0s autopkgtest [21:21:05]: starting date and time: 2024-03-25 21:21:05+0000 0s autopkgtest [21:21:05]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:21:05]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vfu0r2_n/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:reapr,src:curl,src:gnutls28,src:htslib,src:libpsl,src:libtabixpp,src:nettle,src:openssl --apt-upgrade reapr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=reapr/1.0.18+dfsg-5ubuntu1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 libtabixpp/1.1.2-2.1 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-s390x-22.secgroup --name adt-noble-s390x-reapr-20240325-212105-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-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/ 208s autopkgtest [21:24:33]: testbed dpkg architecture: s390x 208s autopkgtest [21:24:33]: testbed apt version: 2.7.12 208s autopkgtest [21:24:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 209s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 210s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 210s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 210s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4038 kB] 212s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 212s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 212s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 212s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 212s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 212s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB] 213s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 213s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 213s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 216s Fetched 9603 kB in 5s (1877 kB/s) 216s Reading package lists... 220s Reading package lists... 220s Building dependency tree... 220s Reading state information... 221s Calculating upgrade... 221s The following packages will be REMOVED: 221s libssl3 221s The following NEW packages will be installed: 221s libssl3t64 221s The following packages have been kept back: 221s curl 221s The following packages will be upgraded: 221s openssl 221s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 221s Need to get 2685 kB of archives. 221s After this operation, 239 kB of additional disk space will be used. 221s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 222s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 223s Fetched 2685 kB in 1s (2139 kB/s) 223s (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 ... 52170 files and directories currently installed.) 223s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 223s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 223s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 223s wget depends on libssl3 (>= 3.0.0). 223s tnftp depends on libssl3 (>= 3.0.0). 223s tcpdump depends on libssl3 (>= 3.0.0). 223s systemd-resolved depends on libssl3 (>= 3.0.0). 223s systemd depends on libssl3 (>= 3.0.0). 223s sudo depends on libssl3 (>= 3.0.0). 223s s390-tools depends on libssl3 (>= 3.0.0). 223s rsync depends on libssl3 (>= 3.0.0). 223s python3-cryptography depends on libssl3 (>= 3.0.0). 223s openssh-server depends on libssl3 (>= 3.0.10). 223s openssh-client depends on libssl3 (>= 3.0.10). 223s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 223s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 223s libssh-4:s390x depends on libssl3 (>= 3.0.0). 223s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 223s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 223s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 223s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 223s libnvme1 depends on libssl3 (>= 3.0.0). 223s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 223s libkmod2:s390x depends on libssl3 (>= 3.0.0). 223s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 223s libcurl4:s390x depends on libssl3 (>= 3.0.0). 223s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 223s kmod depends on libssl3 (>= 3.0.0). 223s dhcpcd-base depends on libssl3 (>= 3.0.0). 223s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 223s 224s (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 ... 52170 files and directories currently installed.) 224s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 224s Selecting previously unselected package libssl3t64:s390x. 224s (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 ... 52159 files and directories currently installed.) 224s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 224s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 224s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 224s Setting up openssl (3.0.13-0ubuntu2) ... 224s Processing triggers for man-db (2.12.0-3) ... 225s Processing triggers for libc-bin (2.39-0ubuntu6) ... 226s Reading package lists... 226s Building dependency tree... 226s Reading state information... 227s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 227s Unknown architecture, assuming PC-style ttyS0 227s sh: Attempting to set up Debian/Ubuntu apt sources automatically 227s sh: Distribution appears to be Ubuntu 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 229s eatmydata is already the newest version (131-1). 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s dbus is already the newest version (1.14.10-4ubuntu1). 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s rng-tools-debian is already the newest version (2.4). 230s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 230s Reading package lists... 231s Building dependency tree... 231s Reading state information... 231s The following packages will be REMOVED: 231s cloud-init* python3-configobj* python3-debconf* 231s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 231s After this operation, 3256 kB disk space will be freed. 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 ... 52172 files and directories currently installed.) 231s Removing cloud-init (24.1.2-0ubuntu1) ... 232s Removing python3-configobj (5.0.8-3) ... 232s Removing python3-debconf (1.5.86) ... 232s Processing triggers for man-db (2.12.0-3) ... 233s (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 ... 51783 files and directories currently installed.) 233s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 234s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 234s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 234s invoke-rc.d: policy-rc.d denied execution of try-restart. 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 235s linux-generic is already the newest version (6.8.0-11.11+1). 235s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 235s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 235s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 235s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 239s Reading package lists... 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 239s Calculating upgrade... 240s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 240s Reading package lists... 240s Building dependency tree... 240s Reading state information... 240s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 240s autopkgtest [21:25:05]: rebooting testbed after setup commands that affected boot 259s autopkgtest [21:25:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 262s autopkgtest [21:25:27]: @@@@@@@@@@@@@@@@@@@@ apt-source reapr 264s Get:1 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (dsc) [2293 B] 264s Get:2 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (tar) [74.6 kB] 264s Get:3 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (diff) [320 kB] 264s gpgv: Signature made Sat Nov 19 21:52:27 2022 UTC 264s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 264s gpgv: issuer "steve.langasek@ubuntu.com" 264s gpgv: Can't check signature: No public key 264s dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-5build2.dsc: no acceptable signature found 264s autopkgtest [21:25:29]: testing package reapr version 1.0.18+dfsg-5build2 265s autopkgtest [21:25:30]: build not needed 266s autopkgtest [21:25:31]: test test-example: preparing testbed 268s Reading package lists... 269s Building dependency tree... 269s Reading state information... 269s Starting pkgProblemResolver with broken count: 0 269s Starting 2 pkgProblemResolver with broken count: 0 269s Done 269s The following additional packages will be installed: 269s bamtools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 269s libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 libdeflate0 269s libfile-copy-link-perl libfontconfig1 libfreetype6 libgfortran5 libgomp1 269s libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 269s libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 libpango-1.0-0 269s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 269s libsharpyuv0 libsm6 libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 269s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 269s libxt6 r-base r-base-core r-cran-boot r-cran-class r-cran-cluster 269s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass 269s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart 269s r-cran-spatial r-cran-survival r-recommended reapr samtools smalt snpomatic 269s tabix unzip x11-common xdg-utils zip 269s Suggested packages: 269s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html cwltool 269s Recommended packages: 269s r-base-html r-doc-html r-base-dev libfile-mimeinfo-perl libnet-dbus-perl 269s libx11-protocol-perl x11-utils x11-xserver-utils 269s The following NEW packages will be installed: 269s autopkgtest-satdep bamtools fontconfig fontconfig-config fonts-dejavu-core 269s fonts-dejavu-mono libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 269s libdeflate0 libfile-copy-link-perl libfontconfig1 libfreetype6 libgfortran5 269s libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 269s libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 libpango-1.0-0 269s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 269s libsharpyuv0 libsm6 libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 269s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 269s libxt6 r-base r-base-core r-cran-boot r-cran-class r-cran-cluster 269s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass 269s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart 269s r-cran-spatial r-cran-survival r-recommended reapr samtools smalt snpomatic 269s tabix unzip x11-common xdg-utils zip 269s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 269s Need to get 61.7 MB/61.7 MB of archives. 269s After this operation, 115 MB of additional disk space will be used. 269s Get:1 /tmp/autopkgtest.iw3I62/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 270s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-4 [134 kB] 270s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libjsoncpp25 s390x 1.9.5-6 [75.5 kB] 270s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x bamtools s390x 2.5.2+dfsg-4 [163 kB] 270s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 271s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 271s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 272s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 272s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 272s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1ubuntu1 [191 kB] 272s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x libbambamc0 s390x 0.0.50-6 [39.3 kB] 272s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 272s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 272s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 272s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 272s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 272s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 273s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] 273s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 273s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x libfile-copy-link-perl all 0.140-5 [12.3 kB] 273s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 273s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 273s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 273s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 274s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 274s Get:26 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 274s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 274s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] 274s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 274s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 274s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 276s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] 276s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] 276s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libpango-1.0-0 s390x 1.51.0+ds-4 [240 kB] 276s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libpangoft2-1.0-0 s390x 1.51.0+ds-4 [43.6 kB] 276s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libpangocairo-1.0-0 s390x 1.51.0+ds-4 [28.9 kB] 276s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29 [13.3 kB] 276s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] 276s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 276s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] 276s Get:41 http://ftpmaster.internal/ubuntu noble/universe s390x libtabixpp0 s390x 1.1.2-2 [10.3 kB] 276s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libtcl8.6 s390x 8.6.13+dfsg-2 [948 kB] 277s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 277s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 277s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 277s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] 277s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build2 [8192 B] 277s Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.14-1 [833 kB] 278s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libxt6 s390x 1:1.2.1-1.1 [166 kB] 278s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13 [175 kB] 278s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu3 [180 kB] 278s Get:52 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 278s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-core s390x 4.3.2-1build1 [27.1 MB] 288s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-boot all 1.3-30-1 [619 kB] 288s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cluster s390x 2.1.6-1 [562 kB] 288s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-foreign s390x 0.8.86-1 [247 kB] 288s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mass s390x 7.3-60.0.1-1 [1122 kB] 289s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-kernsmooth s390x 2.23-22-1 [93.0 kB] 289s Get:59 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lattice s390x 0.22-5-1 [1341 kB] 289s Get:60 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nlme s390x 3.1.164-1 [2268 kB] 290s Get:61 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-matrix s390x 1.6-5-1 [3983 kB] 291s Get:62 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 292s Get:63 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-survival s390x 3.5-8-1 [6161 kB] 293s Get:64 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rpart s390x 4.1.23-1 [667 kB] 294s Get:65 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-class s390x 7.3-22-2 [88.6 kB] 294s Get:66 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nnet s390x 7.3-19-2 [112 kB] 294s Get:67 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatial s390x 7.3-17-1 [134 kB] 294s Get:68 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-codetools all 0.2-19-1 [90.5 kB] 294s Get:69 http://ftpmaster.internal/ubuntu noble/universe s390x r-recommended all 4.3.2-1build1 [2636 B] 294s Get:70 http://ftpmaster.internal/ubuntu noble/universe s390x r-base all 4.3.2-1build1 [9302 B] 294s Get:71 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 294s Get:72 http://ftpmaster.internal/ubuntu noble/universe s390x smalt s390x 0.7.6-13 [109 kB] 294s Get:73 http://ftpmaster.internal/ubuntu noble/universe s390x snpomatic s390x 1.0-7 [92.2 kB] 294s Get:74 http://ftpmaster.internal/ubuntu noble/universe s390x tabix s390x 1.18+ds-1 [527 kB] 294s Get:75 http://ftpmaster.internal/ubuntu noble/universe s390x reapr s390x 1.0.18+dfsg-5build2 [206 kB] 295s Preconfiguring packages ... 295s Fetched 61.7 MB in 25s (2496 kB/s) 295s Selecting previously unselected package libbamtools2.5.2:s390x. 295s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51728 files and directories currently installed.) 295s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_s390x.deb ... 295s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 295s Selecting previously unselected package libjsoncpp25:s390x. 295s Preparing to unpack .../01-libjsoncpp25_1.9.5-6_s390x.deb ... 295s Unpacking libjsoncpp25:s390x (1.9.5-6) ... 295s Selecting previously unselected package bamtools. 295s Preparing to unpack .../02-bamtools_2.5.2+dfsg-4_s390x.deb ... 295s Unpacking bamtools (2.5.2+dfsg-4) ... 295s Selecting previously unselected package libfreetype6:s390x. 295s Preparing to unpack .../03-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 295s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 295s Selecting previously unselected package fonts-dejavu-mono. 295s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 295s Unpacking fonts-dejavu-mono (2.37-8) ... 295s Selecting previously unselected package fonts-dejavu-core. 295s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 295s Unpacking fonts-dejavu-core (2.37-8) ... 295s Selecting previously unselected package fontconfig-config. 295s Preparing to unpack .../06-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 295s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 295s Selecting previously unselected package libfontconfig1:s390x. 295s Preparing to unpack .../07-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 295s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 295s Selecting previously unselected package fontconfig. 295s Preparing to unpack .../08-fontconfig_2.15.0-1ubuntu1_s390x.deb ... 295s Unpacking fontconfig (2.15.0-1ubuntu1) ... 295s Selecting previously unselected package libbambamc0:s390x. 295s Preparing to unpack .../09-libbambamc0_0.0.50-6_s390x.deb ... 295s Unpacking libbambamc0:s390x (0.0.50-6) ... 295s Selecting previously unselected package libblas3:s390x. 295s Preparing to unpack .../10-libblas3_3.12.0-3_s390x.deb ... 295s Unpacking libblas3:s390x (3.12.0-3) ... 295s Selecting previously unselected package libpixman-1-0:s390x. 295s Preparing to unpack .../11-libpixman-1-0_0.42.2-1_s390x.deb ... 295s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 295s Selecting previously unselected package libxcb-render0:s390x. 295s Preparing to unpack .../12-libxcb-render0_1.15-1_s390x.deb ... 295s Unpacking libxcb-render0:s390x (1.15-1) ... 295s Selecting previously unselected package libxcb-shm0:s390x. 295s Preparing to unpack .../13-libxcb-shm0_1.15-1_s390x.deb ... 295s Unpacking libxcb-shm0:s390x (1.15-1) ... 295s Selecting previously unselected package libxrender1:s390x. 295s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 295s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 295s Selecting previously unselected package libcairo2:s390x. 295s Preparing to unpack .../15-libcairo2_1.18.0-1_s390x.deb ... 295s Unpacking libcairo2:s390x (1.18.0-1) ... 295s Selecting previously unselected package libdatrie1:s390x. 295s Preparing to unpack .../16-libdatrie1_0.2.13-3_s390x.deb ... 295s Unpacking libdatrie1:s390x (0.2.13-3) ... 295s Selecting previously unselected package libdeflate0:s390x. 295s Preparing to unpack .../17-libdeflate0_1.19-1_s390x.deb ... 295s Unpacking libdeflate0:s390x (1.19-1) ... 295s Selecting previously unselected package libfile-copy-link-perl. 295s Preparing to unpack .../18-libfile-copy-link-perl_0.140-5_all.deb ... 295s Unpacking libfile-copy-link-perl (0.140-5) ... 295s Selecting previously unselected package libgfortran5:s390x. 296s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 296s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 296s Selecting previously unselected package libgomp1:s390x. 296s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 296s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 296s Selecting previously unselected package libgraphite2-3:s390x. 296s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_s390x.deb ... 296s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 296s Selecting previously unselected package libharfbuzz0b:s390x. 296s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_s390x.deb ... 296s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 296s Selecting previously unselected package libhtscodecs2:s390x. 296s Preparing to unpack .../23-libhtscodecs2_1.6.0-1_s390x.deb ... 296s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 296s Selecting previously unselected package libhts3:s390x. 296s Preparing to unpack .../24-libhts3_1.18+ds-1_s390x.deb ... 296s Unpacking libhts3:s390x (1.18+ds-1) ... 296s Selecting previously unselected package x11-common. 296s Preparing to unpack .../25-x11-common_1%3a7.7+23ubuntu2_all.deb ... 296s Unpacking x11-common (1:7.7+23ubuntu2) ... 296s Selecting previously unselected package libice6:s390x. 296s Preparing to unpack .../26-libice6_2%3a1.0.10-1build2_s390x.deb ... 296s Unpacking libice6:s390x (2:1.0.10-1build2) ... 296s Selecting previously unselected package libjpeg-turbo8:s390x. 296s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 296s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 296s Selecting previously unselected package libjpeg8:s390x. 296s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_s390x.deb ... 296s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 296s Selecting previously unselected package liblapack3:s390x. 296s Preparing to unpack .../29-liblapack3_3.12.0-3_s390x.deb ... 296s Unpacking liblapack3:s390x (3.12.0-3) ... 296s Selecting previously unselected package libthai-data. 296s Preparing to unpack .../30-libthai-data_0.1.29-2_all.deb ... 296s Unpacking libthai-data (0.1.29-2) ... 296s Selecting previously unselected package libthai0:s390x. 296s Preparing to unpack .../31-libthai0_0.1.29-2_s390x.deb ... 296s Unpacking libthai0:s390x (0.1.29-2) ... 296s Selecting previously unselected package libpango-1.0-0:s390x. 296s Preparing to unpack .../32-libpango-1.0-0_1.51.0+ds-4_s390x.deb ... 296s Unpacking libpango-1.0-0:s390x (1.51.0+ds-4) ... 296s Selecting previously unselected package libpangoft2-1.0-0:s390x. 296s Preparing to unpack .../33-libpangoft2-1.0-0_1.51.0+ds-4_s390x.deb ... 296s Unpacking libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 296s Selecting previously unselected package libpangocairo-1.0-0:s390x. 296s Preparing to unpack .../34-libpangocairo-1.0-0_1.51.0+ds-4_s390x.deb ... 296s Unpacking libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 296s Selecting previously unselected package libpaper1:s390x. 296s Preparing to unpack .../35-libpaper1_1.1.29_s390x.deb ... 296s Unpacking libpaper1:s390x (1.1.29) ... 296s Selecting previously unselected package libpaper-utils. 296s Preparing to unpack .../36-libpaper-utils_1.1.29_s390x.deb ... 296s Unpacking libpaper-utils (1.1.29) ... 296s Selecting previously unselected package libsharpyuv0:s390x. 296s Preparing to unpack .../37-libsharpyuv0_1.3.2-0.4_s390x.deb ... 296s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 296s Selecting previously unselected package libsm6:s390x. 296s Preparing to unpack .../38-libsm6_2%3a1.2.3-1build2_s390x.deb ... 296s Unpacking libsm6:s390x (2:1.2.3-1build2) ... 296s Selecting previously unselected package libtabixpp0:s390x. 296s Preparing to unpack .../39-libtabixpp0_1.1.2-2_s390x.deb ... 296s Unpacking libtabixpp0:s390x (1.1.2-2) ... 296s Selecting previously unselected package libtcl8.6:s390x. 296s Preparing to unpack .../40-libtcl8.6_8.6.13+dfsg-2_s390x.deb ... 296s Unpacking libtcl8.6:s390x (8.6.13+dfsg-2) ... 296s Selecting previously unselected package libjbig0:s390x. 296s Preparing to unpack .../41-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 296s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 296s Selecting previously unselected package libwebp7:s390x. 296s Preparing to unpack .../42-libwebp7_1.3.2-0.4_s390x.deb ... 296s Unpacking libwebp7:s390x (1.3.2-0.4) ... 296s Selecting previously unselected package libtiff6:s390x. 296s Preparing to unpack .../43-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 296s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 296s Selecting previously unselected package libxft2:s390x. 296s Preparing to unpack .../44-libxft2_2.3.6-1_s390x.deb ... 296s Unpacking libxft2:s390x (2.3.6-1) ... 296s Selecting previously unselected package libxss1:s390x. 296s Preparing to unpack .../45-libxss1_1%3a1.2.3-1build2_s390x.deb ... 296s Unpacking libxss1:s390x (1:1.2.3-1build2) ... 296s Selecting previously unselected package libtk8.6:s390x. 296s Preparing to unpack .../46-libtk8.6_8.6.14-1_s390x.deb ... 296s Unpacking libtk8.6:s390x (8.6.14-1) ... 296s Selecting previously unselected package libxt6:s390x. 296s Preparing to unpack .../47-libxt6_1%3a1.2.1-1.1_s390x.deb ... 296s Unpacking libxt6:s390x (1:1.2.1-1.1) ... 296s Selecting previously unselected package zip. 296s Preparing to unpack .../48-zip_3.0-13_s390x.deb ... 296s Unpacking zip (3.0-13) ... 296s Selecting previously unselected package unzip. 296s Preparing to unpack .../49-unzip_6.0-28ubuntu3_s390x.deb ... 296s Unpacking unzip (6.0-28ubuntu3) ... 296s Selecting previously unselected package xdg-utils. 296s Preparing to unpack .../50-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 296s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 297s Selecting previously unselected package r-base-core. 297s Preparing to unpack .../51-r-base-core_4.3.2-1build1_s390x.deb ... 297s Unpacking r-base-core (4.3.2-1build1) ... 297s Selecting previously unselected package r-cran-boot. 297s Preparing to unpack .../52-r-cran-boot_1.3-30-1_all.deb ... 297s Unpacking r-cran-boot (1.3-30-1) ... 297s Selecting previously unselected package r-cran-cluster. 297s Preparing to unpack .../53-r-cran-cluster_2.1.6-1_s390x.deb ... 297s Unpacking r-cran-cluster (2.1.6-1) ... 297s Selecting previously unselected package r-cran-foreign. 297s Preparing to unpack .../54-r-cran-foreign_0.8.86-1_s390x.deb ... 297s Unpacking r-cran-foreign (0.8.86-1) ... 297s Selecting previously unselected package r-cran-mass. 297s Preparing to unpack .../55-r-cran-mass_7.3-60.0.1-1_s390x.deb ... 297s Unpacking r-cran-mass (7.3-60.0.1-1) ... 297s Selecting previously unselected package r-cran-kernsmooth. 297s Preparing to unpack .../56-r-cran-kernsmooth_2.23-22-1_s390x.deb ... 297s Unpacking r-cran-kernsmooth (2.23-22-1) ... 297s Selecting previously unselected package r-cran-lattice. 297s Preparing to unpack .../57-r-cran-lattice_0.22-5-1_s390x.deb ... 297s Unpacking r-cran-lattice (0.22-5-1) ... 297s Selecting previously unselected package r-cran-nlme. 297s Preparing to unpack .../58-r-cran-nlme_3.1.164-1_s390x.deb ... 297s Unpacking r-cran-nlme (3.1.164-1) ... 297s Selecting previously unselected package r-cran-matrix. 297s Preparing to unpack .../59-r-cran-matrix_1.6-5-1_s390x.deb ... 297s Unpacking r-cran-matrix (1.6-5-1) ... 297s Selecting previously unselected package r-cran-mgcv. 297s Preparing to unpack .../60-r-cran-mgcv_1.9-1-1_s390x.deb ... 297s Unpacking r-cran-mgcv (1.9-1-1) ... 297s Selecting previously unselected package r-cran-survival. 297s Preparing to unpack .../61-r-cran-survival_3.5-8-1_s390x.deb ... 297s Unpacking r-cran-survival (3.5-8-1) ... 297s Selecting previously unselected package r-cran-rpart. 297s Preparing to unpack .../62-r-cran-rpart_4.1.23-1_s390x.deb ... 297s Unpacking r-cran-rpart (4.1.23-1) ... 297s Selecting previously unselected package r-cran-class. 297s Preparing to unpack .../63-r-cran-class_7.3-22-2_s390x.deb ... 297s Unpacking r-cran-class (7.3-22-2) ... 298s Selecting previously unselected package r-cran-nnet. 298s Preparing to unpack .../64-r-cran-nnet_7.3-19-2_s390x.deb ... 298s Unpacking r-cran-nnet (7.3-19-2) ... 298s Selecting previously unselected package r-cran-spatial. 298s Preparing to unpack .../65-r-cran-spatial_7.3-17-1_s390x.deb ... 298s Unpacking r-cran-spatial (7.3-17-1) ... 298s Selecting previously unselected package r-cran-codetools. 298s Preparing to unpack .../66-r-cran-codetools_0.2-19-1_all.deb ... 298s Unpacking r-cran-codetools (0.2-19-1) ... 298s Selecting previously unselected package r-recommended. 298s Preparing to unpack .../67-r-recommended_4.3.2-1build1_all.deb ... 298s Unpacking r-recommended (4.3.2-1build1) ... 298s Selecting previously unselected package r-base. 298s Preparing to unpack .../68-r-base_4.3.2-1build1_all.deb ... 298s Unpacking r-base (4.3.2-1build1) ... 298s Selecting previously unselected package samtools. 298s Preparing to unpack .../69-samtools_1.19.2-1_s390x.deb ... 298s Unpacking samtools (1.19.2-1) ... 298s Selecting previously unselected package smalt. 298s Preparing to unpack .../70-smalt_0.7.6-13_s390x.deb ... 298s Unpacking smalt (0.7.6-13) ... 298s Selecting previously unselected package snpomatic. 298s Preparing to unpack .../71-snpomatic_1.0-7_s390x.deb ... 298s Unpacking snpomatic (1.0-7) ... 298s Selecting previously unselected package tabix. 298s Preparing to unpack .../72-tabix_1.18+ds-1_s390x.deb ... 298s Unpacking tabix (1.18+ds-1) ... 298s Selecting previously unselected package reapr. 298s Preparing to unpack .../73-reapr_1.0.18+dfsg-5build2_s390x.deb ... 298s Unpacking reapr (1.0.18+dfsg-5build2) ... 298s Selecting previously unselected package autopkgtest-satdep. 298s Preparing to unpack .../74-1-autopkgtest-satdep.deb ... 298s Unpacking autopkgtest-satdep (0) ... 298s Setting up libhtscodecs2:s390x (1.6.0-1) ... 298s Setting up libgraphite2-3:s390x (1.3.14-2) ... 298s Setting up libpixman-1-0:s390x (0.42.2-1) ... 298s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 298s Setting up libpaper1:s390x (1.1.29) ... 298s 298s Creating config file /etc/papersize with new version 298s Setting up libfile-copy-link-perl (0.140-5) ... 298s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 298s Setting up libdatrie1:s390x (0.2.13-3) ... 298s Setting up libxcb-render0:s390x (1.15-1) ... 298s Setting up unzip (6.0-28ubuntu3) ... 298s Setting up x11-common (1:7.7+23ubuntu2) ... 298s Setting up libdeflate0:s390x (1.19-1) ... 298s Setting up libxcb-shm0:s390x (1.15-1) ... 298s Setting up libpaper-utils (1.1.29) ... 298s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 298s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 298s Setting up zip (3.0-13) ... 298s Setting up libblas3:s390x (3.12.0-3) ... 298s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 298s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 298s Setting up libbambamc0:s390x (0.0.50-6) ... 298s Setting up fonts-dejavu-mono (2.37-8) ... 298s Setting up libtcl8.6:s390x (8.6.13+dfsg-2) ... 298s Setting up libjsoncpp25:s390x (1.9.5-6) ... 298s Setting up fonts-dejavu-core (2.37-8) ... 298s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 298s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 298s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 298s Setting up libwebp7:s390x (1.3.2-0.4) ... 298s Setting up bamtools (2.5.2+dfsg-4) ... 298s Setting up snpomatic (1.0-7) ... 298s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 298s Setting up libthai-data (0.1.29-2) ... 298s Setting up libxss1:s390x (1:1.2.3-1build2) ... 298s Setting up tabix (1.18+ds-1) ... 298s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 298s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 298s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 298s Setting up smalt (0.7.6-13) ... 298s Setting up libice6:s390x (2:1.0.10-1build2) ... 298s Setting up liblapack3:s390x (3.12.0-3) ... 298s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 298s Setting up libhts3:s390x (1.18+ds-1) ... 298s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 299s Setting up samtools (1.19.2-1) ... 299s Setting up libthai0:s390x (0.1.29-2) ... 299s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 299s Setting up libtabixpp0:s390x (1.1.2-2) ... 299s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 299s Setting up libsm6:s390x (2:1.2.3-1build2) ... 299s Setting up fontconfig (2.15.0-1ubuntu1) ... 301s Regenerating fonts cache... done. 301s Setting up libxft2:s390x (2.3.6-1) ... 301s Setting up libtk8.6:s390x (8.6.14-1) ... 301s Setting up libpango-1.0-0:s390x (1.51.0+ds-4) ... 301s Setting up libcairo2:s390x (1.18.0-1) ... 301s Setting up libxt6:s390x (1:1.2.1-1.1) ... 301s Setting up libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 301s Setting up libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 301s Setting up r-base-core (4.3.2-1build1) ... 301s 301s Creating config file /etc/R/Renviron with new version 301s Setting up r-cran-lattice (0.22-5-1) ... 301s Setting up r-cran-nlme (3.1.164-1) ... 301s Setting up r-cran-cluster (2.1.6-1) ... 301s Setting up r-cran-nnet (7.3-19-2) ... 301s Setting up r-cran-codetools (0.2-19-1) ... 301s Setting up r-cran-boot (1.3-30-1) ... 301s Setting up r-cran-spatial (7.3-17-1) ... 301s Setting up r-cran-mass (7.3-60.0.1-1) ... 301s Setting up r-cran-foreign (0.8.86-1) ... 301s Setting up r-cran-matrix (1.6-5-1) ... 301s Setting up r-cran-kernsmooth (2.23-22-1) ... 301s Setting up r-cran-mgcv (1.9-1-1) ... 301s Setting up r-cran-class (7.3-22-2) ... 301s Setting up r-cran-survival (3.5-8-1) ... 301s Setting up r-cran-rpart (4.1.23-1) ... 301s Setting up r-recommended (4.3.2-1build1) ... 301s Setting up r-base (4.3.2-1build1) ... 301s Setting up reapr (1.0.18+dfsg-5build2) ... 301s Setting up autopkgtest-satdep (0) ... 301s Processing triggers for man-db (2.12.0-3) ... 302s Processing triggers for install-info (7.1-3) ... 302s Processing triggers for libc-bin (2.39-0ubuntu6) ... 306s (Reading database ... 54920 files and directories currently installed.) 306s Removing autopkgtest-satdep (0) ... 307s autopkgtest [21:26:12]: test test-example: [----------------------- 307s [wgsim] seed = 42 307s [wgsim_core] calculating the total length of the reference sequence... 307s [wgsim_core] 1 sequences, total length: 1000111 307s foo 1384 T K + 307s foo 4961 T W + 307s foo 5885 - T - 307s foo 9598 A C - 307s foo 10177 G R + 307s foo 11305 G K + 307s foo 11592 G R + 307s foo 13931 T - - 307s foo 15907 C A - 307s foo 17264 G K + 307s foo 17780 A - - 307s foo 18711 A W + 307s foo 19249 T W + 307s foo 19522 C S + 307s foo 23053 T K + 307s foo 23681 A R + 307s foo 23730 C S + 307s foo 24075 G S + 307s foo 24555 G C - 307s foo 26775 G K + 307s foo 26896 C M + 307s foo 27253 G K + 307s foo 28210 T Y + 307s foo 28224 A W + 307s foo 28377 - G + 307s foo 29035 G K + 307s foo 29898 C M + 307s foo 30274 A R + 307s foo 30542 G K + 307s foo 31566 A C - 307s foo 32252 - A - 307s foo 33303 T K + 307s foo 33390 - G + 307s foo 34073 A R + 307s foo 34171 G R + 307s foo 34718 T Y + 307s foo 34801 - C + 307s foo 35204 T W + 307s foo 35342 G S + 307s foo 35489 G T - 307s foo 36153 A M + 307s foo 36273 C S + 307s foo 37356 G T - 307s foo 37596 C S + 307s foo 39308 T - - 307s foo 40333 C G - 307s foo 42295 T K + 307s foo 42372 T Y + 307s foo 44433 C G - 307s foo 44630 - AG + 307s foo 44902 T C - 307s foo 47156 C A - 307s foo 48210 C M + 307s foo 48390 A R + 307s foo 49652 C M + 307s foo 52739 T Y + 307s foo 52858 A M + 307s foo 54737 A G - 307s foo 55306 C T - 307s foo 55434 C T - 307s foo 59204 A W + 307s foo 59300 G C - 307s foo 59335 T Y + 307s foo 59444 T - - 307s foo 59531 C S + 307s foo 59766 C Y + 307s foo 61950 C S + 307s foo 62887 G S + 307s foo 63390 A G - 307s foo 64365 G K + 307s foo 64703 C S + 307s foo 64932 C Y + 307s foo 68383 - CG + 307s foo 68464 A W + 307s foo 68727 A W + 307s foo 69080 A M + 307s foo 72071 T C - 307s foo 72720 - G - 307s foo 73354 C T - 307s foo 73637 G T - 307s foo 74741 A M + 307s foo 75101 C T - 307s foo 75207 T K + 307s foo 76400 T Y + 307s foo 76780 A C - 307s foo 77172 A W + 307s foo 78385 C Y + 307s foo 80705 C M + 307s foo 82440 A R + 307s foo 83021 G K + 307s foo 83116 A - - 307s foo 83846 T K + 307s foo 84633 G S + 307s foo 85891 G S + 307s foo 87759 A C - 307s foo 87778 T W + 307s foo 88581 T K + 307s foo 88606 T Y + 307s foo 88880 A G - 307s foo 89945 G C - 307s foo 90728 T K + 307s foo 91798 G R + 307s foo 95957 G C - 307s foo 96173 T W + 307s foo 96665 A M + 307s foo 98019 - G + 307s foo 98131 A M + 307s foo 98669 A R + 307s foo 98719 G T - 307s foo 99062 A W + 307s foo 99590 A T - 307s foo 100532 - TC + 307s foo 103015 A W + 307s foo 103172 G S + 307s foo 103609 G R + 307s foo 106549 T Y + 307s foo 108808 C Y + 307s foo 109191 G C - 307s foo 111686 C G - 307s foo 113436 C A - 307s foo 113763 A W + 307s foo 115671 C T - 307s foo 117460 - A - 307s foo 118193 G - - 307s foo 118585 T K + 307s foo 121219 A M + 307s foo 121876 T K + 307s foo 122071 T A - 307s foo 124918 C G - 307s foo 125300 G S + 307s foo 125967 C S + 307s foo 127443 G S + 307s foo 127565 C Y + 307s foo 128700 C A - 307s foo 129912 G A - 307s foo 130847 T W + 307s foo 131677 G S + 307s foo 132189 T C - 307s foo 135878 CGGC - - 307s foo 136825 T K + 307s foo 138881 TGT - - 307s foo 139288 A W + 307s foo 141054 A W + 307s foo 141055 - T + 307s foo 141101 C S + 307s foo 141404 A R + 307s foo 142698 T C - 307s foo 143990 C A - 307s foo 144167 T Y + 307s foo 144814 C Y + 307s foo 146381 T Y + 307s foo 146393 C A - 307s foo 146510 A C - 307s foo 147182 A W + 307s foo 148783 T C - 307s foo 149068 G S + 307s foo 150208 T K + 307s foo 151554 T W + 307s foo 151709 C G - 307s foo 153072 G R + 307s foo 153307 T Y + 307s foo 154050 G S + 307s foo 154415 C S + 307s foo 154594 G R + 307s foo 155839 G T - 307s foo 156106 G A - 307s foo 159356 T W + 307s foo 159926 A W + 307s foo 160303 T K + 307s foo 161323 C Y + 307s foo 161904 G S + 307s foo 162533 - ACC - 307s foo 164738 C G - 307s foo 165413 A R + 307s foo 166944 C M + 307s foo 167464 T Y + 307s foo 168420 T C - 307s foo 168579 A M + 307s foo 168787 T W + 307s foo 168959 A T - 307s foo 169884 G S + 307s foo 170032 G T - 307s foo 172058 G K + 307s foo 174942 A R + 307s foo 175014 G K + 307s foo 178406 G A - 307s foo 179028 - A + 307s foo 182394 C M + 307s foo 182735 T Y + 307s foo 183384 T K + 307s foo 183893 - AT - 307s foo 185360 G A - 307s foo 185538 - G - 307s foo 187948 G S + 307s foo 188120 T G - 307s foo 188179 T W + 307s foo 188316 T Y + 307s foo 189963 - G + 307s foo 190093 C Y + 307s foo 192220 C M + 307s foo 192368 A W + 307s foo 192782 T K + 307s foo 193307 A R + 307s foo 193501 G K + 307s foo 194276 G S + 307s foo 194930 C S + 307s foo 196728 A W + 307s foo 197559 G C - 307s foo 198467 T W + 307s foo 199042 C Y + 307s foo 199259 AA - - 307s foo 199687 TT - - 307s foo 200287 C A - 307s foo 200678 A R + 307s foo 201208 C T - 307s foo 201882 A - - 307s foo 204456 T K + 307s foo 206327 G R + 307s foo 207311 G T - 307s foo 209184 G A - 307s foo 209279 C Y + 307s foo 211459 C Y + 307s foo 213807 T Y + 307s foo 213846 T Y + 307s foo 214635 A G - 307s foo 214884 C A - 307s foo 216244 A M + 307s foo 216652 A M + 307s foo 216745 T - - 307s foo 216909 A T - 307s foo 217579 A G - 307s foo 217895 C Y + 307s foo 218870 G K + 307s foo 223098 T A - 307s foo 223283 - C + 307s foo 223666 C A - 307s foo 224011 - C + 307s foo 225681 C S + 307s foo 227345 T C - 307s foo 228778 T G - 307s foo 229926 C - - 307s foo 230778 T K + 307s foo 230939 CG - - 307s foo 231988 CT - - 307s foo 234593 T W + 307s foo 235496 C S + 307s foo 235705 G K + 307s foo 235758 A G - 307s foo 236852 T C - 307s foo 238790 A M + 307s foo 238865 T K + 307s foo 239329 A M + 307s foo 239576 - C + 307s foo 243058 G S + 307s foo 244147 T - - 307s foo 244462 C G - 307s foo 245443 - A + 307s foo 246544 C Y + 307s foo 246744 T W + 307s foo 247473 C M + 307s foo 248129 C T - 307s foo 249060 A C - 307s foo 249515 G T - 307s foo 250138 G S + 307s foo 250567 C A - 307s foo 254381 G R + 307s foo 257864 C M + 307s foo 257879 C Y + 307s foo 259859 A M + 307s foo 260643 C S + 307s foo 261681 C G - 307s foo 262645 T Y + 307s foo 263279 A R + 307s foo 263575 A - - 307s foo 264587 - TA + 307s foo 264689 T K + 307s foo 265758 G K + 307s foo 266272 A M + 307s foo 268550 C M + 307s foo 269986 G S + 307s foo 270321 AC - - 307s foo 273346 C S + 307s foo 275367 C A - 307s foo 277334 C G - 307s foo 277629 G T - 307s foo 278431 C Y + 307s foo 281456 T Y + 307s foo 281556 T G - 307s foo 281737 G K + 307s foo 282290 AC - - 307s foo 282851 - C - 307s foo 284405 A C - 307s foo 288751 A C - 307s foo 290501 TAAA - - 307s foo 291315 A W + 307s foo 291368 C - - 307s foo 292154 A C - 307s foo 292385 C M + 307s foo 292555 G K + 307s foo 297709 G C - 307s foo 298183 A W + 307s foo 298228 T W + 307s foo 299902 T G - 307s foo 302575 A T - 307s foo 304823 G R + 307s foo 305308 T Y + 307s foo 305487 G S + 307s foo 305697 G T - 307s foo 306098 C G - 307s foo 306882 T Y + 307s foo 308201 A M + 307s foo 308833 A T - 307s foo 312033 A - - 307s foo 312895 C G - 307s foo 313889 C - - 307s foo 315109 A R + 307s foo 316083 C - - 307s foo 316466 A R + 307s foo 318040 G C - 307s foo 319446 T C - 307s foo 320236 C S + 307s foo 320652 A - - 307s foo 320716 T K + 307s foo 323644 A - - 307s foo 325359 G T - 307s foo 329476 - CA + 307s foo 329706 T G - 307s foo 330181 T Y + 307s foo 330703 C Y + 307s foo 331315 G S + 307s foo 332351 C A - 307s foo 333408 A R + 307s foo 333468 C S + 307s foo 336247 A G - 307s foo 336586 A M + 307s foo 337364 G K + 307s foo 337686 A T - 307s foo 338043 A - - 307s foo 338292 C G - 307s foo 338962 A C - 307s foo 339353 G K + 307s foo 340647 - A + 307s foo 341705 G R + 307s foo 344283 C M + 307s foo 345898 - AG - 307s foo 347959 T - - 307s foo 349162 C M + 307s foo 352072 T Y + 307s foo 354614 C Y + 307s foo 359304 T - - 307s foo 359312 - G + 307s foo 360972 C S + 307s foo 363857 C Y + 307s foo 366226 A C - 307s foo 367259 C M + 307s foo 372502 T Y + 307s foo 372747 A M + 307s foo 375140 C S + 307s foo 376298 T W + 307s foo 376313 C - - 307s foo 376760 T W + 307s foo 378494 A W + 307s foo 381137 T G - 307s foo 381186 A R + 307s foo 381701 A G - 307s foo 382614 A W + 307s foo 382761 C T - 307s foo 382854 T C - 307s foo 383201 C T - 307s foo 385104 G S + 307s foo 385233 - A + 307s foo 386138 C T - 307s foo 386316 A W + 307s foo 387072 A R + 307s foo 387642 - A + 307s foo 388232 T C - 307s foo 388890 GGG - - 307s foo 390508 C S + 307s foo 390625 C M + 307s foo 391921 C G - 307s foo 395256 G T - 307s foo 395542 G S + 307s foo 397015 A - - 307s foo 397516 C Y + 307s foo 397528 GC - - 307s foo 398152 C T - 307s foo 399802 A W + 307s foo 400972 T K + 307s foo 401419 - T + 307s foo 401477 T W + 307s foo 402437 A M + 307s foo 402722 G R + 307s foo 403452 C M + 307s foo 404234 - A + 307s foo 405344 A W + 307s foo 407040 G S + 307s foo 408483 G R + 307s foo 408586 A C - 307s foo 408721 A R + 307s foo 409494 A M + 307s foo 410078 A G - 307s foo 411170 C A - 307s foo 415342 T Y + 307s foo 416265 C G - 307s foo 417740 C A - 307s foo 418622 C S + 307s foo 420232 A W + 307s foo 420288 T Y + 307s foo 420908 A W + 307s foo 421109 T A - 307s foo 421357 A R + 307s foo 422799 G A - 307s foo 424383 C S + 307s foo 424871 - GCA + 307s foo 427273 T A - 307s foo 429822 C M + 307s foo 429846 T W + 307s foo 432015 A G - 307s foo 432414 G K + 307s foo 433606 C Y + 307s foo 433831 T Y + 307s foo 437721 - A - 307s foo 438402 G - - 307s foo 438799 A T - 307s foo 439422 C M + 307s foo 440734 C A - 307s foo 441840 T G - 307s foo 442021 - C + 307s foo 445021 T A - 307s foo 445591 G A - 307s foo 446138 T W + 307s foo 447757 A W + 307s foo 449156 T - - 307s foo 449161 G K + 307s foo 450114 A W + 307s foo 450688 A W + 307s foo 454421 C G - 307s foo 454718 T Y + 307s foo 455675 TC - - 307s foo 461721 G R + 307s foo 462526 G S + 307s foo 467296 G A - 307s foo 467510 G K + 307s foo 468267 T K + 307s foo 469118 G R + 307s foo 469830 C Y + 307s foo 471073 G T - 307s foo 472056 G A - 307s foo 472773 - A + 307s foo 473046 G R + 307s foo 473188 G A - 307s foo 473742 C - - 307s foo 474789 T A - 307s foo 477763 G R + 307s foo 478246 T W + 307s foo 478975 T G - 307s foo 479038 A R + 307s foo 480275 T Y + 307s foo 480317 G A - 307s foo 481512 T K + 307s foo 482069 G S + 307s foo 482534 A R + 307s foo 483760 C Y + 307s foo 485281 T W + 307s foo 486255 T C - 307s foo 487038 T K + 307s foo 487225 T A - 307s foo 488012 C Y + 307s foo 488795 T C - 307s foo 490241 A R + 307s foo 492595 - CGG + 307s foo 493224 C A - 307s foo 494284 A T - 307s foo 495990 - T - 307s foo 497306 A R + 307s foo 497403 T Y + 307s foo 499569 C Y + 307s foo 499651 T K + 307s foo 503139 T C - 307s foo 504660 A R + 307s foo 508679 C - - 307s foo 513643 G K + 307s foo 515668 CC - - 307s foo 515836 G R + 307s foo 516488 C S + 307s foo 517602 G R + 307s foo 517962 G K + 307s foo 517975 T K + 307s foo 519144 A T - 307s foo 520068 T K + 307s foo 520926 A W + 307s foo 521562 C S + 307s foo 522076 CG - - 307s foo 522838 T Y + 307s foo 523513 - C + 307s foo 523907 - TA + 307s foo 526271 T A - 307s foo 526533 AC - - 307s foo 526767 C Y + 307s foo 528217 C Y + 307s foo 531924 G S + 307s foo 532333 - TT + 307s foo 533132 C M + 307s foo 534689 A T - 307s foo 534779 A W + 307s foo 535594 C A - 307s foo 535795 G R + 307s foo 538368 A R + 307s foo 540879 G K + 307s foo 542530 A - - 307s foo 543620 G R + 307s foo 544733 - C - 307s foo 546300 - TT + 307s foo 548196 A T - 307s foo 548878 C M + 307s foo 548885 G R + 307s foo 549459 T K + 307s foo 550908 A G - 307s foo 551170 A - - 307s foo 553130 T Y + 307s foo 555293 T G - 307s foo 556198 G R + 307s foo 556355 A T - 307s foo 557688 G K + 307s foo 558415 G C - 307s foo 558461 - G + 307s foo 559287 T Y + 307s foo 559465 C M + 307s foo 560184 T W + 307s foo 560252 T W + 307s foo 562579 A M + 307s foo 562961 G A - 307s foo 566986 C A - 307s foo 568134 C A - 307s foo 569698 T C - 307s foo 570180 T K + 307s foo 570451 TG - - 307s foo 570832 - A - 307s foo 571589 A W + 307s foo 572208 C M + 307s foo 572871 C S + 307s foo 574334 G - - 307s foo 575673 T Y + 307s foo 576797 G S + 307s foo 578486 - C - 307s foo 578494 C S + 307s foo 579257 G A - 307s foo 580103 G T - 307s foo 580872 A W + 307s foo 580925 G S + 307s foo 580950 G C - 307s foo 581637 T Y + 307s foo 581654 A G - 307s foo 582538 A T - 307s foo 582691 C M + 307s foo 582938 A W + 307s foo 583104 T K + 307s foo 584763 T W + 307s foo 585723 T W + 307s foo 588253 T Y + 307s foo 588972 T C - 307s foo 589438 - C - 307s foo 591131 C Y + 307s foo 591950 G R + 307s foo 592194 T G - 307s foo 592310 G S + 307s foo 593892 G A - 307s foo 598556 A - - 307s foo 601660 G S + 307s foo 602112 G T - 307s foo 602412 T Y + 307s foo 607282 - C + 307s foo 607394 A M + 307s foo 608438 A T - 307s foo 609255 A W + 307s foo 609365 - T + 307s foo 611161 G K + 307s foo 612224 C G - 307s foo 614493 G R + 307s foo 614601 G A - 307s foo 614607 C Y + 307s foo 619507 C M + 307s foo 619798 T C - 307s foo 621872 C T - 307s foo 622375 C Y + 307s foo 623208 - G - 307s foo 624366 C A - 307s foo 625320 - ACA - 307s foo 626664 - G + 307s foo 627140 T C - 307s foo 627353 G T - 307s foo 628714 T Y + 307s foo 628744 A - - 307s foo 629152 A G - 307s foo 630110 T G - 307s foo 631744 G K + 307s foo 632763 C S + 307s foo 634419 G - - 307s foo 634459 A G - 307s foo 634571 G A - 307s foo 635366 - A + 307s foo 635604 G T - 307s foo 637057 T C - 307s foo 637525 A T - 307s foo 638412 A R + 307s foo 640547 A W + 307s foo 641514 T K + 307s foo 642219 A R + 307s foo 642427 A G - 307s foo 642612 A R + 307s foo 643553 T W + 307s foo 647316 - T + 307s foo 647598 C - - 307s foo 651093 G A - 307s foo 651718 G R + 307s foo 652235 A G - 307s foo 652579 A C - 307s foo 653355 A W + 307s foo 655174 C M + 307s foo 655487 A M + 307s foo 656849 G S + 307s foo 661081 T K + 307s foo 661134 G C - 307s foo 661935 A W + 307s foo 662010 A M + 307s foo 662040 G R + 307s foo 663030 A W + 307s foo 663268 - C + 307s foo 664991 T - - 307s foo 665489 T K + 307s foo 665555 C M + 307s foo 665965 C Y + 307s foo 668725 A C - 307s foo 668834 - G - 307s foo 668873 C S + 307s foo 669654 T W + 307s foo 671041 G S + 307s foo 671485 T W + 307s foo 671690 C M + 307s foo 673022 G R + 307s foo 674137 - T + 307s foo 674782 A C - 307s foo 676373 G T - 307s foo 676793 T C - 307s foo 677409 G S + 307s foo 677536 - AA - 307s foo 677620 G K + 307s foo 677686 C Y + 307s foo 678327 G S + 307s foo 678704 G S + 307s foo 678771 A C - 307s foo 678866 C T - 307s foo 679960 A W + 307s foo 680447 - C + 307s foo 682102 C T - 307s foo 685497 T A - 307s foo 686884 G S + 307s foo 687324 ACA - - 307s foo 687684 - AC + 307s foo 687823 T C - 307s foo 688590 G K + 307s foo 690802 C M + 307s foo 691388 T C - 307s foo 691403 T G - 307s foo 691790 G A - 307s foo 692973 C A - 307s foo 694058 G S + 307s foo 694550 G R + 307s foo 694968 T W + 307s foo 695898 A T - 307s foo 696721 C S + 307s foo 696787 C S + 307s foo 696935 A M + 307s foo 698024 - C + 307s foo 699813 A - - 307s foo 700179 G R + 307s foo 701421 A M + 307s foo 701989 T A - 307s foo 702862 C A - 307s foo 707020 G A - 307s foo 708420 A - - 307s foo 708669 C G - 307s foo 710521 T W + 307s foo 711801 G C - 307s foo 711913 T G - 307s foo 715830 C M + 307s foo 717664 TC - - 307s foo 718845 A W + 307s foo 719069 T Y + 307s foo 719565 A W + 307s foo 721136 T K + 307s foo 726116 T K + 307s foo 727809 T K + 307s foo 728864 G K + 307s foo 728918 G A - 307s foo 730296 - T + 307s foo 731988 C Y + 307s foo 734658 A M + 307s foo 734715 A W + 307s foo 736618 C G - 307s foo 737257 T Y + 307s foo 740864 C A - 307s foo 741640 G - - 307s foo 741859 - TA - 307s foo 742011 T K + 307s foo 742237 A R + 307s foo 742960 G K + 307s foo 743731 G R + 307s foo 743971 A W + 307s foo 744635 T K + 307s foo 746430 C G - 307s foo 746489 - GC - 307s foo 746881 C M + 307s foo 756997 TC - - 307s foo 757776 A M + 307s foo 759870 A T - 307s foo 760224 G K + 307s foo 760799 G C - 307s foo 761692 T C - 307s foo 762569 G S + 307s foo 763140 A G - 307s foo 763842 - T - 307s foo 764192 A M + 307s foo 764334 G A - 307s foo 764889 - AAT + 307s foo 766464 G S + 307s foo 768226 G A - 307s foo 770272 T G - 307s foo 771145 C Y + 307s foo 772209 T A - 307s foo 773672 T K + 307s foo 773932 G C - 307s foo 774658 C S + 307s foo 775969 A M + 307s foo 776816 T G - 307s foo 777591 C Y + 307s foo 777891 A M + 307s foo 778164 C M + 307s foo 778219 T W + 307s foo 779260 G T - 307s foo 779465 A W + 307s foo 779779 G S + 307s foo 780033 G K + 307s foo 783243 C M + 307s foo 783860 A R + 307s foo 788345 A M + 307s foo 789554 G - - 307s foo 790025 G K + 307s foo 791454 T K + 307s foo 792009 C A - 307s foo 792872 C G - 307s foo 794616 T W + 307s foo 795031 G R + 307s foo 796919 C M + 307s foo 797020 G S + 307s foo 797042 G C - 307s foo 797149 G A - 307s foo 797177 A C - 307s foo 799076 G C - 307s foo 799580 G S + 307s foo 800356 A R + 307s foo 802297 G T - 307s foo 802309 T Y + 307s foo 802343 - C + 307s foo 802769 A W + 307s foo 803104 C G - 307s foo 805819 C Y + 307s foo 805972 T Y + 307s foo 807503 T K + 307s foo 807950 C M + 307s foo 807994 - A - 307s foo 809167 A G - 307s foo 809658 A W + 307s foo 810152 A M + 307s foo 811506 G R + 307s foo 813494 A M + 307s foo 814035 G T - 307s foo 814476 A W + 307s foo 819399 T K + 307s foo 820171 T W + 307s foo 820445 G C - 307s foo 822178 C G - 307s foo 822504 C T - 307s foo 823378 C M + 307s foo 823591 CG - - 307s foo 824229 C M + 307s foo 824579 C T - 307s foo 824858 C M + 307s foo 826101 T K + 307s foo 827593 C G - 307s foo 827794 T Y + 307s foo 828228 A M + 307s foo 828367 T K + 307s foo 828788 C M + 307s foo 829002 C Y + 307s foo 830345 C M + 307s foo 831018 C A - 307s foo 831459 T K + 307s foo 832413 A T - 307s foo 832782 T Y + 307s foo 832908 T Y + 307s foo 833130 T - - 307s foo 833142 G S + 307s foo 833241 G A - 307s foo 836727 A T - 307s foo 836829 G S + 307s foo 838452 T G - 307s foo 838543 A T - 307s foo 838605 C M + 307s foo 838954 G C - 307s foo 841829 G K + 307s foo 842324 - TC + 307s foo 842996 - C + 307s foo 844390 C A - 307s foo 844793 A C - 307s foo 844925 C A - 307s foo 845082 G C - 307s foo 846202 G R + 307s foo 846707 A G - 307s foo 848713 G A - 307s foo 849372 C S + 307s foo 849742 G A - 307s foo 850499 C - - 307s foo 850927 GT - - 307s foo 851084 - G + 307s foo 852247 A R + 307s foo 852972 C A - 307s foo 854808 T W + 307s foo 855956 G K + 307s foo 856225 G A - 307s foo 856582 T K + 307s foo 857351 C M + 307s foo 857504 AC - - 307s foo 858324 A T - 307s foo 858858 T C - 307s foo 859488 T Y + 307s foo 862441 T Y + 307s foo 863827 C Y + 307s foo 864165 C A - 307s foo 865997 C M + 307s foo 866370 G S + 307s foo 867653 G S + 307s foo 867722 C Y + 307s foo 868696 C M + 307s foo 869005 T W + 307s foo 869791 T Y + 307s foo 875339 C Y + 307s foo 875347 C M + 307s foo 875584 T G - 307s foo 876780 C T - 307s foo 878368 A C - 307s foo 878916 - CAG + 307s foo 879005 A R + 307s foo 880112 G T - 307s foo 881021 - T - 307s foo 881175 T W + 307s foo 882168 - GGG + 307s foo 882223 - G - 307s foo 883033 TG - - 307s foo 883381 C G - 307s foo 884378 C - - 307s foo 885075 A M + 307s foo 885190 A W + 307s foo 885568 A W + 307s foo 885827 T Y + 307s foo 887610 TG - - 307s foo 889139 G R + 307s foo 890978 T - - 307s foo 891500 C Y + 307s foo 892257 G C - 307s foo 892642 G R + 307s foo 892644 T W + 307s foo 892757 C A - 307s foo 893222 T - - 307s foo 893348 T W + 307s foo 894161 - C - 307s foo 894447 A G - 307s foo 894614 A W + 307s foo 897817 T W + 307s foo 899408 C S + 307s foo 902450 A T - 307s foo 902970 AT - - 307s foo 905836 G K + 307s foo 906524 GA - - 307s foo 907484 A W + 307s foo 907537 C M + 307s foo 908515 G R + 307s foo 908642 C T - 307s foo 911145 T C - 307s foo 912220 T Y + 307s foo 912682 C Y + 307s foo 914260 C S + 307s foo 914757 T Y + 307s foo 916413 G C - 307s foo 916783 T G - 307s foo 917033 G C - 307s foo 917218 A - - 307s foo 918225 G - - 307s foo 918459 A - - 307s foo 918732 A M + 307s foo 919640 TC - - 307s foo 920824 T W + 307s foo 920836 G C - 307s foo 924560 G R + 307s foo 924659 GA - - 307s foo 925868 T A - 307s foo 928254 T G - 307s foo 928369 - A - 307s foo 928641 - AG + 307s foo 929857 C M + 307s foo 930211 T W + 307s foo 930935 C T - 307s foo 931986 A M + 307s foo 932852 G T - 307s foo 933965 T A - 307s foo 935564 A W + 307s foo 936034 T Y + 307s foo 936221 AC - - 307s foo 936670 C S + 307s foo 936704 T A - 307s foo 936786 T W + 307s foo 939218 C S + 307s foo 939312 A W + 307s foo 939467 A W + 307s foo 939934 C S + 307s foo 941603 C Y + 307s foo 942910 A W + 307s foo 944654 T Y + 307s foo 945301 A C - 307s foo 945770 C T - 307s foo 946078 G S + 307s foo 948833 G K + 307s foo 948999 A W + 307s foo 949193 A R + 307s foo 950276 C M + 307s foo 950414 A W + 307s foo 951285 G C - 307s foo 953158 G R + 307s foo 953287 A W + 307s foo 954150 C G - 307s foo 954258 G - - 307s foo 955396 CC - - 307s foo 956490 - AC + 307s foo 958129 A R + 307s foo 959027 T A - 307s foo 959964 A W + 307s foo 962042 A G - 307s foo 962742 C G - 307s foo 963306 T W + 307s foo 963422 G K + 307s foo 964082 G S + 307s foo 965561 C S + 307s foo 966531 T K + 307s foo 967324 T W + 307s foo 968419 - C - 307s foo 969054 G - - 307s foo 969158 G S + 307s foo 972658 C M + 307s foo 974266 T W + 307s foo 974629 G K + 307s foo 975034 A R + 307s foo 975636 T W + 307s foo 977078 - A - 307s foo 978321 G T - 307s foo 978595 C G - 307s foo 979090 C M + 307s foo 983855 TA - - 307s foo 985725 T A - 307s foo 988497 C Y + 307s foo 990171 C M + 307s foo 990804 - CA - 307s foo 990941 T W + 307s foo 991797 A W + 307s foo 992469 A M + 307s foo 994610 C Y + 307s foo 998107 - T + 307s foo 999725 G R + 308s [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.2475.smaltmap.smalt_index foo1.fasta 308s # Command line: smalt index -k 13 -s 2 out.bam.tmp.2475.smaltmap.smalt_index foo1.fasta 308s # Reading sequences ... 308s # Writing sequence set ... 308s # Setting up hash index with collisions ... 308s # word length = 13 bases, skip step = 2 bases ... 308s # number of bits for key = 18 with 0 perfect bits 308s # Counting keys ... 308s # Counting k-tuples ... 308s # Allocating k-tuple arrays ... 308s # Counting k-tuple occurrences ... 308s # Setting the k-tuple positions in index ... 308s # Hash table is set up. 308s # =-=-=-=-= Hash Index Stats =-=-=-=-= 308s # Hash index with collisions. 308s # Word length: 13 bases 308s # Skip step: 2 bases 308s # Number of hash keys: 262144 308s # Number of word positions: 499970 308s # Number of different words: 498076 308s # Maximum number of words per key: 11 308s # Number of keys without words: 39377 308s # =-=-= End of Hash Index Stats =-=-= 308s # Writing table to file ... 308s # smalt: Total elapsed wall clock time: 0 seconds 308s [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.2475.smaltmap.smalt_sample out.bam.tmp.2475.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 308s # Command line: smalt sample -u 1000 -o out.bam.tmp.2475.smaltmap.smalt_sample out.bam.tmp.2475.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 308s # Opening read files ... 308s # Reading reference sequences ... 308s # Reading hash table ... 308s # =-=-=-=-= Hash Index Stats =-=-=-=-= 308s # Hash index with collisions. 308s # Word length: 13 bases 308s # Skip step: 2 bases 308s # Number of hash keys: 262144 308s # Number of word positions: 499970 308s # Number of different words: 498076 308s # Maximum number of words per key: 11 308s # Number of keys without words: 39377 308s # =-=-= End of Hash Index Stats =-=-= 308s # Check of read pairs ok ... 308s # Mate names match ... 308s # Sampling insert size distribution ... 312s # Processed 9999 read pairs. 312s # smalt: Time spent setting up hash index:0 seconds 312s # smalt: Time spent mapping reads:4 seconds 312s # smalt: Total elapsed wall clock time: 4 seconds 312s [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2475.smaltmap.smalt_sample -f samsoft out.bam.tmp.2475.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.2475.smaltmap.raw.bam 312s # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2475.smaltmap.smalt_sample -f samsoft out.bam.tmp.2475.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 312s # Reading distribution of insert sizes from file ... 312s # Sampled histogram 312s # Smoothed histogram 312s # Opening read files ... 312s # Reading reference sequences ... 312s # Reading hash table ... 312s # =-=-=-=-= Hash Index Stats =-=-=-=-= 312s # Hash index with collisions. 312s # Word length: 13 bases 312s # Skip step: 2 bases 312s # Number of hash keys: 262144 312s # Number of word positions: 499970 312s # Number of different words: 498076 312s # Maximum number of words per key: 11 312s # Number of keys without words: 39377 312s # =-=-= End of Hash Index Stats =-=-= 312s # Processing query reads ... 330s # Processed 10000 read pairs. 330s # smalt: Time spent setting up hash index:0 seconds 330s # smalt: Time spent mapping reads:18 seconds 330s # smalt: Total elapsed wall clock time: 18 seconds 330s [REAPR smaltmap] Running: samtools sort out.bam.tmp.2475.smaltmap.raw.bam -O bam -o out.bam.tmp.2475.smaltmap.raw.bam.sort.bam 330s [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.2475.smaltmap.raw.bam.sort.bam out.bam.tmp.2475.smaltmap.rmdup.bam 330s [bam_rmdup_core] processing reference foo... 330s [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' 330s [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.2475.smaltmap.header 330s [REAPR smaltmap] Running: samtools view -H out.bam.tmp.2475.smaltmap.rmdup.bam >> out.bam.tmp.2475.smaltmap.header 330s [REAPR smaltmap] Running: samtools reheader out.bam.tmp.2475.smaltmap.header out.bam.tmp.2475.smaltmap.rmdup.bam > out.bam 330s [REAPR smaltmap] Running: samtools index out.bam 330s [REAPR smaltmap] Running: rm out.bam.tmp.2475.smaltmap.* 330s Running reapr version 1.0.18 pipeline: 330s reapr foo1.fasta out.bam result 330s [REAPR pipeline] Running facheck 330s [REAPR pipeline] Running preprocess 333s [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases 334s [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases 334s [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases 334s [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases 335s [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation 339s [REAPR pipeline] Running stats 361s [REAPR pipeline] Running fcdrate 364s [REAPR pipeline] Running score 372s [REAPR pipeline] Running break 372s [REAPR pipeline] Running summary 372s autopkgtest [21:27:17]: test test-example: -----------------------] 373s autopkgtest [21:27:18]: test test-example: - - - - - - - - - - results - - - - - - - - - - 373s test-example PASS 373s autopkgtest [21:27:18]: @@@@@@@@@@@@@@@@@@@@ summary 373s test-example PASS 385s Creating nova instance adt-noble-s390x-reapr-20240325-212105-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...