0s autopkgtest [17:41:55]: starting date and time: 2024-03-24 17:41:55+0000 0s autopkgtest [17:41:55]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:41:55]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vcsb_nxq/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade reapr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-19.secgroup --name adt-noble-arm64-reapr-20240324-174155-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 96s autopkgtest [17:43:31]: testbed dpkg architecture: arm64 96s autopkgtest [17:43:31]: testbed apt version: 2.7.12 96s autopkgtest [17:43:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 98s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 98s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 98s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 99s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 99s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 99s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 99s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 99s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 99s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 99s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 99s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 105s Fetched 9851 kB in 3s (3225 kB/s) 105s Reading package lists... 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Calculating upgrade... 112s The following packages will be REMOVED: 112s libssl3 112s The following NEW packages will be installed: 112s libssl3t64 112s The following packages have been kept back: 112s curl 112s The following packages will be upgraded: 112s openssl 112s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 112s Need to get 2777 kB of archives. 112s After this operation, 139 kB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 114s Fetched 2777 kB in 1s (3912 kB/s) 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75911 files and directories currently installed.) 114s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 114s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 114s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 114s wget depends on libssl3 (>= 3.0.0). 114s u-boot-tools depends on libssl3 (>= 3.0.0). 114s tnftp depends on libssl3 (>= 3.0.0). 114s tcpdump depends on libssl3 (>= 3.0.0). 114s systemd-resolved depends on libssl3 (>= 3.0.0). 114s systemd depends on libssl3 (>= 3.0.0). 114s sudo depends on libssl3 (>= 3.0.0). 114s sbsigntool depends on libssl3 (>= 3.0.0). 114s rsync depends on libssl3 (>= 3.0.0). 114s python3-cryptography depends on libssl3 (>= 3.0.0). 114s openssh-server depends on libssl3 (>= 3.0.10). 114s openssh-client depends on libssl3 (>= 3.0.10). 114s mtd-utils depends on libssl3 (>= 3.0.0). 114s mokutil depends on libssl3 (>= 3.0.0). 114s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 114s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 114s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 114s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 114s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 114s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 114s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 114s libnvme1 depends on libssl3 (>= 3.0.0). 114s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 114s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 114s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 114s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 114s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 114s kmod depends on libssl3 (>= 3.0.0). 114s dhcpcd-base depends on libssl3 (>= 3.0.0). 114s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 114s 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75911 files and directories currently installed.) 114s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 115s Selecting previously unselected package libssl3t64:arm64. 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75900 files and directories currently installed.) 115s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 115s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 115s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 115s Setting up openssl (3.0.13-0ubuntu2) ... 115s Processing triggers for man-db (2.12.0-3) ... 116s Processing triggers for libc-bin (2.39-0ubuntu6) ... 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 118s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 120s sh: Attempting to set up Debian/Ubuntu apt sources automatically 120s sh: Distribution appears to be Ubuntu 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s eatmydata is already the newest version (131-1). 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s dbus is already the newest version (1.14.10-4ubuntu1). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s rng-tools-debian is already the newest version (2.4). 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s The following packages will be REMOVED: 129s cloud-init* python3-configobj* python3-debconf* 130s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 130s After this operation, 3256 kB disk space will be freed. 130s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75913 files and directories currently installed.) 130s Removing cloud-init (24.1.2-0ubuntu1) ... 131s Removing python3-configobj (5.0.8-3) ... 131s Removing python3-debconf (1.5.86) ... 132s Processing triggers for man-db (2.12.0-3) ... 132s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75524 files and directories currently installed.) 132s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 134s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 135s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 135s invoke-rc.d: policy-rc.d denied execution of try-restart. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 137s linux-generic is already the newest version (6.8.0-11.11+1). 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 137s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 143s Reading package lists... 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s Calculating upgrade... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [17:44:23]: rebooting testbed after setup commands that affected boot 303s autopkgtest [17:46:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 307s autopkgtest [17:47:02]: @@@@@@@@@@@@@@@@@@@@ apt-source reapr 309s Get:1 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (dsc) [2293 B] 309s Get:2 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (tar) [74.6 kB] 309s Get:3 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (diff) [320 kB] 309s gpgv: Signature made Sat Nov 19 21:52:27 2022 UTC 309s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 309s gpgv: issuer "steve.langasek@ubuntu.com" 309s gpgv: Can't check signature: No public key 309s dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-5build2.dsc: no acceptable signature found 310s autopkgtest [17:47:05]: testing package reapr version 1.0.18+dfsg-5build2 310s autopkgtest [17:47:05]: build not needed 310s autopkgtest [17:47:05]: test test-example: preparing testbed 322s Reading package lists... 323s Building dependency tree... 323s Reading state information... 324s Starting pkgProblemResolver with broken count: 0 324s Starting 2 pkgProblemResolver with broken count: 0 324s Done 325s The following additional packages will be installed: 325s bamtools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 325s libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 libdeflate0 325s libfile-copy-link-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 325s libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 libjpeg8 325s libjsoncpp25 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 325s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 325s libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 325s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 r-base 325s r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools 325s r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix 325s r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial 325s r-cran-survival r-recommended reapr samtools smalt snpomatic tabix unzip 325s x11-common xdg-utils zip 325s Suggested packages: 325s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html cwltool 325s Recommended packages: 325s r-base-html r-doc-html r-base-dev libfile-mimeinfo-perl libnet-dbus-perl 325s libx11-protocol-perl x11-utils x11-xserver-utils 325s The following NEW packages will be installed: 325s autopkgtest-satdep bamtools fontconfig fontconfig-config fonts-dejavu-core 325s fonts-dejavu-mono libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 325s libdeflate0 libfile-copy-link-perl libfontconfig1 libgfortran5 libgomp1 325s libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 325s libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 liblerc4 libpango-1.0-0 325s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 325s libsharpyuv0 libsm6 libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 325s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 325s libxt6 r-base r-base-core r-cran-boot r-cran-class r-cran-cluster 325s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass 325s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart 325s r-cran-spatial r-cran-survival r-recommended reapr samtools smalt snpomatic 325s tabix unzip x11-common xdg-utils zip 325s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 325s Need to get 59.4 MB/59.4 MB of archives. 325s After this operation, 112 MB of additional disk space will be used. 325s Get:1 /tmp/autopkgtest.7IbVyd/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 325s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] 326s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libjsoncpp25 arm64 1.9.5-6 [76.0 kB] 326s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 bamtools arm64 2.5.2+dfsg-4 [162 kB] 326s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 326s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 327s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 327s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 327s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 327s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libbambamc0 arm64 0.0.50-6 [37.2 kB] 327s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 327s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 327s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 327s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 327s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 327s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 327s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 327s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 327s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libfile-copy-link-perl all 0.140-5 [12.3 kB] 327s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 327s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 327s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 327s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 327s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 327s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 328s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 328s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 328s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 328s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 328s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 328s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 328s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 328s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 328s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 328s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 328s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 328s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 328s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 328s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 328s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 328s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 libtabixpp0 arm64 1.1.2-2 [9636 B] 328s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 328s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 328s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 328s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 328s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 328s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 328s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.14-1 [767 kB] 328s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 328s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 328s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 329s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 329s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 331s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 331s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cluster arm64 2.1.6-1 [552 kB] 331s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 331s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 331s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-kernsmooth arm64 2.23-22-1 [91.1 kB] 331s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 331s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 332s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 332s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 332s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 333s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 333s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-class arm64 7.3-22-2 [88.2 kB] 333s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 333s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatial arm64 7.3-17-1 [130 kB] 333s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 333s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-recommended all 4.3.2-1build1 [2636 B] 333s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base all 4.3.2-1build1 [9302 B] 333s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 333s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 smalt arm64 0.7.6-13 [95.2 kB] 333s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 snpomatic arm64 1.0-7 [78.4 kB] 333s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 tabix arm64 1.18+ds-1 [505 kB] 333s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 reapr arm64 1.0.18+dfsg-5build2 [182 kB] 334s Preconfiguring packages ... 334s Fetched 59.4 MB in 8s (7921 kB/s) 334s Selecting previously unselected package libbamtools2.5.2:arm64. 334s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75469 files and directories currently installed.) 334s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ... 334s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 334s Selecting previously unselected package libjsoncpp25:arm64. 334s Preparing to unpack .../01-libjsoncpp25_1.9.5-6_arm64.deb ... 334s Unpacking libjsoncpp25:arm64 (1.9.5-6) ... 334s Selecting previously unselected package bamtools. 334s Preparing to unpack .../02-bamtools_2.5.2+dfsg-4_arm64.deb ... 334s Unpacking bamtools (2.5.2+dfsg-4) ... 334s Selecting previously unselected package fonts-dejavu-mono. 334s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 334s Unpacking fonts-dejavu-mono (2.37-8) ... 334s Selecting previously unselected package fonts-dejavu-core. 334s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 334s Unpacking fonts-dejavu-core (2.37-8) ... 334s Selecting previously unselected package fontconfig-config. 334s Preparing to unpack .../05-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 335s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 335s Selecting previously unselected package libfontconfig1:arm64. 335s Preparing to unpack .../06-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 335s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 335s Selecting previously unselected package fontconfig. 335s Preparing to unpack .../07-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 335s Unpacking fontconfig (2.15.0-1ubuntu1) ... 335s Selecting previously unselected package libbambamc0:arm64. 335s Preparing to unpack .../08-libbambamc0_0.0.50-6_arm64.deb ... 335s Unpacking libbambamc0:arm64 (0.0.50-6) ... 335s Selecting previously unselected package libblas3:arm64. 335s Preparing to unpack .../09-libblas3_3.12.0-3_arm64.deb ... 335s Unpacking libblas3:arm64 (3.12.0-3) ... 335s Selecting previously unselected package libpixman-1-0:arm64. 335s Preparing to unpack .../10-libpixman-1-0_0.42.2-1_arm64.deb ... 335s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 335s Selecting previously unselected package libxcb-render0:arm64. 335s Preparing to unpack .../11-libxcb-render0_1.15-1_arm64.deb ... 335s Unpacking libxcb-render0:arm64 (1.15-1) ... 335s Selecting previously unselected package libxcb-shm0:arm64. 335s Preparing to unpack .../12-libxcb-shm0_1.15-1_arm64.deb ... 335s Unpacking libxcb-shm0:arm64 (1.15-1) ... 335s Selecting previously unselected package libxrender1:arm64. 335s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 335s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 335s Selecting previously unselected package libcairo2:arm64. 335s Preparing to unpack .../14-libcairo2_1.18.0-1_arm64.deb ... 335s Unpacking libcairo2:arm64 (1.18.0-1) ... 336s Selecting previously unselected package libdatrie1:arm64. 336s Preparing to unpack .../15-libdatrie1_0.2.13-3_arm64.deb ... 336s Unpacking libdatrie1:arm64 (0.2.13-3) ... 336s Selecting previously unselected package libdeflate0:arm64. 336s Preparing to unpack .../16-libdeflate0_1.19-1_arm64.deb ... 336s Unpacking libdeflate0:arm64 (1.19-1) ... 336s Selecting previously unselected package libfile-copy-link-perl. 336s Preparing to unpack .../17-libfile-copy-link-perl_0.140-5_all.deb ... 336s Unpacking libfile-copy-link-perl (0.140-5) ... 336s Selecting previously unselected package libgfortran5:arm64. 336s Preparing to unpack .../18-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 336s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 336s Selecting previously unselected package libgomp1:arm64. 336s Preparing to unpack .../19-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 336s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 336s Selecting previously unselected package libgraphite2-3:arm64. 336s Preparing to unpack .../20-libgraphite2-3_1.3.14-2_arm64.deb ... 336s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 336s Selecting previously unselected package libharfbuzz0b:arm64. 336s Preparing to unpack .../21-libharfbuzz0b_8.3.0-2_arm64.deb ... 336s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 336s Selecting previously unselected package libhtscodecs2:arm64. 336s Preparing to unpack .../22-libhtscodecs2_1.6.0-1_arm64.deb ... 336s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 336s Selecting previously unselected package libhts3:arm64. 336s Preparing to unpack .../23-libhts3_1.18+ds-1_arm64.deb ... 336s Unpacking libhts3:arm64 (1.18+ds-1) ... 336s Selecting previously unselected package x11-common. 336s Preparing to unpack .../24-x11-common_1%3a7.7+23ubuntu2_all.deb ... 336s Unpacking x11-common (1:7.7+23ubuntu2) ... 336s Selecting previously unselected package libice6:arm64. 336s Preparing to unpack .../25-libice6_2%3a1.0.10-1build2_arm64.deb ... 336s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 336s Selecting previously unselected package libjpeg-turbo8:arm64. 336s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 336s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 336s Selecting previously unselected package libjpeg8:arm64. 336s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_arm64.deb ... 336s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 336s Selecting previously unselected package liblapack3:arm64. 336s Preparing to unpack .../28-liblapack3_3.12.0-3_arm64.deb ... 337s Unpacking liblapack3:arm64 (3.12.0-3) ... 337s Selecting previously unselected package liblerc4:arm64. 337s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 337s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 337s Selecting previously unselected package libthai-data. 337s Preparing to unpack .../30-libthai-data_0.1.29-2_all.deb ... 337s Unpacking libthai-data (0.1.29-2) ... 337s Selecting previously unselected package libthai0:arm64. 337s Preparing to unpack .../31-libthai0_0.1.29-2_arm64.deb ... 337s Unpacking libthai0:arm64 (0.1.29-2) ... 337s Selecting previously unselected package libpango-1.0-0:arm64. 337s Preparing to unpack .../32-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 337s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 337s Selecting previously unselected package libpangoft2-1.0-0:arm64. 337s Preparing to unpack .../33-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 337s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 337s Selecting previously unselected package libpangocairo-1.0-0:arm64. 337s Preparing to unpack .../34-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 337s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 337s Selecting previously unselected package libpaper1:arm64. 337s Preparing to unpack .../35-libpaper1_1.1.29_arm64.deb ... 337s Unpacking libpaper1:arm64 (1.1.29) ... 337s Selecting previously unselected package libpaper-utils. 337s Preparing to unpack .../36-libpaper-utils_1.1.29_arm64.deb ... 337s Unpacking libpaper-utils (1.1.29) ... 337s Selecting previously unselected package libsharpyuv0:arm64. 337s Preparing to unpack .../37-libsharpyuv0_1.3.2-0.4_arm64.deb ... 337s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 337s Selecting previously unselected package libsm6:arm64. 337s Preparing to unpack .../38-libsm6_2%3a1.2.3-1build2_arm64.deb ... 337s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 337s Selecting previously unselected package libtabixpp0:arm64. 337s Preparing to unpack .../39-libtabixpp0_1.1.2-2_arm64.deb ... 337s Unpacking libtabixpp0:arm64 (1.1.2-2) ... 337s Selecting previously unselected package libtcl8.6:arm64. 337s Preparing to unpack .../40-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 337s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 338s Selecting previously unselected package libjbig0:arm64. 338s Preparing to unpack .../41-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 338s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 338s Selecting previously unselected package libwebp7:arm64. 338s Preparing to unpack .../42-libwebp7_1.3.2-0.4_arm64.deb ... 338s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 338s Selecting previously unselected package libtiff6:arm64. 338s Preparing to unpack .../43-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 338s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 338s Selecting previously unselected package libxft2:arm64. 338s Preparing to unpack .../44-libxft2_2.3.6-1_arm64.deb ... 338s Unpacking libxft2:arm64 (2.3.6-1) ... 338s Selecting previously unselected package libxss1:arm64. 338s Preparing to unpack .../45-libxss1_1%3a1.2.3-1build2_arm64.deb ... 338s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 338s Selecting previously unselected package libtk8.6:arm64. 338s Preparing to unpack .../46-libtk8.6_8.6.14-1_arm64.deb ... 338s Unpacking libtk8.6:arm64 (8.6.14-1) ... 338s Selecting previously unselected package libxt6:arm64. 338s Preparing to unpack .../47-libxt6_1%3a1.2.1-1.1_arm64.deb ... 338s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 338s Selecting previously unselected package zip. 338s Preparing to unpack .../48-zip_3.0-13_arm64.deb ... 338s Unpacking zip (3.0-13) ... 338s Selecting previously unselected package unzip. 338s Preparing to unpack .../49-unzip_6.0-28ubuntu3_arm64.deb ... 338s Unpacking unzip (6.0-28ubuntu3) ... 338s Selecting previously unselected package xdg-utils. 338s Preparing to unpack .../50-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 338s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 338s Selecting previously unselected package r-base-core. 338s Preparing to unpack .../51-r-base-core_4.3.2-1build1_arm64.deb ... 338s Unpacking r-base-core (4.3.2-1build1) ... 339s Selecting previously unselected package r-cran-boot. 339s Preparing to unpack .../52-r-cran-boot_1.3-30-1_all.deb ... 339s Unpacking r-cran-boot (1.3-30-1) ... 339s Selecting previously unselected package r-cran-cluster. 339s Preparing to unpack .../53-r-cran-cluster_2.1.6-1_arm64.deb ... 339s Unpacking r-cran-cluster (2.1.6-1) ... 340s Selecting previously unselected package r-cran-foreign. 340s Preparing to unpack .../54-r-cran-foreign_0.8.86-1_arm64.deb ... 340s Unpacking r-cran-foreign (0.8.86-1) ... 340s Selecting previously unselected package r-cran-mass. 340s Preparing to unpack .../55-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 340s Unpacking r-cran-mass (7.3-60.0.1-1) ... 340s Selecting previously unselected package r-cran-kernsmooth. 340s Preparing to unpack .../56-r-cran-kernsmooth_2.23-22-1_arm64.deb ... 340s Unpacking r-cran-kernsmooth (2.23-22-1) ... 340s Selecting previously unselected package r-cran-lattice. 340s Preparing to unpack .../57-r-cran-lattice_0.22-5-1_arm64.deb ... 340s Unpacking r-cran-lattice (0.22-5-1) ... 340s Selecting previously unselected package r-cran-nlme. 340s Preparing to unpack .../58-r-cran-nlme_3.1.164-1_arm64.deb ... 340s Unpacking r-cran-nlme (3.1.164-1) ... 340s Selecting previously unselected package r-cran-matrix. 340s Preparing to unpack .../59-r-cran-matrix_1.6-5-1_arm64.deb ... 340s Unpacking r-cran-matrix (1.6-5-1) ... 340s Selecting previously unselected package r-cran-mgcv. 340s Preparing to unpack .../60-r-cran-mgcv_1.9-1-1_arm64.deb ... 340s Unpacking r-cran-mgcv (1.9-1-1) ... 340s Selecting previously unselected package r-cran-survival. 340s Preparing to unpack .../61-r-cran-survival_3.5-8-1_arm64.deb ... 340s Unpacking r-cran-survival (3.5-8-1) ... 340s Selecting previously unselected package r-cran-rpart. 341s Preparing to unpack .../62-r-cran-rpart_4.1.23-1_arm64.deb ... 341s Unpacking r-cran-rpart (4.1.23-1) ... 341s Selecting previously unselected package r-cran-class. 341s Preparing to unpack .../63-r-cran-class_7.3-22-2_arm64.deb ... 341s Unpacking r-cran-class (7.3-22-2) ... 341s Selecting previously unselected package r-cran-nnet. 341s Preparing to unpack .../64-r-cran-nnet_7.3-19-2_arm64.deb ... 341s Unpacking r-cran-nnet (7.3-19-2) ... 341s Selecting previously unselected package r-cran-spatial. 341s Preparing to unpack .../65-r-cran-spatial_7.3-17-1_arm64.deb ... 341s Unpacking r-cran-spatial (7.3-17-1) ... 341s Selecting previously unselected package r-cran-codetools. 341s Preparing to unpack .../66-r-cran-codetools_0.2-19-1_all.deb ... 341s Unpacking r-cran-codetools (0.2-19-1) ... 341s Selecting previously unselected package r-recommended. 341s Preparing to unpack .../67-r-recommended_4.3.2-1build1_all.deb ... 341s Unpacking r-recommended (4.3.2-1build1) ... 341s Selecting previously unselected package r-base. 341s Preparing to unpack .../68-r-base_4.3.2-1build1_all.deb ... 341s Unpacking r-base (4.3.2-1build1) ... 341s Selecting previously unselected package samtools. 341s Preparing to unpack .../69-samtools_1.19.2-1_arm64.deb ... 341s Unpacking samtools (1.19.2-1) ... 341s Selecting previously unselected package smalt. 341s Preparing to unpack .../70-smalt_0.7.6-13_arm64.deb ... 341s Unpacking smalt (0.7.6-13) ... 341s Selecting previously unselected package snpomatic. 341s Preparing to unpack .../71-snpomatic_1.0-7_arm64.deb ... 341s Unpacking snpomatic (1.0-7) ... 341s Selecting previously unselected package tabix. 341s Preparing to unpack .../72-tabix_1.18+ds-1_arm64.deb ... 341s Unpacking tabix (1.18+ds-1) ... 341s Selecting previously unselected package reapr. 341s Preparing to unpack .../73-reapr_1.0.18+dfsg-5build2_arm64.deb ... 341s Unpacking reapr (1.0.18+dfsg-5build2) ... 341s Selecting previously unselected package autopkgtest-satdep. 341s Preparing to unpack .../74-1-autopkgtest-satdep.deb ... 341s Unpacking autopkgtest-satdep (0) ... 342s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 342s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 342s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 342s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 342s Setting up libpaper1:arm64 (1.1.29) ... 342s 342s Creating config file /etc/papersize with new version 342s Setting up libfile-copy-link-perl (0.140-5) ... 342s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 342s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 342s Setting up libdatrie1:arm64 (0.2.13-3) ... 342s Setting up libxcb-render0:arm64 (1.15-1) ... 342s Setting up unzip (6.0-28ubuntu3) ... 342s Setting up x11-common (1:7.7+23ubuntu2) ... 343s Setting up libdeflate0:arm64 (1.19-1) ... 343s Setting up libxcb-shm0:arm64 (1.15-1) ... 343s Setting up libpaper-utils (1.1.29) ... 343s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 343s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 343s Setting up zip (3.0-13) ... 343s Setting up libblas3:arm64 (3.12.0-3) ... 343s 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 343s Setting up libbambamc0:arm64 (0.0.50-6) ... 343s Setting up fonts-dejavu-mono (2.37-8) ... 343s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 343s Setting up libjsoncpp25:arm64 (1.9.5-6) ... 343s Setting up fonts-dejavu-core (2.37-8) ... 343s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 343s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 343s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 343s Setting up libwebp7:arm64 (1.3.2-0.4) ... 343s Setting up bamtools (2.5.2+dfsg-4) ... 343s Setting up snpomatic (1.0-7) ... 343s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 343s Setting up libthai-data (0.1.29-2) ... 343s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 343s Setting up tabix (1.18+ds-1) ... 343s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 343s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 343s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 343s Setting up smalt (0.7.6-13) ... 343s Setting up libice6:arm64 (2:1.0.10-1build2) ... 343s Setting up liblapack3:arm64 (3.12.0-3) ... 343s 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 343s Setting up libhts3:arm64 (1.18+ds-1) ... 343s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 344s Setting up samtools (1.19.2-1) ... 344s Setting up libthai0:arm64 (0.1.29-2) ... 344s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 344s Setting up libtabixpp0:arm64 (1.1.2-2) ... 344s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 344s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 344s Setting up fontconfig (2.15.0-1ubuntu1) ... 346s Regenerating fonts cache... done. 346s Setting up libxft2:arm64 (2.3.6-1) ... 346s Setting up libtk8.6:arm64 (8.6.14-1) ... 346s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 346s Setting up libcairo2:arm64 (1.18.0-1) ... 346s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 346s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 346s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 346s Setting up r-base-core (4.3.2-1build1) ... 346s 346s Creating config file /etc/R/Renviron with new version 346s Setting up r-cran-lattice (0.22-5-1) ... 346s Setting up r-cran-nlme (3.1.164-1) ... 346s Setting up r-cran-cluster (2.1.6-1) ... 346s Setting up r-cran-nnet (7.3-19-2) ... 346s Setting up r-cran-codetools (0.2-19-1) ... 346s Setting up r-cran-boot (1.3-30-1) ... 346s Setting up r-cran-spatial (7.3-17-1) ... 346s Setting up r-cran-mass (7.3-60.0.1-1) ... 346s Setting up r-cran-foreign (0.8.86-1) ... 346s Setting up r-cran-matrix (1.6-5-1) ... 346s Setting up r-cran-kernsmooth (2.23-22-1) ... 346s Setting up r-cran-mgcv (1.9-1-1) ... 346s Setting up r-cran-class (7.3-22-2) ... 346s Setting up r-cran-survival (3.5-8-1) ... 346s Setting up r-cran-rpart (4.1.23-1) ... 346s Setting up r-recommended (4.3.2-1build1) ... 346s Setting up r-base (4.3.2-1build1) ... 346s Setting up reapr (1.0.18+dfsg-5build2) ... 346s Setting up autopkgtest-satdep (0) ... 346s Processing triggers for man-db (2.12.0-3) ... 348s Processing triggers for install-info (7.1-3) ... 348s Processing triggers for libc-bin (2.39-0ubuntu6) ... 358s (Reading database ... 78660 files and directories currently installed.) 358s Removing autopkgtest-satdep (0) ... 360s autopkgtest [17:47:55]: test test-example: [----------------------- 360s [wgsim] seed = 42 360s [wgsim_core] calculating the total length of the reference sequence... 360s [wgsim_core] 1 sequences, total length: 1000111 360s foo 1384 T K + 360s foo 4961 T W + 360s foo 5885 - T - 360s foo 9598 A C - 360s foo 10177 G R + 360s foo 11305 G K + 360s foo 11592 G R + 360s foo 13931 T - - 360s foo 15907 C A - 360s foo 17264 G K + 360s foo 17780 A - - 360s foo 18711 A W + 360s foo 19249 T W + 360s foo 19522 C S + 360s foo 23053 T K + 360s foo 23681 A R + 360s foo 23730 C S + 360s foo 24075 G S + 360s foo 24555 G C - 360s foo 26775 G K + 360s foo 26896 C M + 360s foo 27253 G K + 360s foo 28210 T Y + 360s foo 28224 A W + 360s foo 28377 - G + 360s foo 29035 G K + 360s foo 29898 C M + 360s foo 30274 A R + 360s foo 30542 G K + 360s foo 31566 A C - 360s foo 32252 - A - 360s foo 33303 T K + 360s foo 33390 - G + 360s foo 34073 A R + 360s foo 34171 G R + 360s foo 34718 T Y + 360s foo 34801 - C + 360s foo 35204 T W + 360s foo 35342 G S + 360s foo 35489 G T - 360s foo 36153 A M + 360s foo 36273 C S + 360s foo 37356 G T - 360s foo 37596 C S + 360s foo 39308 T - - 360s foo 40333 C G - 360s foo 42295 T K + 360s foo 42372 T Y + 360s foo 44433 C G - 360s foo 44630 - AG + 360s foo 44902 T C - 360s foo 47156 C A - 360s foo 48210 C M + 360s foo 48390 A R + 360s foo 49652 C M + 360s foo 52739 T Y + 360s foo 52858 A M + 360s foo 54737 A G - 360s foo 55306 C T - 360s foo 55434 C T - 360s foo 59204 A W + 360s foo 59300 G C - 360s foo 59335 T Y + 360s foo 59444 T - - 360s foo 59531 C S + 360s foo 59766 C Y + 360s foo 61950 C S + 360s foo 62887 G S + 360s foo 63390 A G - 360s foo 64365 G K + 360s foo 64703 C S + 360s foo 64932 C Y + 360s foo 68383 - CG + 360s foo 68464 A W + 360s foo 68727 A W + 360s foo 69080 A M + 360s foo 72071 T C - 360s foo 72720 - G - 360s foo 73354 C T - 360s foo 73637 G T - 360s foo 74741 A M + 360s foo 75101 C T - 360s foo 75207 T K + 360s foo 76400 T Y + 360s foo 76780 A C - 360s foo 77172 A W + 360s foo 78385 C Y + 360s foo 80705 C M + 360s foo 82440 A R + 360s foo 83021 G K + 360s foo 83116 A - - 360s foo 83846 T K + 360s foo 84633 G S + 360s foo 85891 G S + 360s foo 87759 A C - 360s foo 87778 T W + 360s foo 88581 T K + 360s foo 88606 T Y + 360s foo 88880 A G - 360s foo 89945 G C - 360s foo 90728 T K + 360s foo 91798 G R + 360s foo 95957 G C - 360s foo 96173 T W + 360s foo 96665 A M + 360s foo 98019 - G + 360s foo 98131 A M + 360s foo 98669 A R + 360s foo 98719 G T - 360s foo 99062 A W + 360s foo 99590 A T - 360s foo 100532 - TC + 360s foo 103015 A W + 360s foo 103172 G S + 360s foo 103609 G R + 360s foo 106549 T Y + 360s foo 108808 C Y + 360s foo 109191 G C - 360s foo 111686 C G - 360s foo 113436 C A - 360s foo 113763 A W + 360s foo 115671 C T - 360s foo 117460 - A - 360s foo 118193 G - - 360s foo 118585 T K + 360s foo 121219 A M + 360s foo 121876 T K + 360s foo 122071 T A - 360s foo 124918 C G - 360s foo 125300 G S + 360s foo 125967 C S + 360s foo 127443 G S + 360s foo 127565 C Y + 360s foo 128700 C A - 360s foo 129912 G A - 360s foo 130847 T W + 360s foo 131677 G S + 360s foo 132189 T C - 360s foo 135878 CGGC - - 360s foo 136825 T K + 360s foo 138881 TGT - - 360s foo 139288 A W + 360s foo 141054 A W + 360s foo 141055 - T + 360s foo 141101 C S + 360s foo 141404 A R + 360s foo 142698 T C - 360s foo 143990 C A - 360s foo 144167 T Y + 360s foo 144814 C Y + 360s foo 146381 T Y + 360s foo 146393 C A - 360s foo 146510 A C - 360s foo 147182 A W + 360s foo 148783 T C - 360s foo 149068 G S + 360s foo 150208 T K + 360s foo 151554 T W + 360s foo 151709 C G - 360s foo 153072 G R + 360s foo 153307 T Y + 360s foo 154050 G S + 360s foo 154415 C S + 360s foo 154594 G R + 360s foo 155839 G T - 360s foo 156106 G A - 360s foo 159356 T W + 360s foo 159926 A W + 360s foo 160303 T K + 360s foo 161323 C Y + 360s foo 161904 G S + 360s foo 162533 - ACC - 360s foo 164738 C G - 360s foo 165413 A R + 360s foo 166944 C M + 360s foo 167464 T Y + 360s foo 168420 T C - 360s foo 168579 A M + 360s foo 168787 T W + 360s foo 168959 A T - 360s foo 169884 G S + 360s foo 170032 G T - 360s foo 172058 G K + 360s foo 174942 A R + 360s foo 175014 G K + 360s foo 178406 G A - 360s foo 179028 - A + 360s foo 182394 C M + 360s foo 182735 T Y + 360s foo 183384 T K + 360s foo 183893 - AT - 360s foo 185360 G A - 360s foo 185538 - G - 360s foo 187948 G S + 360s foo 188120 T G - 360s foo 188179 T W + 360s foo 188316 T Y + 360s foo 189963 - G + 360s foo 190093 C Y + 360s foo 192220 C M + 360s foo 192368 A W + 360s foo 192782 T K + 360s foo 193307 A R + 360s foo 193501 G K + 360s foo 194276 G S + 360s foo 194930 C S + 360s foo 196728 A W + 360s foo 197559 G C - 360s foo 198467 T W + 360s foo 199042 C Y + 360s foo 199259 AA - - 360s foo 199687 TT - - 360s foo 200287 C A - 360s foo 200678 A R + 360s foo 201208 C T - 360s foo 201882 A - - 360s foo 204456 T K + 360s foo 206327 G R + 360s foo 207311 G T - 360s foo 209184 G A - 360s foo 209279 C Y + 360s foo 211459 C Y + 360s foo 213807 T Y + 360s foo 213846 T Y + 360s foo 214635 A G - 360s foo 214884 C A - 360s foo 216244 A M + 360s foo 216652 A M + 360s foo 216745 T - - 360s foo 216909 A T - 360s foo 217579 A G - 360s foo 217895 C Y + 360s foo 218870 G K + 360s foo 223098 T A - 360s foo 223283 - C + 360s foo 223666 C A - 360s foo 224011 - C + 360s foo 225681 C S + 360s foo 227345 T C - 360s foo 228778 T G - 360s foo 229926 C - - 360s foo 230778 T K + 360s foo 230939 CG - - 360s foo 231988 CT - - 360s foo 234593 T W + 360s foo 235496 C S + 360s foo 235705 G K + 360s foo 235758 A G - 360s foo 236852 T C - 360s foo 238790 A M + 360s foo 238865 T K + 360s foo 239329 A M + 360s foo 239576 - C + 360s foo 243058 G S + 360s foo 244147 T - - 360s foo 244462 C G - 360s foo 245443 - A + 360s foo 246544 C Y + 360s foo 246744 T W + 360s foo 247473 C M + 360s foo 248129 C T - 360s foo 249060 A C - 360s foo 249515 G T - 360s foo 250138 G S + 360s foo 250567 C A - 360s foo 254381 G R + 360s foo 257864 C M + 360s foo 257879 C Y + 360s foo 259859 A M + 360s foo 260643 C S + 360s foo 261681 C G - 360s foo 262645 T Y + 360s foo 263279 A R + 360s foo 263575 A - - 360s foo 264587 - TA + 360s foo 264689 T K + 360s foo 265758 G K + 360s foo 266272 A M + 360s foo 268550 C M + 360s foo 269986 G S + 360s foo 270321 AC - - 360s foo 273346 C S + 360s foo 275367 C A - 360s foo 277334 C G - 360s foo 277629 G T - 360s foo 278431 C Y + 360s foo 281456 T Y + 360s foo 281556 T G - 360s foo 281737 G K + 360s foo 282290 AC - - 360s foo 282851 - C - 360s foo 284405 A C - 360s foo 288751 A C - 360s foo 290501 TAAA - - 360s foo 291315 A W + 360s foo 291368 C - - 360s foo 292154 A C - 360s foo 292385 C M + 360s foo 292555 G K + 360s foo 297709 G C - 360s foo 298183 A W + 360s foo 298228 T W + 360s foo 299902 T G - 360s foo 302575 A T - 360s foo 304823 G R + 360s foo 305308 T Y + 360s foo 305487 G S + 360s foo 305697 G T - 360s foo 306098 C G - 360s foo 306882 T Y + 360s foo 308201 A M + 360s foo 308833 A T - 360s foo 312033 A - - 360s foo 312895 C G - 360s foo 313889 C - - 360s foo 315109 A R + 360s foo 316083 C - - 360s foo 316466 A R + 360s foo 318040 G C - 360s foo 319446 T C - 360s foo 320236 C S + 360s foo 320652 A - - 360s foo 320716 T K + 360s foo 323644 A - - 360s foo 325359 G T - 360s foo 329476 - CA + 360s foo 329706 T G - 360s foo 330181 T Y + 360s foo 330703 C Y + 360s foo 331315 G S + 360s foo 332351 C A - 360s foo 333408 A R + 360s foo 333468 C S + 360s foo 336247 A G - 360s foo 336586 A M + 360s foo 337364 G K + 360s foo 337686 A T - 360s foo 338043 A - - 360s foo 338292 C G - 360s foo 338962 A C - 360s foo 339353 G K + 360s foo 340647 - A + 360s foo 341705 G R + 360s foo 344283 C M + 360s foo 345898 - AG - 360s foo 347959 T - - 360s foo 349162 C M + 360s foo 352072 T Y + 360s foo 354614 C Y + 360s foo 359304 T - - 360s foo 359312 - G + 360s foo 360972 C S + 360s foo 363857 C Y + 360s foo 366226 A C - 360s foo 367259 C M + 360s foo 372502 T Y + 360s foo 372747 A M + 360s foo 375140 C S + 360s foo 376298 T W + 360s foo 376313 C - - 360s foo 376760 T W + 360s foo 378494 A W + 360s foo 381137 T G - 360s foo 381186 A R + 360s foo 381701 A G - 360s foo 382614 A W + 360s foo 382761 C T - 360s foo 382854 T C - 360s foo 383201 C T - 360s foo 385104 G S + 360s foo 385233 - A + 360s foo 386138 C T - 360s foo 386316 A W + 360s foo 387072 A R + 360s foo 387642 - A + 360s foo 388232 T C - 360s foo 388890 GGG - - 360s foo 390508 C S + 360s foo 390625 C M + 360s foo 391921 C G - 360s foo 395256 G T - 360s foo 395542 G S + 360s foo 397015 A - - 360s foo 397516 C Y + 360s foo 397528 GC - - 360s foo 398152 C T - 360s foo 399802 A W + 360s foo 400972 T K + 360s foo 401419 - T + 360s foo 401477 T W + 360s foo 402437 A M + 360s foo 402722 G R + 360s foo 403452 C M + 360s foo 404234 - A + 360s foo 405344 A W + 360s foo 407040 G S + 360s foo 408483 G R + 360s foo 408586 A C - 360s foo 408721 A R + 360s foo 409494 A M + 360s foo 410078 A G - 360s foo 411170 C A - 360s foo 415342 T Y + 360s foo 416265 C G - 360s foo 417740 C A - 360s foo 418622 C S + 360s foo 420232 A W + 360s foo 420288 T Y + 360s foo 420908 A W + 360s foo 421109 T A - 360s foo 421357 A R + 360s foo 422799 G A - 360s foo 424383 C S + 360s foo 424871 - GCA + 360s foo 427273 T A - 360s foo 429822 C M + 360s foo 429846 T W + 360s foo 432015 A G - 360s foo 432414 G K + 360s foo 433606 C Y + 360s foo 433831 T Y + 360s foo 437721 - A - 360s foo 438402 G - - 360s foo 438799 A T - 360s foo 439422 C M + 360s foo 440734 C A - 360s foo 441840 T G - 360s foo 442021 - C + 360s foo 445021 T A - 360s foo 445591 G A - 360s foo 446138 T W + 360s foo 447757 A W + 360s foo 449156 T - - 360s foo 449161 G K + 360s foo 450114 A W + 360s foo 450688 A W + 360s foo 454421 C G - 360s foo 454718 T Y + 360s foo 455675 TC - - 360s foo 461721 G R + 360s foo 462526 G S + 360s foo 467296 G A - 360s foo 467510 G K + 360s foo 468267 T K + 360s foo 469118 G R + 360s foo 469830 C Y + 360s foo 471073 G T - 360s foo 472056 G A - 360s foo 472773 - A + 360s foo 473046 G R + 360s foo 473188 G A - 360s foo 473742 C - - 360s foo 474789 T A - 360s foo 477763 G R + 360s foo 478246 T W + 360s foo 478975 T G - 360s foo 479038 A R + 360s foo 480275 T Y + 360s foo 480317 G A - 360s foo 481512 T K + 360s foo 482069 G S + 360s foo 482534 A R + 360s foo 483760 C Y + 360s foo 485281 T W + 360s foo 486255 T C - 360s foo 487038 T K + 360s foo 487225 T A - 360s foo 488012 C Y + 360s foo 488795 T C - 360s foo 490241 A R + 360s foo 492595 - CGG + 360s foo 493224 C A - 360s foo 494284 A T - 360s foo 495990 - T - 360s foo 497306 A R + 360s foo 497403 T Y + 360s foo 499569 C Y + 360s foo 499651 T K + 360s foo 503139 T C - 360s foo 504660 A R + 360s foo 508679 C - - 360s foo 513643 G K + 360s foo 515668 CC - - 360s foo 515836 G R + 360s foo 516488 C S + 360s foo 517602 G R + 360s foo 517962 G K + 360s foo 517975 T K + 360s foo 519144 A T - 360s foo 520068 T K + 360s foo 520926 A W + 360s foo 521562 C S + 360s foo 522076 CG - - 360s foo 522838 T Y + 360s foo 523513 - C + 360s foo 523907 - TA + 360s foo 526271 T A - 360s foo 526533 AC - - 360s foo 526767 C Y + 360s foo 528217 C Y + 360s foo 531924 G S + 360s foo 532333 - TT + 360s foo 533132 C M + 360s foo 534689 A T - 360s foo 534779 A W + 360s foo 535594 C A - 360s foo 535795 G R + 360s foo 538368 A R + 360s foo 540879 G K + 360s foo 542530 A - - 360s foo 543620 G R + 360s foo 544733 - C - 360s foo 546300 - TT + 360s foo 548196 A T - 360s foo 548878 C M + 360s foo 548885 G R + 360s foo 549459 T K + 360s foo 550908 A G - 360s foo 551170 A - - 360s foo 553130 T Y + 360s foo 555293 T G - 360s foo 556198 G R + 360s foo 556355 A T - 360s foo 557688 G K + 360s foo 558415 G C - 360s foo 558461 - G + 360s foo 559287 T Y + 360s foo 559465 C M + 360s foo 560184 T W + 360s foo 560252 T W + 360s foo 562579 A M + 360s foo 562961 G A - 360s foo 566986 C A - 360s foo 568134 C A - 360s foo 569698 T C - 360s foo 570180 T K + 360s foo 570451 TG - - 360s foo 570832 - A - 360s foo 571589 A W + 360s foo 572208 C M + 360s foo 572871 C S + 360s foo 574334 G - - 360s foo 575673 T Y + 360s foo 576797 G S + 360s foo 578486 - C - 360s foo 578494 C S + 360s foo 579257 G A - 360s foo 580103 G T - 360s foo 580872 A W + 360s foo 580925 G S + 360s foo 580950 G C - 360s foo 581637 T Y + 360s foo 581654 A G - 360s foo 582538 A T - 360s foo 582691 C M + 360s foo 582938 A W + 360s foo 583104 T K + 360s foo 584763 T W + 360s foo 585723 T W + 360s foo 588253 T Y + 360s foo 588972 T C - 360s foo 589438 - C - 360s foo 591131 C Y + 360s foo 591950 G R + 360s foo 592194 T G - 360s foo 592310 G S + 360s foo 593892 G A - 360s foo 598556 A - - 360s foo 601660 G S + 360s foo 602112 G T - 360s foo 602412 T Y + 360s foo 607282 - C + 360s foo 607394 A M + 360s foo 608438 A T - 360s foo 609255 A W + 360s foo 609365 - T + 360s foo 611161 G K + 360s foo 612224 C G - 360s foo 614493 G R + 360s foo 614601 G A - 360s foo 614607 C Y + 360s foo 619507 C M + 360s foo 619798 T C - 360s foo 621872 C T - 360s foo 622375 C Y + 360s foo 623208 - G - 360s foo 624366 C A - 360s foo 625320 - ACA - 360s foo 626664 - G + 360s foo 627140 T C - 360s foo 627353 G T - 360s foo 628714 T Y + 360s foo 628744 A - - 360s foo 629152 A G - 360s foo 630110 T G - 360s foo 631744 G K + 360s foo 632763 C S + 360s foo 634419 G - - 360s foo 634459 A G - 360s foo 634571 G A - 360s foo 635366 - A + 360s foo 635604 G T - 360s foo 637057 T C - 360s foo 637525 A T - 360s foo 638412 A R + 360s foo 640547 A W + 360s foo 641514 T K + 360s foo 642219 A R + 360s foo 642427 A G - 360s foo 642612 A R + 360s foo 643553 T W + 360s foo 647316 - T + 360s foo 647598 C - - 360s foo 651093 G A - 360s foo 651718 G R + 360s foo 652235 A G - 360s foo 652579 A C - 360s foo 653355 A W + 360s foo 655174 C M + 360s foo 655487 A M + 360s foo 656849 G S + 360s foo 661081 T K + 360s foo 661134 G C - 360s foo 661935 A W + 360s foo 662010 A M + 360s foo 662040 G R + 360s foo 663030 A W + 360s foo 663268 - C + 360s foo 664991 T - - 360s foo 665489 T K + 360s foo 665555 C M + 360s foo 665965 C Y + 360s foo 668725 A C - 360s foo 668834 - G - 360s foo 668873 C S + 360s foo 669654 T W + 360s foo 671041 G S + 360s foo 671485 T W + 360s foo 671690 C M + 360s foo 673022 G R + 360s foo 674137 - T + 360s foo 674782 A C - 360s foo 676373 G T - 360s foo 676793 T C - 360s foo 677409 G S + 360s foo 677536 - AA - 360s foo 677620 G K + 360s foo 677686 C Y + 360s foo 678327 G S + 360s foo 678704 G S + 360s foo 678771 A C - 360s foo 678866 C T - 360s foo 679960 A W + 360s foo 680447 - C + 360s foo 682102 C T - 360s foo 685497 T A - 360s foo 686884 G S + 360s foo 687324 ACA - - 360s foo 687684 - AC + 360s foo 687823 T C - 360s foo 688590 G K + 360s foo 690802 C M + 360s foo 691388 T C - 360s foo 691403 T G - 360s foo 691790 G A - 360s foo 692973 C A - 360s foo 694058 G S + 360s foo 694550 G R + 360s foo 694968 T W + 360s foo 695898 A T - 360s foo 696721 C S + 360s foo 696787 C S + 360s foo 696935 A M + 360s foo 698024 - C + 360s foo 699813 A - - 360s foo 700179 G R + 360s foo 701421 A M + 360s foo 701989 T A - 360s foo 702862 C A - 360s foo 707020 G A - 360s foo 708420 A - - 360s foo 708669 C G - 360s foo 710521 T W + 360s foo 711801 G C - 360s foo 711913 T G - 360s foo 715830 C M + 360s foo 717664 TC - - 360s foo 718845 A W + 360s foo 719069 T Y + 360s foo 719565 A W + 360s foo 721136 T K + 360s foo 726116 T K + 360s foo 727809 T K + 360s foo 728864 G K + 360s foo 728918 G A - 360s foo 730296 - T + 360s foo 731988 C Y + 360s foo 734658 A M + 360s foo 734715 A W + 360s foo 736618 C G - 360s foo 737257 T Y + 360s foo 740864 C A - 360s foo 741640 G - - 360s foo 741859 - TA - 360s foo 742011 T K + 360s foo 742237 A R + 360s foo 742960 G K + 360s foo 743731 G R + 360s foo 743971 A W + 360s foo 744635 T K + 360s foo 746430 C G - 360s foo 746489 - GC - 360s foo 746881 C M + 360s foo 756997 TC - - 360s foo 757776 A M + 360s foo 759870 A T - 360s foo 760224 G K + 360s foo 760799 G C - 360s foo 761692 T C - 360s foo 762569 G S + 360s foo 763140 A G - 360s foo 763842 - T - 360s foo 764192 A M + 360s foo 764334 G A - 360s foo 764889 - AAT + 360s foo 766464 G S + 360s foo 768226 G A - 360s foo 770272 T G - 360s foo 771145 C Y + 360s foo 772209 T A - 360s foo 773672 T K + 360s foo 773932 G C - 360s foo 774658 C S + 360s foo 775969 A M + 360s foo 776816 T G - 360s foo 777591 C Y + 360s foo 777891 A M + 360s foo 778164 C M + 360s foo 778219 T W + 360s foo 779260 G T - 360s foo 779465 A W + 360s foo 779779 G S + 360s foo 780033 G K + 360s foo 783243 C M + 360s foo 783860 A R + 360s foo 788345 A M + 360s foo 789554 G - - 360s foo 790025 G K + 360s foo 791454 T K + 360s foo 792009 C A - 360s foo 792872 C G - 360s foo 794616 T W + 360s foo 795031 G R + 360s foo 796919 C M + 360s foo 797020 G S + 360s foo 797042 G C - 360s foo 797149 G A - 360s foo 797177 A C - 360s foo 799076 G C - 360s foo 799580 G S + 360s foo 800356 A R + 360s foo 802297 G T - 360s foo 802309 T Y + 360s foo 802343 - C + 360s foo 802769 A W + 360s foo 803104 C G - 360s foo 805819 C Y + 360s foo 805972 T Y + 360s foo 807503 T K + 360s foo 807950 C M + 360s foo 807994 - A - 360s foo 809167 A G - 360s foo 809658 A W + 360s foo 810152 A M + 360s foo 811506 G R + 360s foo 813494 A M + 360s foo 814035 G T - 360s foo 814476 A W + 360s foo 819399 T K + 360s foo 820171 T W + 360s foo 820445 G C - 360s foo 822178 C G - 360s foo 822504 C T - 360s foo 823378 C M + 360s foo 823591 CG - - 360s foo 824229 C M + 360s foo 824579 C T - 360s foo 824858 C M + 360s foo 826101 T K + 360s foo 827593 C G - 360s foo 827794 T Y + 360s foo 828228 A M + 360s foo 828367 T K + 360s foo 828788 C M + 360s foo 829002 C Y + 360s foo 830345 C M + 360s foo 831018 C A - 360s foo 831459 T K + 360s foo 832413 A T - 360s foo 832782 T Y + 360s foo 832908 T Y + 360s foo 833130 T - - 360s foo 833142 G S + 360s foo 833241 G A - 360s foo 836727 A T - 360s foo 836829 G S + 360s foo 838452 T G - 360s foo 838543 A T - 360s foo 838605 C M + 360s foo 838954 G C - 360s foo 841829 G K + 360s foo 842324 - TC + 360s foo 842996 - C + 360s foo 844390 C A - 360s foo 844793 A C - 360s foo 844925 C A - 360s foo 845082 G C - 360s foo 846202 G R + 360s foo 846707 A G - 360s foo 848713 G A - 360s foo 849372 C S + 360s foo 849742 G A - 360s foo 850499 C - - 360s foo 850927 GT - - 360s foo 851084 - G + 360s foo 852247 A R + 360s foo 852972 C A - 360s foo 854808 T W + 360s foo 855956 G K + 360s foo 856225 G A - 360s foo 856582 T K + 360s foo 857351 C M + 360s foo 857504 AC - - 360s foo 858324 A T - 360s foo 858858 T C - 360s foo 859488 T Y + 360s foo 862441 T Y + 360s foo 863827 C Y + 360s foo 864165 C A - 360s foo 865997 C M + 360s foo 866370 G S + 360s foo 867653 G S + 360s foo 867722 C Y + 360s foo 868696 C M + 360s foo 869005 T W + 360s foo 869791 T Y + 360s foo 875339 C Y + 360s foo 875347 C M + 360s foo 875584 T G - 360s foo 876780 C T - 360s foo 878368 A C - 360s foo 878916 - CAG + 360s foo 879005 A R + 360s foo 880112 G T - 360s foo 881021 - T - 360s foo 881175 T W + 360s foo 882168 - GGG + 360s foo 882223 - G - 360s foo 883033 TG - - 360s foo 883381 C G - 360s foo 884378 C - - 360s foo 885075 A M + 360s foo 885190 A W + 360s foo 885568 A W + 360s foo 885827 T Y + 360s foo 887610 TG - - 360s foo 889139 G R + 360s foo 890978 T - - 360s foo 891500 C Y + 360s foo 892257 G C - 360s foo 892642 G R + 360s foo 892644 T W + 360s foo 892757 C A - 360s foo 893222 T - - 360s foo 893348 T W + 360s foo 894161 - C - 360s foo 894447 A G - 360s foo 894614 A W + 360s foo 897817 T W + 360s foo 899408 C S + 360s foo 902450 A T - 360s foo 902970 AT - - 360s foo 905836 G K + 360s foo 906524 GA - - 360s foo 907484 A W + 360s foo 907537 C M + 360s foo 908515 G R + 360s foo 908642 C T - 360s foo 911145 T C - 360s foo 912220 T Y + 360s foo 912682 C Y + 360s foo 914260 C S + 360s foo 914757 T Y + 360s foo 916413 G C - 360s foo 916783 T G - 360s foo 917033 G C - 360s foo 917218 A - - 360s foo 918225 G - - 360s foo 918459 A - - 360s foo 918732 A M + 360s foo 919640 TC - - 360s foo 920824 T W + 360s foo 920836 G C - 360s foo 924560 G R + 360s foo 924659 GA - - 360s foo 925868 T A - 360s foo 928254 T G - 360s foo 928369 - A - 360s foo 928641 - AG + 360s foo 929857 C M + 360s foo 930211 T W + 360s foo 930935 C T - 360s foo 931986 A M + 360s foo 932852 G T - 360s foo 933965 T A - 360s foo 935564 A W + 360s foo 936034 T Y + 360s foo 936221 AC - - 360s foo 936670 C S + 360s foo 936704 T A - 360s foo 936786 T W + 360s foo 939218 C S + 360s foo 939312 A W + 360s foo 939467 A W + 360s foo 939934 C S + 360s foo 941603 C Y + 360s foo 942910 A W + 360s foo 944654 T Y + 360s foo 945301 A C - 360s foo 945770 C T - 360s foo 946078 G S + 360s foo 948833 G K + 360s foo 948999 A W + 360s foo 949193 A R + 360s foo 950276 C M + 360s foo 950414 A W + 360s foo 951285 G C - 360s foo 953158 G R + 360s foo 953287 A W + 360s foo 954150 C G - 360s foo 954258 G - - 360s foo 955396 CC - - 360s foo 956490 - AC + 360s foo 958129 A R + 360s foo 959027 T A - 360s foo 959964 A W + 360s foo 962042 A G - 360s foo 962742 C G - 360s foo 963306 T W + 360s foo 963422 G K + 360s foo 964082 G S + 360s foo 965561 C S + 360s foo 966531 T K + 360s foo 967324 T W + 360s foo 968419 - C - 360s foo 969054 G - - 360s foo 969158 G S + 360s foo 972658 C M + 360s foo 974266 T W + 360s foo 974629 G K + 360s foo 975034 A R + 360s foo 975636 T W + 360s foo 977078 - A - 360s foo 978321 G T - 360s foo 978595 C G - 360s foo 979090 C M + 360s foo 983855 TA - - 360s foo 985725 T A - 360s foo 988497 C Y + 360s foo 990171 C M + 360s foo 990804 - CA - 360s foo 990941 T W + 360s foo 991797 A W + 360s foo 992469 A M + 360s foo 994610 C Y + 360s foo 998107 - T + 360s foo 999725 G R + 361s [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.2483.smaltmap.smalt_index foo1.fasta 361s # Command line: smalt index -k 13 -s 2 out.bam.tmp.2483.smaltmap.smalt_index foo1.fasta 361s # Reading sequences ... 361s # Writing sequence set ... 361s # Setting up hash index with collisions ... 361s # word length = 13 bases, skip step = 2 bases ... 361s # number of bits for key = 18 with 0 perfect bits 361s # Counting keys ... 361s # Counting k-tuples ... 361s # Allocating k-tuple arrays ... 361s # Counting k-tuple occurrences ... 361s # Setting the k-tuple positions in index ... 361s # Hash table is set up. 361s # =-=-=-=-= Hash Index Stats =-=-=-=-= 361s # Hash index with collisions. 361s # Word length: 13 bases 361s # Skip step: 2 bases 361s # Number of hash keys: 262144 361s # Number of word positions: 499970 361s # Number of different words: 498076 361s # Maximum number of words per key: 11 361s # Number of keys without words: 39377 361s # =-=-= End of Hash Index Stats =-=-= 361s # Writing table to file ... 361s # smalt: Total elapsed wall clock time: 0 seconds 361s [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.2483.smaltmap.smalt_sample out.bam.tmp.2483.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 361s # Command line: smalt sample -u 1000 -o out.bam.tmp.2483.smaltmap.smalt_sample out.bam.tmp.2483.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 361s # Opening read files ... 361s # Reading reference sequences ... 361s # Reading hash table ... 361s # =-=-=-=-= Hash Index Stats =-=-=-=-= 361s # Hash index with collisions. 361s # Word length: 13 bases 361s # Skip step: 2 bases 361s # Number of hash keys: 262144 361s # Number of word positions: 499970 361s # Number of different words: 498076 361s # Maximum number of words per key: 11 361s # Number of keys without words: 39377 361s # =-=-= End of Hash Index Stats =-=-= 361s # Check of read pairs ok ... 361s # Mate names match ... 361s # Sampling insert size distribution ... 366s # Processed 9999 read pairs. 366s # smalt: Time spent setting up hash index:0 seconds 366s # smalt: Time spent mapping reads:5 seconds 366s # smalt: Total elapsed wall clock time: 5 seconds 366s [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2483.smaltmap.smalt_sample -f samsoft out.bam.tmp.2483.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.2483.smaltmap.raw.bam 366s # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2483.smaltmap.smalt_sample -f samsoft out.bam.tmp.2483.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 366s # Reading distribution of insert sizes from file ... 366s # Sampled histogram 366s # Smoothed histogram 366s # Opening read files ... 366s # Reading reference sequences ... 366s # Reading hash table ... 366s # =-=-=-=-= Hash Index Stats =-=-=-=-= 366s # Hash index with collisions. 366s # Word length: 13 bases 366s # Skip step: 2 bases 366s # Number of hash keys: 262144 366s # Number of word positions: 499970 366s # Number of different words: 498076 366s # Maximum number of words per key: 11 366s # Number of keys without words: 39377 366s # =-=-= End of Hash Index Stats =-=-= 366s # Processing query reads ... 385s # Processed 10000 read pairs. 385s # smalt: Time spent setting up hash index:0 seconds 385s # smalt: Time spent mapping reads:19 seconds 385s # smalt: Total elapsed wall clock time: 19 seconds 385s [REAPR smaltmap] Running: samtools sort out.bam.tmp.2483.smaltmap.raw.bam -O bam -o out.bam.tmp.2483.smaltmap.raw.bam.sort.bam 386s [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.2483.smaltmap.raw.bam.sort.bam out.bam.tmp.2483.smaltmap.rmdup.bam 386s [bam_rmdup_core] processing reference foo... 386s [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' 386s [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.2483.smaltmap.header 386s [REAPR smaltmap] Running: samtools view -H out.bam.tmp.2483.smaltmap.rmdup.bam >> out.bam.tmp.2483.smaltmap.header 386s [REAPR smaltmap] Running: samtools reheader out.bam.tmp.2483.smaltmap.header out.bam.tmp.2483.smaltmap.rmdup.bam > out.bam 386s [REAPR smaltmap] Running: samtools index out.bam 386s [REAPR smaltmap] Running: rm out.bam.tmp.2483.smaltmap.* 386s Running reapr version 1.0.18 pipeline: 386s reapr foo1.fasta out.bam result 386s [REAPR pipeline] Running facheck 386s [REAPR pipeline] Running preprocess 390s [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases 390s [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases 390s [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases 390s [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases 392s [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation 399s [REAPR pipeline] Running stats 434s [REAPR pipeline] Running fcdrate 437s [REAPR pipeline] Running score 444s [REAPR pipeline] Running break 444s [REAPR pipeline] Running summary 445s autopkgtest [17:49:20]: test test-example: -----------------------] 446s test-example PASS 446s autopkgtest [17:49:21]: test test-example: - - - - - - - - - - results - - - - - - - - - - 446s autopkgtest [17:49:21]: @@@@@@@@@@@@@@@@@@@@ summary 446s test-example PASS 460s Creating nova instance adt-noble-arm64-reapr-20240324-174155-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...