s Setting up r-cran-class (7.3-23-1) ... 350s Setting up r-cran-survival (3.8-3-1) ... 350s Setting up r-cran-rpart (4.1.24-1) ... 350s Setting up r-recommended (4.4.3-1) ... 350s Setting up r-base (4.4.3-1) ... 350s Setting up reapr (1.0.18+dfsg-7) ... 350s Processing triggers for man-db (2.13.0-1) ... 351s Processing triggers for install-info (7.1.1-1) ... 352s Processing triggers for libc-bin (2.41-1ubuntu2) ... 353s autopkgtest [16:16:06]: test test-example: [----------------------- 353s [wgsim] seed = 42 353s [wgsim_core] calculating the total length of the reference sequence... 353s [wgsim_core] 1 sequences, total length: 1000111 353s foo 1384 T K + 353s foo 4961 T W + 353s foo 5885 - T - 353s foo 9598 A C - 353s foo 10177 G R + 353s foo 11305 G K + 353s foo 11592 G R + 353s foo 13931 T - - 353s foo 15907 C A - 353s foo 17264 G K + 353s foo 17780 A - - 353s foo 18711 A W + 353s foo 19249 T W + 353s foo 19522 C S + 353s foo 23053 T K + 353s foo 23681 A R + 353s foo 23730 C S + 353s foo 24075 G S + 353s foo 24555 G C - 353s foo 26775 G K + 353s foo 26896 C M + 353s foo 27253 G K + 353s foo 28210 T Y + 353s foo 28224 A W + 353s foo 28377 - G + 353s foo 29035 G K + 353s foo 29898 C M + 353s foo 30274 A R + 353s foo 30542 G K + 353s foo 31566 A C - 353s foo 32252 - A - 353s foo 33303 T K + 353s foo 33390 - G + 353s foo 34073 A R + 353s foo 34171 G R + 353s foo 34718 T Y + 353s foo 34801 - C + 353s foo 35204 T W + 353s foo 35342 G S + 353s foo 35489 G T - 353s foo 36153 A M + 353s foo 36273 C S + 353s foo 37356 G T - 353s foo 37596 C S + 353s foo 39308 T - - 353s foo 40333 C G - 353s foo 42295 T K + 353s foo 42372 T Y + 353s foo 44433 C G - 353s foo 44630 - AG + 353s foo 44902 T C - 353s foo 47156 C A - 353s foo 48210 C M + 353s foo 48390 A R + 353s foo 49652 C M + 353s foo 52739 T Y + 353s foo 52858 A M + 353s foo 54737 A G - 353s foo 55306 C T - 353s foo 55434 C T - 353s foo 59204 A W + 353s foo 59300 G C - 353s foo 59335 T Y + 353s foo 59444 T - - 353s foo 59531 C S + 353s foo 59766 C Y + 353s foo 61950 C S + 353s foo 62887 G S + 353s foo 63390 A G - 353s foo 64365 G K + 353s foo 64703 C S + 353s foo 64932 C Y + 353s foo 68383 - CG + 353s foo 68464 A W + 353s foo 68727 A W + 353s foo 69080 A M + 353s foo 72071 T C - 353s foo 72720 - G - 353s foo 73354 C T - 353s foo 73637 G T - 353s foo 74741 A M + 353s foo 75101 C T - 353s foo 75207 T K + 353s foo 76400 T Y + 353s foo 76780 A C - 353s foo 77172 A W + 353s foo 78385 C Y + 353s foo 80705 C M + 353s foo 82440 A R + 353s foo 83021 G K + 353s foo 83116 A - - 353s foo 83846 T K + 353s foo 84633 G S + 353s foo 85891 G S + 353s foo 87759 A C - 353s foo 87778 T W + 353s foo 88581 T K + 353s foo 88606 T Y + 353s foo 88880 A G - 353s foo 89945 G C - 353s foo 90728 T K + 353s foo 91798 G R + 353s foo 95957 G C - 353s foo 96173 T W + 353s foo 96665 A M + 353s foo 98019 - G + 353s foo 98131 A M + 353s foo 98669 A R + 353s foo 98719 G T - 353s foo 99062 A W + 353s foo 99590 A T - 353s foo 100532 - TC + 353s foo 103015 A W + 353s foo 103172 G S + 353s foo 103609 G R + 353s foo 106549 T Y + 353s foo 108808 C Y + 353s foo 109191 G C - 353s foo 111686 C G - 353s foo 113436 C A - 353s foo 113763 A W + 353s foo 115671 C T - 353s foo 117460 - A - 353s foo 118193 G - - 353s foo 118585 T K + 353s foo 121219 A M + 353s foo 121876 T K + 353s foo 122071 T A - 353s foo 124918 C G - 353s foo 125300 G S + 353s foo 125967 C S + 353s foo 127443 G S + 353s foo 127565 C Y + 353s foo 128700 C A - 353s foo 129912 G A - 353s foo 130847 T W + 353s foo 131677 G S + 353s foo 132189 T C - 353s foo 135878 CGGC - - 353s foo 136825 T K + 353s foo 138881 TGT - - 353s foo 139288 A W + 353s foo 141054 A W + 353s foo 141055 - T + 353s foo 141101 C S + 353s foo 141404 A R + 353s foo 142698 T C - 353s foo 143990 C A - 353s foo 144167 T Y + 353s foo 144814 C Y + 353s foo 146381 T Y + 353s foo 146393 C A - 353s foo 146510 A C - 353s foo 147182 A W + 353s foo 148783 T C - 353s foo 149068 G S + 353s foo 150208 T K + 353s foo 151554 T W + 353s foo 151709 C G - 353s foo 153072 G R + 353s foo 153307 T Y + 353s foo 154050 G S + 353s foo 154415 C S + 353s foo 154594 G R + 353s foo 155839 G T - 353s foo 156106 G A - 353s foo 159356 T W + 353s foo 159926 A W + 353s foo 160303 T K + 353s foo 161323 C Y + 353s foo 161904 G S + 353s foo 162533 - ACC - 353s foo 164738 C G - 353s foo 165413 A R + 353s foo 166944 C M + 353s foo 167464 T Y + 353s foo 168420 T C - 353s foo 168579 A M + 353s foo 168787 T W + 353s foo 168959 A T - 353s foo 169884 G S + 353s foo 170032 G T - 353s foo 172058 G K + 353s foo 174942 A R + 353s foo 175014 G K + 353s foo 178406 G A - 353s foo 179028 - A + 353s foo 182394 C M + 353s foo 182735 T Y + 353s foo 183384 T K + 353s foo 183893 - AT - 353s foo 185360 G A - 353s foo 185538 - G - 353s foo 187948 G S + 353s foo 188120 T G - 353s foo 188179 T W + 353s foo 188316 T Y + 353s foo 189963 - G + 353s foo 190093 C Y + 353s foo 192220 C M + 353s foo 192368 A W + 353s foo 192782 T K + 353s foo 193307 A R + 353s foo 193501 G K + 353s foo 194276 G S + 353s foo 194930 C S + 353s foo 196728 A W + 353s foo 197559 G C - 353s foo 198467 T W + 353s foo 199042 C Y + 353s foo 199259 AA - - 353s foo 199687 TT - - 353s foo 200287 C A - 353s foo 200678 A R + 353s foo 201208 C T - 353s foo 201882 A - - 353s foo 204456 T K + 353s foo 206327 G R + 353s foo 207311 G T - 353s foo 209184 G A - 353s foo 209279 C Y + 353s foo 211459 C Y + 353s foo 213807 T Y + 353s foo 213846 T Y + 353s foo 214635 A G - 353s foo 214884 C A - 353s foo 216244 A M + 353s foo 216652 A M + 353s foo 216745 T - - 353s foo 216909 A T - 353s foo 217579 A G - 353s foo 217895 C Y + 353s foo 218870 G K + 353s foo 223098 T A - 353s foo 223283 - C + 353s foo 223666 C A - 353s foo 224011 - C + 353s foo 225681 C S + 353s foo 227345 T C - 353s foo 228778 T G - 353s foo 229926 C - - 353s foo 230778 T K + 353s foo 230939 CG - - 353s foo 231988 CT - - 353s foo 234593 T W + 353s foo 235496 C S + 353s foo 235705 G K + 353s foo 235758 A G - 353s foo 236852 T C - 353s foo 238790 A M + 353s foo 238865 T K + 353s foo 239329 A M + 353s foo 239576 - C + 353s foo 243058 G S + 353s foo 244147 T - - 353s foo 244462 C G - 353s foo 245443 - A + 353s foo 246544 C Y + 353s foo 246744 T W + 353s foo 247473 C M + 353s foo 248129 C T - 353s foo 249060 A C - 353s foo 249515 G T - 353s foo 250138 G S + 353s foo 250567 C A - 353s foo 254381 G R + 353s foo 257864 C M + 353s foo 257879 C Y + 353s foo 259859 A M + 353s foo 260643 C S + 353s foo 261681 C G - 353s foo 262645 T Y + 353s foo 263279 A R + 353s foo 263575 A - - 353s foo 264587 - TA + 353s foo 264689 T K + 353s foo 265758 G K + 353s foo 266272 A M + 353s foo 268550 C M + 353s foo 269986 G S + 353s foo 270321 AC - - 353s foo 273346 C S + 353s foo 275367 C A - 353s foo 277334 C G - 353s foo 277629 G T - 353s foo 278431 C Y + 353s foo 281456 T Y + 353s foo 281556 T G - 353s foo 281737 G K + 353s foo 282290 AC - - 353s foo 282851 - C - 353s foo 284405 A C - 353s foo 288751 A C - 353s foo 290501 TAAA - - 353s foo 291315 A W + 353s foo 291368 C - - 353s foo 292154 A C - 353s foo 292385 C M + 353s foo 292555 G K + 353s foo 297709 G C - 353s foo 298183 A W + 353s foo 298228 T W + 353s foo 299902 T G - 353s foo 302575 A T - 353s foo 304823 G R + 353s foo 305308 T Y + 353s foo 305487 G S + 353s foo 305697 G T - 353s foo 306098 C G - 353s foo 306882 T Y + 353s foo 308201 A M + 353s foo 308833 A T - 353s foo 312033 A - - 353s foo 312895 C G - 353s foo 313889 C - - 353s foo 315109 A R + 353s foo 316083 C - - 353s foo 316466 A R + 353s foo 318040 G C - 353s foo 319446 T C - 353s foo 320236 C S + 353s foo 320652 A - - 353s foo 320716 T K + 353s foo 323644 A - - 353s foo 325359 G T - 353s foo 329476 - CA + 353s foo 329706 T G - 353s foo 330181 T Y + 353s foo 330703 C Y + 353s foo 331315 G S + 353s foo 332351 C A - 353s foo 333408 A R + 353s foo 333468 C S + 353s foo 336247 A G - 353s foo 336586 A M + 353s foo 337364 G K + 353s foo 337686 A T - 353s foo 338043 A - - 353s foo 338292 C G - 353s foo 338962 A C - 353s foo 339353 G K + 353s foo 340647 - A + 353s foo 341705 G R + 353s foo 344283 C M + 353s foo 345898 - AG - 353s foo 347959 T - - 353s foo 349162 C M + 353s foo 352072 T Y + 353s foo 354614 C Y + 353s foo 359304 T - - 353s foo 359312 - G + 353s foo 360972 C S + 353s foo 363857 C Y + 353s foo 366226 A C - 353s foo 367259 C M + 353s foo 372502 T Y + 353s foo 372747 A M + 353s foo 375140 C S + 353s foo 376298 T W + 353s foo 376313 C - - 353s foo 376760 T W + 353s foo 378494 A W + 353s foo 381137 T G - 353s foo 381186 A R + 353s foo 381701 A G - 353s foo 382614 A W + 353s foo 382761 C T - 353s foo 382854 T C - 353s foo 383201 C T - 353s foo 385104 G S + 353s foo 385233 - A + 353s foo 386138 C T - 353s foo 386316 A W + 353s foo 387072 A R + 353s foo 387642 - A + 353s foo 388232 T C - 353s foo 388890 GGG - - 353s foo 390508 C S + 353s foo 390625 C M + 353s foo 391921 C G - 353s foo 395256 G T - 353s foo 395542 G S + 353s foo 397015 A - - 353s foo 397516 C Y + 353s foo 397528 GC - - 353s foo 398152 C T - 353s foo 399802 A W + 353s foo 400972 T K + 353s foo 401419 - T + 353s foo 401477 T W + 353s foo 402437 A M + 353s foo 402722 G R + 353s foo 403452 C M + 353s foo 404234 - A + 353s foo 405344 A W + 353s foo 407040 G S + 353s foo 408483 G R + 353s foo 408586 A C - 353s foo 408721 A R + 353s foo 409494 A M + 353s foo 410078 A G - 353s foo 411170 C A - 353s foo 415342 T Y + 353s foo 416265 C G - 353s foo 417740 C A - 353s foo 418622 C S + 353s foo 420232 A W + 353s foo 420288 T Y + 353s foo 420908 A W + 353s foo 421109 T A - 353s foo 421357 A R + 353s foo 422799 G A - 353s foo 424383 C S + 353s foo 424871 - GCA + 353s foo 427273 T A - 353s foo 429822 C M + 353s foo 429846 T W + 353s foo 432015 A G - 353s foo 432414 G K + 353s foo 433606 C Y + 353s foo 433831 T Y + 353s foo 437721 - A - 353s foo 438402 G - - 353s foo 438799 A T - 353s foo 439422 C M + 353s foo 440734 C A - 353s foo 441840 T G - 353s foo 442021 - C + 353s foo 445021 T A - 353s foo 445591 G A - 353s foo 446138 T W + 353s foo 447757 A W + 353s foo 449156 T - - 353s foo 449161 G K + 353s foo 450114 A W + 353s foo 450688 A W + 353s foo 454421 C G - 353s foo 454718 T Y + 353s foo 455675 TC - - 353s foo 461721 G R + 353s foo 462526 G S + 353s foo 467296 G A - 353s foo 467510 G K + 353s foo 468267 T K + 353s foo 469118 G R + 353s foo 469830 C Y + 353s foo 471073 G T - 353s foo 472056 G A - 353s foo 472773 - A + 353s foo 473046 G R + 353s foo 473188 G A - 353s foo 473742 C - - 353s foo 474789 T A - 353s foo 477763 G R + 353s foo 478246 T W + 353s foo 478975 T G - 353s foo 479038 A R + 353s foo 480275 T Y + 353s foo 480317 G A - 353s foo 481512 T K + 353s foo 482069 G S + 353s foo 482534 A R + 353s foo 483760 C Y + 353s foo 485281 T W + 353s foo 486255 T C - 353s foo 487038 T K + 353s foo 487225 T A - 353s foo 488012 C Y + 353s foo 488795 T C - 353s foo 490241 A R + 353s foo 492595 - CGG + 353s foo 493224 C A - 353s foo 494284 A T - 353s foo 495990 - T - 353s foo 497306 A R + 353s foo 497403 T Y + 353s foo 499569 C Y + 353s foo 499651 T K + 353s foo 503139 T C - 353s foo 504660 A R + 353s foo 508679 C - - 353s foo 513643 G K + 353s foo 515668 CC - - 353s foo 515836 G R + 353s foo 516488 C S + 353s foo 517602 G R + 353s foo 517962 G K + 353s foo 517975 T K + 353s foo 519144 A T - 353s foo 520068 T K + 353s foo 520926 A W + 353s foo 521562 C S + 353s foo 522076 CG - - 353s foo 522838 T Y + 353s foo 523513 - C + 353s foo 523907 - TA + 353s foo 526271 T A - 353s foo 526533 AC - - 353s foo 526767 C Y + 353s foo 528217 C Y + 353s foo 531924 G S + 353s foo 532333 - TT + 353s foo 533132 C M + 353s foo 534689 A T - 353s foo 534779 A W + 353s foo 535594 C A - 353s foo 535795 G R + 353s foo 538368 A R + 353s foo 540879 G K + 353s foo 542530 A - - 353s foo 543620 G R + 353s foo 544733 - C - 353s foo 546300 - TT + 353s foo 548196 A T - 353s foo 548878 C M + 353s foo 548885 G R + 353s foo 549459 T K + 353s foo 550908 A G - 353s foo 551170 A - - 353s foo 553130 T Y + 353s foo 555293 T G - 353s foo 556198 G R + 353s foo 556355 A T - 353s foo 557688 G K + 353s foo 558415 G C - 353s foo 558461 - G + 353s foo 559287 T Y + 353s foo 559465 C M + 353s foo 560184 T W + 353s foo 560252 T W + 353s foo 562579 A M + 353s foo 562961 G A - 353s foo 566986 C A - 353s foo 568134 C A - 353s foo 569698 T C - 353s foo 570180 T K + 353s foo 570451 TG - - 353s foo 570832 - A - 353s foo 571589 A W + 353s foo 572208 C M + 353s foo 572871 C S + 353s foo 574334 G - - 353s foo 575673 T Y + 353s foo 576797 G S + 353s foo 578486 - C - 353s foo 578494 C S + 353s foo 579257 G A - 353s foo 580103 G T - 353s foo 580872 A W + 353s foo 580925 G S + 353s foo 580950 G C - 353s foo 581637 T Y + 353s foo 581654 A G - 353s foo 582538 A T - 353s foo 582691 C M + 353s foo 582938 A W + 353s foo 583104 T K + 353s foo 584763 T W + 353s foo 585723 T W + 353s foo 588253 T Y + 353s foo 588972 T C - 353s foo 589438 - C - 353s foo 591131 C Y + 353s foo 591950 G R + 353s foo 592194 T G - 353s foo 592310 G S + 353s foo 593892 G A - 353s foo 598556 A - - 353s foo 601660 G S + 353s foo 602112 G T - 353s foo 602412 T Y + 353s foo 607282 - C + 353s foo 607394 A M + 353s foo 608438 A T - 353s foo 609255 A W + 353s foo 609365 - T + 353s foo 611161 G K + 353s foo 612224 C G - 353s foo 614493 G R + 353s foo 614601 G A - 353s foo 614607 C Y + 353s foo 619507 C M + 353s foo 619798 T C - 353s foo 621872 C T - 353s foo 622375 C Y + 353s foo 623208 - G - 353s foo 624366 C A - 353s foo 625320 - ACA - 353s foo 626664 - G + 353s foo 627140 T C - 353s foo 627353 G T - 353s foo 628714 T Y + 353s foo 628744 A - - 353s foo 629152 A G - 353s foo 630110 T G - 353s foo 631744 G K + 353s foo 632763 C S + 353s foo 634419 G - - 353s foo 634459 A G - 353s foo 634571 G A - 353s foo 635366 - A + 353s foo 635604 G T - 353s foo 637057 T C - 353s foo 637525 A T - 353s foo 638412 A R + 353s foo 640547 A W + 353s foo 641514 T K + 353s foo 642219 A R + 353s foo 642427 A G - 353s foo 642612 A R + 353s foo 643553 T W + 353s foo 647316 - T + 353s foo 647598 C - - 353s foo 651093 G A - 353s foo 651718 G R + 353s foo 652235 A G - 353s foo 652579 A C - 353s foo 653355 A W + 353s foo 655174 C M + 353s foo 655487 A M + 353s foo 656849 G S + 353s foo 661081 T K + 353s foo 661134 G C - 353s foo 661935 A W + 353s foo 662010 A M + 353s foo 662040 G R + 353s foo 663030 A W + 353s foo 663268 - C + 353s foo 664991 T - - 353s foo 665489 T K + 353s foo 665555 C M + 353s foo 665965 C Y + 353s foo 668725 A C - 353s foo 668834 - G - 353s foo 668873 C S + 353s foo 669654 T W + 353s foo 671041 G S + 353s foo 671485 T W + 353s foo 671690 C M + 353s foo 673022 G R + 353s foo 674137 - T + 353s foo 674782 A C - 353s foo 676373 G T - 353s foo 676793 T C - 353s foo 677409 G S + 353s foo 677536 - AA - 353s foo 677620 G K + 353s foo 677686 C Y + 353s foo 678327 G S + 353s foo 678704 G S + 353s foo 678771 A C - 353s foo 678866 C T - 353s foo 679960 A W + 353s foo 680447 - C + 353s foo 682102 C T - 353s foo 685497 T A - 353s foo 686884 G S + 353s foo 687324 ACA - - 353s foo 687684 - AC + 353s foo 687823 T C - 353s foo 688590 G K + 353s foo 690802 C M + 353s foo 691388 T C - 353s foo 691403 T G - 353s foo 691790 G A - 353s foo 692973 C A - 353s foo 694058 G S + 353s foo 694550 G R + 353s foo 694968 T W + 353s foo 695898 A T - 353s foo 696721 C S + 353s foo 696787 C S + 353s foo 696935 A M + 353s foo 698024 - C + 353s foo 699813 A - - 353s foo 700179 G R + 353s foo 701421 A M + 353s foo 701989 T A - 353s foo 702862 C A - 353s foo 707020 G A - 353s foo 708420 A - - 353s foo 708669 C G - 353s foo 710521 T W + 353s foo 711801 G C - 353s foo 711913 T G - 353s foo 715830 C M + 353s foo 717664 TC - - 353s foo 718845 A W + 353s foo 719069 T Y + 353s foo 719565 A W + 353s foo 721136 T K + 353s foo 726116 T K + 353s foo 727809 T K + 353s foo 728864 G K + 353s foo 728918 G A - 353s foo 730296 - T + 353s foo 731988 C Y + 353s foo 734658 A M + 353s foo 734715 A W + 353s foo 736618 C G - 353s foo 737257 T Y + 353s foo 740864 C A - 353s foo 741640 G - - 353s foo 741859 - TA - 353s foo 742011 T K + 353s foo 742237 A R + 353s foo 742960 G K + 353s foo 743731 G R + 353s foo 743971 A W + 353s foo 744635 T K + 353s foo 746430 C G - 353s foo 746489 - GC - 353s foo 746881 C M + 353s foo 756997 TC - - 353s foo 757776 A M + 353s foo 759870 A T - 353s foo 760224 G K + 353s foo 760799 G C - 353s foo 761692 T C - 353s foo 762569 G S + 353s foo 763140 A G - 353s foo 763842 - T - 353s foo 764192 A M + 353s foo 764334 G A - 353s foo 764889 - AAT + 353s foo 766464 G S + 353s foo 768226 G A - 353s foo 770272 T G - 353s foo 771145 C Y + 353s foo 772209 T A - 353s foo 773672 T K + 353s foo 773932 G C - 353s foo 774658 C S + 353s foo 775969 A M + 353s foo 776816 T G - 353s foo 777591 C Y + 353s foo 777891 A M + 353s foo 778164 C M + 353s foo 778219 T W + 353s foo 779260 G T - 353s foo 779465 A W + 353s foo 779779 G S + 353s foo 780033 G K + 353s foo 783243 C M + 353s foo 783860 A R + 353s foo 788345 A M + 353s foo 789554 G - - 353s foo 790025 G K + 353s foo 791454 T K + 353s foo 792009 C A - 353s foo 792872 C G - 353s foo 794616 T W + 353s foo 795031 G R + 353s foo 796919 C M + 353s foo 797020 G S + 353s foo 797042 G C - 353s foo 797149 G A - 353s foo 797177 A C - 353s foo 799076 G C - 353s foo 799580 G S + 353s foo 800356 A R + 353s foo 802297 G T - 353s foo 802309 T Y + 353s foo 802343 - C + 353s foo 802769 A W + 353s foo 803104 C G - 353s foo 805819 C Y + 353s foo 805972 T Y + 353s foo 807503 T K + 353s foo 807950 C M + 353s foo 807994 - A - 353s foo 809167 A G - 353s foo 809658 A W + 353s foo 810152 A M + 353s foo 811506 G R + 353s foo 813494 A M + 353s foo 814035 G T - 353s foo 814476 A W + 353s foo 819399 T K + 353s foo 820171 T W + 353s foo 820445 G C - 353s foo 822178 C G - 353s foo 822504 C T - 353s foo 823378 C M + 353s foo 823591 CG - - 353s foo 824229 C M + 353s foo 824579 C T - 353s foo 824858 C M + 353s foo 826101 T K + 353s foo 827593 C G - 353s foo 827794 T Y + 353s foo 828228 A M + 353s foo 828367 T K + 353s foo 828788 C M + 353s foo 829002 C Y + 353s foo 830345 C M + 353s foo 831018 C A - 353s foo 831459 T K + 353s foo 832413 A T - 353s foo 832782 T Y + 353s foo 832908 T Y + 353s foo 833130 T - - 353s foo 833142 G S + 353s foo 833241 G A - 353s foo 836727 A T - 353s foo 836829 G S + 353s foo 838452 T G - 353s foo 838543 A T - 353s foo 838605 C M + 353s foo 838954 G C - 353s foo 841829 G K + 353s foo 842324 - TC + 353s foo 842996 - C + 353s foo 844390 C A - 353s foo 844793 A C - 353s foo 844925 C A - 353s foo 845082 G C - 353s foo 846202 G R + 353s foo 846707 A G - 353s foo 848713 G A - 353s foo 849372 C S + 353s foo 849742 G A - 353s foo 850499 C - - 353s foo 850927 GT - - 353s foo 851084 - G + 353s foo 852247 A R + 353s foo 852972 C A - 353s foo 854808 T W + 353s foo 855956 G K + 353s foo 856225 G A - 353s foo 856582 T K + 353s foo 857351 C M + 353s foo 857504 AC - - 353s foo 858324 A T - 353s foo 858858 T C - 353s foo 859488 T Y + 353s foo 862441 T Y + 353s foo 863827 C Y + 353s foo 864165 C A - 353s foo 865997 C M + 353s foo 866370 G S + 353s foo 867653 G S + 353s foo 867722 C Y + 353s foo 868696 C M + 353s foo 869005 T W + 353s foo 869791 T Y + 353s foo 875339 C Y + 353s foo 875347 C M + 353s foo 875584 T G - 353s foo 876780 C T - 353s foo 878368 A C - 353s foo 878916 - CAG + 353s foo 879005 A R + 353s foo 880112 G T - 353s foo 881021 - T - 353s foo 881175 T W + 353s foo 882168 - GGG + 353s foo 882223 - G - 353s foo 883033 TG - - 353s foo 883381 C G - 353s foo 884378 C - - 353s foo 885075 A M + 353s foo 885190 A W + 353s foo 885568 A W + 353s foo 885827 T Y + 353s foo 887610 TG - - 353s foo 889139 G R + 353s foo 890978 T - - 353s foo 891500 C Y + 353s foo 892257 G C - 353s foo 892642 G R + 353s foo 892644 T W + 353s foo 892757 C A - 353s foo 893222 T - - 353s foo 893348 T W + 353s foo 894161 - C - 353s foo 894447 A G - 353s foo 894614 A W + 353s foo 897817 T W + 353s foo 899408 C S + 353s foo 902450 A T - 353s foo 902970 AT - - 353s foo 905836 G K + 353s foo 906524 GA - - 353s foo 907484 A W + 353s foo 907537 C M + 353s foo 908515 G R + 353s foo 908642 C T - 353s foo 911145 T C - 353s foo 912220 T Y + 353s foo 912682 C Y + 353s foo 914260 C S + 353s foo 914757 T Y + 353s foo 916413 G C - 353s foo 916783 T G - 353s foo 917033 G C - 353s foo 917218 A - - 353s foo 918225 G - - 353s foo 918459 A - - 353s foo 918732 A M + 353s foo 919640 TC - - 353s foo 920824 T W + 353s foo 920836 G C - 353s foo 924560 G R + 353s foo 924659 GA - - 353s foo 925868 T A - 353s foo 928254 T G - 353s foo 928369 - A - 353s foo 928641 - AG + 353s foo 929857 C M + 353s foo 930211 T W + 353s foo 930935 C T - 353s foo 931986 A M + 353s foo 932852 G T - 353s foo 933965 T A - 353s foo 935564 A W + 353s foo 936034 T Y + 353s foo 936221 AC - - 353s foo 936670 C S + 353s foo 936704 T A - 353s foo 936786 T W + 353s foo 939218 C S + 353s foo 939312 A W + 353s foo 939467 A W + 353s foo 939934 C S + 353s foo 941603 C Y + 353s foo 942910 A W + 353s foo 944654 T Y + 353s foo 945301 A C - 353s foo 945770 C T - 353s foo 946078 G S + 353s foo 948833 G K + 353s foo 948999 A W + 353s foo 949193 A R + 353s foo 950276 C M + 353s foo 950414 A W + 353s foo 951285 G C - 353s foo 953158 G R + 353s foo 953287 A W + 353s foo 954150 C G - 353s foo 954258 G - - 353s foo 955396 CC - - 353s foo 956490 - AC + 353s foo 958129 A R + 353s foo 959027 T A - 353s foo 959964 A W + 353s foo 962042 A G - 353s foo 962742 C G - 353s foo 963306 T W + 353s foo 963422 G K + 353s foo 964082 G S + 353s foo 965561 C S + 353s foo 966531 T K + 353s foo 967324 T W + 353s foo 968419 - C - 353s foo 969054 G - - 353s foo 969158 G S + 353s foo 972658 C M + 353s foo 974266 T W + 353s foo 974629 G K + 353s foo 975034 A R + 353s foo 975636 T W + 353s foo 977078 - A - 353s foo 978321 G T - 353s foo 978595 C G - 353s foo 979090 C M + 353s foo 983855 TA - - 353s foo 985725 T A - 353s foo 988497 C Y + 353s foo 990171 C M + 353s foo 990804 - CA - 353s foo 990941 T W + 353s foo 991797 A W + 353s foo 992469 A M + 353s foo 994610 C Y + 353s foo 998107 - T + 353s foo 999725 G R + 353s # Command line: smalt index -k 13 -s 2 out.bam.tmp.2522.smaltmap.smalt_index foo1.fasta 353s # Reading sequences ... 353s [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.2522.smaltmap.smalt_index foo1.fasta 353s # Writing sequence set ... 353s # Setting up hash index with collisions ... 353s # word length = 13 bases, skip step = 2 bases ... 353s # number of bits for key = 18 with 0 perfect bits 353s # Counting keys ... 353s # Counting k-tuples ... 354s # Allocating k-tuple arrays ... 354s # Counting k-tuple occurrences ... 354s # Setting the k-tuple positions in index ... 354s # Hash table is set up. 354s # =-=-=-=-= Hash Index Stats =-=-=-=-= 354s # Hash index with collisions. 354s # Word length: 13 bases 354s # Skip step: 2 bases 354s # Number of hash keys: 262144 354s # Number of word positions: 499970 354s # Number of different words: 498076 354s # Maximum number of words per key: 11 354s # Number of keys without words: 39377 354s # =-=-= End of Hash Index Stats =-=-= 354s # Writing table to file ... 354s # smalt: Total elapsed wall clock time: 1 seconds 354s # Command line: smalt sample -u 1000 -o out.bam.tmp.2522.smaltmap.smalt_sample out.bam.tmp.2522.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 354s # Opening read files ... 354s # Reading reference sequences ... 354s # Reading hash table ... 354s # =-=-=-=-= Hash Index Stats =-=-=-=-= 354s # Hash index with collisions. 354s # Word length: 13 bases 354s # Skip step: 2 bases 354s # Number of hash keys: 262144 354s # Number of word positions: 499970 354s # Number of different words: 498076 354s # Maximum number of words per key: 11 354s [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.2522.smaltmap.smalt_sample out.bam.tmp.2522.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 354s # Number of keys without words: 39377 354s # =-=-= End of Hash Index Stats =-=-= 354s # Check of read pairs ok ... 354s # Mate names match ... 354s # Sampling insert size distribution ... 356s # Processed 9999 read pairs. 356s # smalt: Time spent setting up hash index:0 seconds 356s # smalt: Time spent mapping reads:2 seconds 356s # smalt: Total elapsed wall clock time: 2 seconds 356s # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2522.smaltmap.smalt_sample -f samsoft out.bam.tmp.2522.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 356s # Reading distribution of insert sizes from file ... 356s # Sampled histogram 356s # Smoothed histogram 356s # Opening read files ... 356s # Reading reference sequences ... 356s # Reading hash table ... 356s # =-=-=-=-= Hash Index Stats =-=-=-=-= 356s # Hash index with collisions. 356s # Word length: 13 bases 356s # Skip step: 2 bases 356s # Number of hash keys: 262144 356s # Number of word positions: 499970 356s [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2522.smaltmap.smalt_sample -f samsoft out.bam.tmp.2522.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.2522.smaltmap.raw.bam 356s # Number of different words: 498076 356s # Maximum number of words per key: 11 356s # Number of keys without words: 39377 356s # =-=-= End of Hash Index Stats =-=-= 356s # Processing query reads ... 369s # Processed 10000 read pairs. 369s # smalt: Time spent setting up hash index:0 seconds 369s # smalt: Time spent mapping reads:13 seconds 369s # smalt: Total elapsed wall clock time: 13 seconds 369s [REAPR smaltmap] Running: samtools sort out.bam.tmp.2522.smaltmap.raw.bam -O bam -o out.bam.tmp.2522.smaltmap.raw.bam.sort.bam 369s [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.2522.smaltmap.raw.bam.sort.bam out.bam.tmp.2522.smaltmap.rmdup.bam 369s [bam_rmdup_core] processing reference foo... 369s [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' 369s [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.2522.smaltmap.header 369s [REAPR smaltmap] Running: samtools view -H out.bam.tmp.2522.smaltmap.rmdup.bam >> out.bam.tmp.2522.smaltmap.header 369s [REAPR smaltmap] Running: samtools reheader out.bam.tmp.2522.smaltmap.header out.bam.tmp.2522.smaltmap.rmdup.bam > out.bam 369s [REAPR smaltmap] Running: samtools index out.bam 369s [REAPR smaltmap] Running: rm out.bam.tmp.2522.smaltmap.* 369s Running reapr version 1.0.18 pipeline: 369s reapr foo1.fasta out.bam result 369s [REAPR pipeline] Running facheck 369s [REAPR pipeline] Running preprocess 370s [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases 370s [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases 370s [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases 371s [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases 372s [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation 375s [REAPR pipeline] Running stats 386s [REAPR pipeline] Running fcdrate 387s [REAPR pipeline] Running score 391s [REAPR pipeline] Running break 391s [REAPR pipeline] Running summary 391s autopkgtest [16:16:44]: test test-example: -----------------------] 392s autopkgtest [16:16:45]: test test-example: - - - - - - - - - - results - - - - - - - - - - 392s test-example PASS 392s autopkgtest [16:16:45]: @@@@@@@@@@@@@@@@@@@@ summary 392s test-example PASS 411s nova [W] Using flock in prodstack6-arm64 411s Creating nova instance adt-plucky-arm64-reapr-20250315-161013-juju-7f2275-prod-proposed-migration-environment-2-68c94139-5575-491b-8c30-b3a9c5505f28 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 411s nova [W] Timed out waiting for 38ce204d-65d7-4e00-a724-0262ab509940 to get deleted.