0s autopkgtest [15:48:35]: starting date and time: 2024-03-23 15:48:35+0000 0s autopkgtest [15:48:35]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:48:35]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r3wfmplw/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-ppc64el-25.secgroup --name adt-noble-ppc64el-reapr-20240323-154835-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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/ 272s autopkgtest [15:53:07]: testbed dpkg architecture: ppc64el 273s autopkgtest [15:53:08]: testbed apt version: 2.7.12 273s autopkgtest [15:53:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 273s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 274s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 274s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 274s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 274s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 274s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 275s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 275s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 275s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 275s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 275s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 275s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 275s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 279s Fetched 9623 kB in 3s (3524 kB/s) 279s Reading package lists... 282s Reading package lists... 282s Building dependency tree... 282s Reading state information... 282s Calculating upgrade... 282s The following packages will be REMOVED: 282s libssl3 282s The following NEW packages will be installed: 282s libssl3t64 282s The following packages have been kept back: 282s curl 282s The following packages will be upgraded: 282s openssl 282s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 282s Need to get 3151 kB of archives. 282s After this operation, 73.7 kB of additional disk space will be used. 282s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 283s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 283s Fetched 3151 kB in 1s (3985 kB/s) 283s (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 ... 70156 files and directories currently installed.) 283s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 283s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 283s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 283s wget depends on libssl3 (>= 3.0.0). 283s tnftp depends on libssl3 (>= 3.0.0). 283s tcpdump depends on libssl3 (>= 3.0.0). 283s systemd-resolved depends on libssl3 (>= 3.0.0). 283s systemd depends on libssl3 (>= 3.0.0). 283s sudo depends on libssl3 (>= 3.0.0). 283s rsync depends on libssl3 (>= 3.0.0). 283s python3-cryptography depends on libssl3 (>= 3.0.0). 283s openssh-server depends on libssl3 (>= 3.0.10). 283s openssh-client depends on libssl3 (>= 3.0.10). 283s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 283s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 283s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 283s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 283s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 283s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 283s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 283s libnvme1 depends on libssl3 (>= 3.0.0). 283s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 283s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 283s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 283s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 283s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 283s kmod depends on libssl3 (>= 3.0.0). 283s dhcpcd-base depends on libssl3 (>= 3.0.0). 283s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 283s 284s (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 ... 70156 files and directories currently installed.) 284s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 284s Selecting previously unselected package libssl3t64:ppc64el. 284s (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 ... 70145 files and directories currently installed.) 284s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 284s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 284s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 284s Setting up openssl (3.0.13-0ubuntu2) ... 284s Processing triggers for man-db (2.12.0-3) ... 284s Processing triggers for libc-bin (2.39-0ubuntu6) ... 284s Reading package lists... 285s Building dependency tree... 285s Reading state information... 285s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 286s sh: Attempting to set up Debian/Ubuntu apt sources automatically 286s sh: Distribution appears to be Ubuntu 287s Reading package lists... 287s Building dependency tree... 287s Reading state information... 287s eatmydata is already the newest version (131-1). 287s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 287s Reading package lists... 287s Building dependency tree... 287s Reading state information... 287s dbus is already the newest version (1.14.10-4ubuntu1). 287s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 287s Reading package lists... 288s Building dependency tree... 288s Reading state information... 288s rng-tools-debian is already the newest version (2.4). 288s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 288s The following packages will be REMOVED: 288s cloud-init* python3-configobj* python3-debconf* 288s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 288s After this operation, 3256 kB disk space will be freed. 289s (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 ... 70158 files and directories currently installed.) 289s Removing cloud-init (24.1.2-0ubuntu1) ... 289s Removing python3-configobj (5.0.8-3) ... 289s Removing python3-debconf (1.5.86) ... 289s Processing triggers for man-db (2.12.0-3) ... 290s (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 ... 69769 files and directories currently installed.) 290s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 290s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 290s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 290s invoke-rc.d: policy-rc.d denied execution of try-restart. 290s Reading package lists... 291s Building dependency tree... 291s Reading state information... 291s linux-generic is already the newest version (6.8.0-11.11+1). 291s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 291s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 291s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 291s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 294s Reading package lists... 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 295s Calculating upgrade... 295s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 295s Reading package lists... 295s Building dependency tree... 295s Reading state information... 295s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 295s autopkgtest [15:53:30]: rebooting testbed after setup commands that affected boot 339s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 347s autopkgtest [15:54:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 349s autopkgtest [15:54:24]: @@@@@@@@@@@@@@@@@@@@ apt-source reapr 351s Get:1 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (dsc) [2293 B] 351s Get:2 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (tar) [74.6 kB] 351s Get:3 http://ftpmaster.internal/ubuntu noble/universe reapr 1.0.18+dfsg-5build2 (diff) [320 kB] 351s gpgv: Signature made Sat Nov 19 21:52:27 2022 UTC 351s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 351s gpgv: issuer "steve.langasek@ubuntu.com" 351s gpgv: Can't check signature: No public key 351s dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-5build2.dsc: no acceptable signature found 351s autopkgtest [15:54:26]: testing package reapr version 1.0.18+dfsg-5build2 352s autopkgtest [15:54:27]: build not needed 352s autopkgtest [15:54:27]: test test-example: preparing testbed 359s Reading package lists... 359s Building dependency tree... 359s Reading state information... 359s Starting pkgProblemResolver with broken count: 0 359s Starting 2 pkgProblemResolver with broken count: 0 359s Done 359s The following additional packages will be installed: 359s bamtools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 359s libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 libdeflate0 359s libfile-copy-link-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 359s libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 libjpeg-turbo8 libjpeg8 359s libjsoncpp25 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 359s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 359s libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 359s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 r-base 359s r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools 360s r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix 360s r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial 360s r-cran-survival r-recommended reapr samtools smalt snpomatic tabix unzip 360s x11-common xdg-utils zip 360s Suggested packages: 360s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html cwltool 360s Recommended packages: 360s r-base-html r-doc-html r-base-dev libfile-mimeinfo-perl libnet-dbus-perl 360s libx11-protocol-perl x11-utils x11-xserver-utils 360s The following NEW packages will be installed: 360s autopkgtest-satdep bamtools fontconfig fontconfig-config fonts-dejavu-core 360s fonts-dejavu-mono libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 360s libdeflate0 libfile-copy-link-perl libfontconfig1 libgfortran5 libgomp1 360s libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 360s libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 liblerc4 libpango-1.0-0 360s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 360s libsharpyuv0 libsm6 libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 360s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 360s libxt6 r-base r-base-core r-cran-boot r-cran-class r-cran-cluster 360s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass 360s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart 360s r-cran-spatial r-cran-survival r-recommended reapr samtools smalt snpomatic 360s tabix unzip x11-common xdg-utils zip 360s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 360s Need to get 63.4 MB/63.4 MB of archives. 360s After this operation, 126 MB of additional disk space will be used. 360s Get:1 /tmp/autopkgtest.F2A3Jr/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 360s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbamtools2.5.2 ppc64el 2.5.2+dfsg-4 [161 kB] 360s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libjsoncpp25 ppc64el 1.9.5-6 [86.8 kB] 360s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el bamtools ppc64el 2.5.2+dfsg-4 [187 kB] 360s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 360s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 360s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 360s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 360s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 360s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbambamc0 ppc64el 0.0.50-6 [43.9 kB] 360s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 360s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 360s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 360s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 360s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 360s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 360s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 360s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 360s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfile-copy-link-perl all 0.140-5 [12.3 kB] 360s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 360s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 360s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 360s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 360s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 360s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 360s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 360s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 360s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 360s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 360s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 360s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 360s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 360s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 360s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 360s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 360s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 360s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 360s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 360s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 361s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 361s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtabixpp0 ppc64el 1.1.2-2 [10.0 kB] 361s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 361s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 361s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 361s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 361s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 361s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 361s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 361s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 361s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 361s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 361s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 361s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 361s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-boot all 1.3-30-1 [619 kB] 361s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-cluster ppc64el 2.1.6-1 [568 kB] 361s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-foreign ppc64el 0.8.86-1 [251 kB] 361s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mass ppc64el 7.3-60.0.1-1 [1126 kB] 361s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-kernsmooth ppc64el 2.23-22-1 [94.6 kB] 361s Get:59 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-lattice ppc64el 0.22-5-1 [1343 kB] 361s Get:60 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nlme ppc64el 3.1.164-1 [2281 kB] 361s Get:61 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-matrix ppc64el 1.6-5-1 [4057 kB] 362s Get:62 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mgcv ppc64el 1.9-1-1 [3393 kB] 362s Get:63 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-survival ppc64el 3.5-8-1 [6160 kB] 362s Get:64 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rpart ppc64el 4.1.23-1 [672 kB] 362s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-class ppc64el 7.3-22-2 [92.5 kB] 362s Get:66 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nnet ppc64el 7.3-19-2 [118 kB] 362s Get:67 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatial ppc64el 7.3-17-1 [137 kB] 362s Get:68 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-codetools all 0.2-19-1 [90.5 kB] 362s Get:69 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-recommended all 4.3.2-1build1 [2636 B] 362s Get:70 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base all 4.3.2-1build1 [9302 B] 362s Get:71 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 362s Get:72 http://ftpmaster.internal/ubuntu noble/universe ppc64el smalt ppc64el 0.7.6-13 [132 kB] 362s Get:73 http://ftpmaster.internal/ubuntu noble/universe ppc64el snpomatic ppc64el 1.0-7 [88.0 kB] 362s Get:74 http://ftpmaster.internal/ubuntu noble/universe ppc64el tabix ppc64el 1.18+ds-1 [692 kB] 362s Get:75 http://ftpmaster.internal/ubuntu noble/universe ppc64el reapr ppc64el 1.0.18+dfsg-5build2 [197 kB] 363s Preconfiguring packages ... 363s Fetched 63.4 MB in 3s (24.0 MB/s) 363s Selecting previously unselected package libbamtools2.5.2:ppc64el. 363s (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 ... 69714 files and directories currently installed.) 363s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_ppc64el.deb ... 363s Unpacking libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ... 363s Selecting previously unselected package libjsoncpp25:ppc64el. 363s Preparing to unpack .../01-libjsoncpp25_1.9.5-6_ppc64el.deb ... 363s Unpacking libjsoncpp25:ppc64el (1.9.5-6) ... 363s Selecting previously unselected package bamtools. 363s Preparing to unpack .../02-bamtools_2.5.2+dfsg-4_ppc64el.deb ... 363s Unpacking bamtools (2.5.2+dfsg-4) ... 363s Selecting previously unselected package fonts-dejavu-mono. 363s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 363s Unpacking fonts-dejavu-mono (2.37-8) ... 363s Selecting previously unselected package fonts-dejavu-core. 363s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 363s Unpacking fonts-dejavu-core (2.37-8) ... 363s Selecting previously unselected package fontconfig-config. 363s Preparing to unpack .../05-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 363s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 363s Selecting previously unselected package libfontconfig1:ppc64el. 363s Preparing to unpack .../06-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 363s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 363s Selecting previously unselected package fontconfig. 363s Preparing to unpack .../07-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 363s Unpacking fontconfig (2.15.0-1ubuntu1) ... 363s Selecting previously unselected package libbambamc0:ppc64el. 363s Preparing to unpack .../08-libbambamc0_0.0.50-6_ppc64el.deb ... 363s Unpacking libbambamc0:ppc64el (0.0.50-6) ... 363s Selecting previously unselected package libblas3:ppc64el. 363s Preparing to unpack .../09-libblas3_3.12.0-3_ppc64el.deb ... 363s Unpacking libblas3:ppc64el (3.12.0-3) ... 363s Selecting previously unselected package libpixman-1-0:ppc64el. 363s Preparing to unpack .../10-libpixman-1-0_0.42.2-1_ppc64el.deb ... 363s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 363s Selecting previously unselected package libxcb-render0:ppc64el. 363s Preparing to unpack .../11-libxcb-render0_1.15-1_ppc64el.deb ... 363s Unpacking libxcb-render0:ppc64el (1.15-1) ... 363s Selecting previously unselected package libxcb-shm0:ppc64el. 363s Preparing to unpack .../12-libxcb-shm0_1.15-1_ppc64el.deb ... 363s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 363s Selecting previously unselected package libxrender1:ppc64el. 363s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 363s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 363s Selecting previously unselected package libcairo2:ppc64el. 363s Preparing to unpack .../14-libcairo2_1.18.0-1_ppc64el.deb ... 363s Unpacking libcairo2:ppc64el (1.18.0-1) ... 363s Selecting previously unselected package libdatrie1:ppc64el. 363s Preparing to unpack .../15-libdatrie1_0.2.13-3_ppc64el.deb ... 363s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 363s Selecting previously unselected package libdeflate0:ppc64el. 363s Preparing to unpack .../16-libdeflate0_1.19-1_ppc64el.deb ... 363s Unpacking libdeflate0:ppc64el (1.19-1) ... 363s Selecting previously unselected package libfile-copy-link-perl. 363s Preparing to unpack .../17-libfile-copy-link-perl_0.140-5_all.deb ... 363s Unpacking libfile-copy-link-perl (0.140-5) ... 363s Selecting previously unselected package libgfortran5:ppc64el. 363s Preparing to unpack .../18-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 363s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 363s Selecting previously unselected package libgomp1:ppc64el. 363s Preparing to unpack .../19-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 363s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 363s Selecting previously unselected package libgraphite2-3:ppc64el. 363s Preparing to unpack .../20-libgraphite2-3_1.3.14-2_ppc64el.deb ... 363s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 363s Selecting previously unselected package libharfbuzz0b:ppc64el. 363s Preparing to unpack .../21-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 363s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 363s Selecting previously unselected package libhtscodecs2:ppc64el. 363s Preparing to unpack .../22-libhtscodecs2_1.6.0-1_ppc64el.deb ... 363s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 363s Selecting previously unselected package libhts3:ppc64el. 363s Preparing to unpack .../23-libhts3_1.18+ds-1_ppc64el.deb ... 363s Unpacking libhts3:ppc64el (1.18+ds-1) ... 363s Selecting previously unselected package x11-common. 363s Preparing to unpack .../24-x11-common_1%3a7.7+23ubuntu2_all.deb ... 364s Unpacking x11-common (1:7.7+23ubuntu2) ... 364s Selecting previously unselected package libice6:ppc64el. 364s Preparing to unpack .../25-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 364s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 364s Selecting previously unselected package libjpeg-turbo8:ppc64el. 364s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 364s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 364s Selecting previously unselected package libjpeg8:ppc64el. 364s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 364s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 364s Selecting previously unselected package liblapack3:ppc64el. 364s Preparing to unpack .../28-liblapack3_3.12.0-3_ppc64el.deb ... 364s Unpacking liblapack3:ppc64el (3.12.0-3) ... 364s Selecting previously unselected package liblerc4:ppc64el. 364s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 364s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 364s Selecting previously unselected package libthai-data. 364s Preparing to unpack .../30-libthai-data_0.1.29-2_all.deb ... 364s Unpacking libthai-data (0.1.29-2) ... 364s Selecting previously unselected package libthai0:ppc64el. 364s Preparing to unpack .../31-libthai0_0.1.29-2_ppc64el.deb ... 364s Unpacking libthai0:ppc64el (0.1.29-2) ... 364s Selecting previously unselected package libpango-1.0-0:ppc64el. 364s Preparing to unpack .../32-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 364s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 364s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 364s Preparing to unpack .../33-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 364s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 364s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 364s Preparing to unpack .../34-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 364s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 364s Selecting previously unselected package libpaper1:ppc64el. 364s Preparing to unpack .../35-libpaper1_1.1.29_ppc64el.deb ... 364s Unpacking libpaper1:ppc64el (1.1.29) ... 364s Selecting previously unselected package libpaper-utils. 364s Preparing to unpack .../36-libpaper-utils_1.1.29_ppc64el.deb ... 364s Unpacking libpaper-utils (1.1.29) ... 364s Selecting previously unselected package libsharpyuv0:ppc64el. 364s Preparing to unpack .../37-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 364s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 364s Selecting previously unselected package libsm6:ppc64el. 364s Preparing to unpack .../38-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 364s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 364s Selecting previously unselected package libtabixpp0:ppc64el. 364s Preparing to unpack .../39-libtabixpp0_1.1.2-2_ppc64el.deb ... 364s Unpacking libtabixpp0:ppc64el (1.1.2-2) ... 364s Selecting previously unselected package libtcl8.6:ppc64el. 364s Preparing to unpack .../40-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 364s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 364s Selecting previously unselected package libjbig0:ppc64el. 364s Preparing to unpack .../41-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 364s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 364s Selecting previously unselected package libwebp7:ppc64el. 364s Preparing to unpack .../42-libwebp7_1.3.2-0.4_ppc64el.deb ... 364s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 364s Selecting previously unselected package libtiff6:ppc64el. 364s Preparing to unpack .../43-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 364s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 364s Selecting previously unselected package libxft2:ppc64el. 364s Preparing to unpack .../44-libxft2_2.3.6-1_ppc64el.deb ... 364s Unpacking libxft2:ppc64el (2.3.6-1) ... 364s Selecting previously unselected package libxss1:ppc64el. 364s Preparing to unpack .../45-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 364s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 364s Selecting previously unselected package libtk8.6:ppc64el. 364s Preparing to unpack .../46-libtk8.6_8.6.14-1_ppc64el.deb ... 364s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 364s Selecting previously unselected package libxt6:ppc64el. 364s Preparing to unpack .../47-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 364s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 364s Selecting previously unselected package zip. 364s Preparing to unpack .../48-zip_3.0-13_ppc64el.deb ... 364s Unpacking zip (3.0-13) ... 364s Selecting previously unselected package unzip. 364s Preparing to unpack .../49-unzip_6.0-28ubuntu3_ppc64el.deb ... 364s Unpacking unzip (6.0-28ubuntu3) ... 364s Selecting previously unselected package xdg-utils. 364s Preparing to unpack .../50-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 364s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 364s Selecting previously unselected package r-base-core. 364s Preparing to unpack .../51-r-base-core_4.3.2-1build1_ppc64el.deb ... 364s Unpacking r-base-core (4.3.2-1build1) ... 365s Selecting previously unselected package r-cran-boot. 365s Preparing to unpack .../52-r-cran-boot_1.3-30-1_all.deb ... 365s Unpacking r-cran-boot (1.3-30-1) ... 365s Selecting previously unselected package r-cran-cluster. 365s Preparing to unpack .../53-r-cran-cluster_2.1.6-1_ppc64el.deb ... 365s Unpacking r-cran-cluster (2.1.6-1) ... 365s Selecting previously unselected package r-cran-foreign. 365s Preparing to unpack .../54-r-cran-foreign_0.8.86-1_ppc64el.deb ... 365s Unpacking r-cran-foreign (0.8.86-1) ... 365s Selecting previously unselected package r-cran-mass. 365s Preparing to unpack .../55-r-cran-mass_7.3-60.0.1-1_ppc64el.deb ... 365s Unpacking r-cran-mass (7.3-60.0.1-1) ... 365s Selecting previously unselected package r-cran-kernsmooth. 365s Preparing to unpack .../56-r-cran-kernsmooth_2.23-22-1_ppc64el.deb ... 365s Unpacking r-cran-kernsmooth (2.23-22-1) ... 365s Selecting previously unselected package r-cran-lattice. 365s Preparing to unpack .../57-r-cran-lattice_0.22-5-1_ppc64el.deb ... 365s Unpacking r-cran-lattice (0.22-5-1) ... 365s Selecting previously unselected package r-cran-nlme. 365s Preparing to unpack .../58-r-cran-nlme_3.1.164-1_ppc64el.deb ... 365s Unpacking r-cran-nlme (3.1.164-1) ... 365s Selecting previously unselected package r-cran-matrix. 365s Preparing to unpack .../59-r-cran-matrix_1.6-5-1_ppc64el.deb ... 365s Unpacking r-cran-matrix (1.6-5-1) ... 365s Selecting previously unselected package r-cran-mgcv. 365s Preparing to unpack .../60-r-cran-mgcv_1.9-1-1_ppc64el.deb ... 365s Unpacking r-cran-mgcv (1.9-1-1) ... 365s Selecting previously unselected package r-cran-survival. 365s Preparing to unpack .../61-r-cran-survival_3.5-8-1_ppc64el.deb ... 365s Unpacking r-cran-survival (3.5-8-1) ... 365s Selecting previously unselected package r-cran-rpart. 365s Preparing to unpack .../62-r-cran-rpart_4.1.23-1_ppc64el.deb ... 365s Unpacking r-cran-rpart (4.1.23-1) ... 365s Selecting previously unselected package r-cran-class. 365s Preparing to unpack .../63-r-cran-class_7.3-22-2_ppc64el.deb ... 365s Unpacking r-cran-class (7.3-22-2) ... 365s Selecting previously unselected package r-cran-nnet. 365s Preparing to unpack .../64-r-cran-nnet_7.3-19-2_ppc64el.deb ... 365s Unpacking r-cran-nnet (7.3-19-2) ... 365s Selecting previously unselected package r-cran-spatial. 365s Preparing to unpack .../65-r-cran-spatial_7.3-17-1_ppc64el.deb ... 365s Unpacking r-cran-spatial (7.3-17-1) ... 365s Selecting previously unselected package r-cran-codetools. 365s Preparing to unpack .../66-r-cran-codetools_0.2-19-1_all.deb ... 365s Unpacking r-cran-codetools (0.2-19-1) ... 365s Selecting previously unselected package r-recommended. 365s Preparing to unpack .../67-r-recommended_4.3.2-1build1_all.deb ... 365s Unpacking r-recommended (4.3.2-1build1) ... 365s Selecting previously unselected package r-base. 365s Preparing to unpack .../68-r-base_4.3.2-1build1_all.deb ... 365s Unpacking r-base (4.3.2-1build1) ... 365s Selecting previously unselected package samtools. 365s Preparing to unpack .../69-samtools_1.19.2-1_ppc64el.deb ... 365s Unpacking samtools (1.19.2-1) ... 365s Selecting previously unselected package smalt. 365s Preparing to unpack .../70-smalt_0.7.6-13_ppc64el.deb ... 365s Unpacking smalt (0.7.6-13) ... 365s Selecting previously unselected package snpomatic. 365s Preparing to unpack .../71-snpomatic_1.0-7_ppc64el.deb ... 365s Unpacking snpomatic (1.0-7) ... 365s Selecting previously unselected package tabix. 365s Preparing to unpack .../72-tabix_1.18+ds-1_ppc64el.deb ... 365s Unpacking tabix (1.18+ds-1) ... 365s Selecting previously unselected package reapr. 365s Preparing to unpack .../73-reapr_1.0.18+dfsg-5build2_ppc64el.deb ... 365s Unpacking reapr (1.0.18+dfsg-5build2) ... 365s Selecting previously unselected package autopkgtest-satdep. 365s Preparing to unpack .../74-1-autopkgtest-satdep.deb ... 365s Unpacking autopkgtest-satdep (0) ... 365s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 365s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 365s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 365s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 365s Setting up libpaper1:ppc64el (1.1.29) ... 366s 366s Creating config file /etc/papersize with new version 366s Setting up libfile-copy-link-perl (0.140-5) ... 366s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 366s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 366s Setting up libdatrie1:ppc64el (0.2.13-3) ... 366s Setting up libxcb-render0:ppc64el (1.15-1) ... 366s Setting up unzip (6.0-28ubuntu3) ... 366s Setting up x11-common (1:7.7+23ubuntu2) ... 366s Setting up libdeflate0:ppc64el (1.19-1) ... 366s Setting up libxcb-shm0:ppc64el (1.15-1) ... 366s Setting up libpaper-utils (1.1.29) ... 366s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 366s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 366s Setting up zip (3.0-13) ... 366s Setting up libblas3:ppc64el (3.12.0-3) ... 366s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 366s Setting up libbambamc0:ppc64el (0.0.50-6) ... 366s Setting up fonts-dejavu-mono (2.37-8) ... 366s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 366s Setting up libjsoncpp25:ppc64el (1.9.5-6) ... 366s Setting up fonts-dejavu-core (2.37-8) ... 366s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 366s Setting up libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ... 366s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 366s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 366s Setting up bamtools (2.5.2+dfsg-4) ... 366s Setting up snpomatic (1.0-7) ... 366s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 366s Setting up libthai-data (0.1.29-2) ... 366s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 366s Setting up tabix (1.18+ds-1) ... 366s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 366s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 366s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 366s Setting up smalt (0.7.6-13) ... 366s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 366s Setting up liblapack3:ppc64el (3.12.0-3) ... 366s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 366s Setting up libhts3:ppc64el (1.18+ds-1) ... 366s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 366s Setting up samtools (1.19.2-1) ... 366s Setting up libthai0:ppc64el (0.1.29-2) ... 366s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 366s Setting up libtabixpp0:ppc64el (1.1.2-2) ... 366s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 366s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 366s Setting up fontconfig (2.15.0-1ubuntu1) ... 368s Regenerating fonts cache... done. 368s Setting up libxft2:ppc64el (2.3.6-1) ... 368s Setting up libtk8.6:ppc64el (8.6.14-1) ... 368s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 368s Setting up libcairo2:ppc64el (1.18.0-1) ... 368s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 368s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 368s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 368s Setting up r-base-core (4.3.2-1build1) ... 369s 369s Creating config file /etc/R/Renviron with new version 369s Setting up r-cran-lattice (0.22-5-1) ... 369s Setting up r-cran-nlme (3.1.164-1) ... 369s Setting up r-cran-cluster (2.1.6-1) ... 369s Setting up r-cran-nnet (7.3-19-2) ... 369s Setting up r-cran-codetools (0.2-19-1) ... 369s Setting up r-cran-boot (1.3-30-1) ... 369s Setting up r-cran-spatial (7.3-17-1) ... 369s Setting up r-cran-mass (7.3-60.0.1-1) ... 369s Setting up r-cran-foreign (0.8.86-1) ... 369s Setting up r-cran-matrix (1.6-5-1) ... 369s Setting up r-cran-kernsmooth (2.23-22-1) ... 369s Setting up r-cran-mgcv (1.9-1-1) ... 369s Setting up r-cran-class (7.3-22-2) ... 369s Setting up r-cran-survival (3.5-8-1) ... 369s Setting up r-cran-rpart (4.1.23-1) ... 369s Setting up r-recommended (4.3.2-1build1) ... 369s Setting up r-base (4.3.2-1build1) ... 369s Setting up reapr (1.0.18+dfsg-5build2) ... 369s Setting up autopkgtest-satdep (0) ... 369s Processing triggers for man-db (2.12.0-3) ... 370s Processing triggers for install-info (7.1-3) ... 370s Processing triggers for libc-bin (2.39-0ubuntu6) ... 374s (Reading database ... 72905 files and directories currently installed.) 374s Removing autopkgtest-satdep (0) ... 375s autopkgtest [15:54:50]: test test-example: [----------------------- 375s [wgsim] seed = 42 375s [wgsim_core] calculating the total length of the reference sequence... 375s [wgsim_core] 1 sequences, total length: 1000111 375s foo 1384 T K + 375s foo 4961 T W + 375s foo 5885 - T - 375s foo 9598 A C - 375s foo 10177 G R + 375s foo 11305 G K + 375s foo 11592 G R + 375s foo 13931 T - - 375s foo 15907 C A - 375s foo 17264 G K + 375s foo 17780 A - - 375s foo 18711 A W + 375s foo 19249 T W + 375s foo 19522 C S + 375s foo 23053 T K + 375s foo 23681 A R + 375s foo 23730 C S + 375s foo 24075 G S + 375s foo 24555 G C - 375s foo 26775 G K + 375s foo 26896 C M + 375s foo 27253 G K + 375s foo 28210 T Y + 375s foo 28224 A W + 375s foo 28377 - G + 375s foo 29035 G K + 375s foo 29898 C M + 375s foo 30274 A R + 375s foo 30542 G K + 375s foo 31566 A C - 375s foo 32252 - A - 375s foo 33303 T K + 375s foo 33390 - G + 375s foo 34073 A R + 375s foo 34171 G R + 375s foo 34718 T Y + 375s foo 34801 - C + 375s foo 35204 T W + 375s foo 35342 G S + 375s foo 35489 G T - 375s foo 36153 A M + 375s foo 36273 C S + 375s foo 37356 G T - 375s foo 37596 C S + 375s foo 39308 T - - 375s foo 40333 C G - 375s foo 42295 T K + 375s foo 42372 T Y + 375s foo 44433 C G - 375s foo 44630 - AG + 375s foo 44902 T C - 375s foo 47156 C A - 375s foo 48210 C M + 375s foo 48390 A R + 375s foo 49652 C M + 375s foo 52739 T Y + 375s foo 52858 A M + 375s foo 54737 A G - 375s foo 55306 C T - 375s foo 55434 C T - 375s foo 59204 A W + 375s foo 59300 G C - 375s foo 59335 T Y + 375s foo 59444 T - - 375s foo 59531 C S + 375s foo 59766 C Y + 375s foo 61950 C S + 375s foo 62887 G S + 375s foo 63390 A G - 375s foo 64365 G K + 375s foo 64703 C S + 375s foo 64932 C Y + 375s foo 68383 - CG + 375s foo 68464 A W + 375s foo 68727 A W + 375s foo 69080 A M + 375s foo 72071 T C - 375s foo 72720 - G - 375s foo 73354 C T - 375s foo 73637 G T - 375s foo 74741 A M + 375s foo 75101 C T - 375s foo 75207 T K + 375s foo 76400 T Y + 375s foo 76780 A C - 375s foo 77172 A W + 375s foo 78385 C Y + 375s foo 80705 C M + 375s foo 82440 A R + 375s foo 83021 G K + 375s foo 83116 A - - 375s foo 83846 T K + 375s foo 84633 G S + 375s foo 85891 G S + 375s foo 87759 A C - 375s foo 87778 T W + 375s foo 88581 T K + 375s foo 88606 T Y + 375s foo 88880 A G - 375s foo 89945 G C - 375s foo 90728 T K + 375s foo 91798 G R + 375s foo 95957 G C - 375s foo 96173 T W + 375s foo 96665 A M + 375s foo 98019 - G + 375s foo 98131 A M + 375s foo 98669 A R + 375s foo 98719 G T - 375s foo 99062 A W + 375s foo 99590 A T - 375s foo 100532 - TC + 375s foo 103015 A W + 375s foo 103172 G S + 375s foo 103609 G R + 375s foo 106549 T Y + 375s foo 108808 C Y + 375s foo 109191 G C - 375s foo 111686 C G - 375s foo 113436 C A - 375s foo 113763 A W + 375s foo 115671 C T - 375s foo 117460 - A - 375s foo 118193 G - - 375s foo 118585 T K + 375s foo 121219 A M + 375s foo 121876 T K + 375s foo 122071 T A - 375s foo 124918 C G - 375s foo 125300 G S + 375s foo 125967 C S + 375s foo 127443 G S + 375s foo 127565 C Y + 375s foo 128700 C A - 375s foo 129912 G A - 375s foo 130847 T W + 375s foo 131677 G S + 375s foo 132189 T C - 375s foo 135878 CGGC - - 375s foo 136825 T K + 375s foo 138881 TGT - - 375s foo 139288 A W + 375s foo 141054 A W + 375s foo 141055 - T + 375s foo 141101 C S + 375s foo 141404 A R + 375s foo 142698 T C - 375s foo 143990 C A - 375s foo 144167 T Y + 375s foo 144814 C Y + 375s foo 146381 T Y + 375s foo 146393 C A - 375s foo 146510 A C - 375s foo 147182 A W + 375s foo 148783 T C - 375s foo 149068 G S + 375s foo 150208 T K + 375s foo 151554 T W + 375s foo 151709 C G - 375s foo 153072 G R + 375s foo 153307 T Y + 375s foo 154050 G S + 375s foo 154415 C S + 375s foo 154594 G R + 375s foo 155839 G T - 375s foo 156106 G A - 375s foo 159356 T W + 375s foo 159926 A W + 375s foo 160303 T K + 375s foo 161323 C Y + 375s foo 161904 G S + 375s foo 162533 - ACC - 375s foo 164738 C G - 375s foo 165413 A R + 375s foo 166944 C M + 375s foo 167464 T Y + 375s foo 168420 T C - 375s foo 168579 A M + 375s foo 168787 T W + 375s foo 168959 A T - 375s foo 169884 G S + 375s foo 170032 G T - 375s foo 172058 G K + 375s foo 174942 A R + 375s foo 175014 G K + 375s foo 178406 G A - 375s foo 179028 - A + 375s foo 182394 C M + 375s foo 182735 T Y + 375s foo 183384 T K + 375s foo 183893 - AT - 375s foo 185360 G A - 375s foo 185538 - G - 375s foo 187948 G S + 375s foo 188120 T G - 375s foo 188179 T W + 375s foo 188316 T Y + 375s foo 189963 - G + 375s foo 190093 C Y + 375s foo 192220 C M + 375s foo 192368 A W + 375s foo 192782 T K + 375s foo 193307 A R + 375s foo 193501 G K + 375s foo 194276 G S + 375s foo 194930 C S + 375s foo 196728 A W + 375s foo 197559 G C - 375s foo 198467 T W + 375s foo 199042 C Y + 375s foo 199259 AA - - 375s foo 199687 TT - - 375s foo 200287 C A - 375s foo 200678 A R + 375s foo 201208 C T - 375s foo 201882 A - - 375s foo 204456 T K + 375s foo 206327 G R + 375s foo 207311 G T - 375s foo 209184 G A - 375s foo 209279 C Y + 375s foo 211459 C Y + 375s foo 213807 T Y + 375s foo 213846 T Y + 375s foo 214635 A G - 375s foo 214884 C A - 375s foo 216244 A M + 375s foo 216652 A M + 375s foo 216745 T - - 375s foo 216909 A T - 375s foo 217579 A G - 375s foo 217895 C Y + 375s foo 218870 G K + 375s foo 223098 T A - 375s foo 223283 - C + 375s foo 223666 C A - 375s foo 224011 - C + 375s foo 225681 C S + 375s foo 227345 T C - 375s foo 228778 T G - 375s foo 229926 C - - 375s foo 230778 T K + 375s foo 230939 CG - - 375s foo 231988 CT - - 375s foo 234593 T W + 375s foo 235496 C S + 375s foo 235705 G K + 375s foo 235758 A G - 375s foo 236852 T C - 375s foo 238790 A M + 375s foo 238865 T K + 375s foo 239329 A M + 375s foo 239576 - C + 375s foo 243058 G S + 375s foo 244147 T - - 375s foo 244462 C G - 375s foo 245443 - A + 375s foo 246544 C Y + 375s foo 246744 T W + 375s foo 247473 C M + 375s foo 248129 C T - 375s foo 249060 A C - 375s foo 249515 G T - 375s foo 250138 G S + 375s foo 250567 C A - 375s foo 254381 G R + 375s foo 257864 C M + 375s foo 257879 C Y + 375s foo 259859 A M + 375s foo 260643 C S + 375s foo 261681 C G - 375s foo 262645 T Y + 375s foo 263279 A R + 375s foo 263575 A - - 375s foo 264587 - TA + 375s foo 264689 T K + 375s foo 265758 G K + 375s foo 266272 A M + 375s foo 268550 C M + 375s foo 269986 G S + 375s foo 270321 AC - - 375s foo 273346 C S + 375s foo 275367 C A - 375s foo 277334 C G - 375s foo 277629 G T - 375s foo 278431 C Y + 375s foo 281456 T Y + 375s foo 281556 T G - 375s foo 281737 G K + 375s foo 282290 AC - - 375s foo 282851 - C - 375s foo 284405 A C - 375s foo 288751 A C - 375s foo 290501 TAAA - - 375s foo 291315 A W + 375s foo 291368 C - - 375s foo 292154 A C - 375s foo 292385 C M + 375s foo 292555 G K + 375s foo 297709 G C - 375s foo 298183 A W + 375s foo 298228 T W + 375s foo 299902 T G - 375s foo 302575 A T - 375s foo 304823 G R + 375s foo 305308 T Y + 375s foo 305487 G S + 375s foo 305697 G T - 375s foo 306098 C G - 375s foo 306882 T Y + 375s foo 308201 A M + 375s foo 308833 A T - 375s foo 312033 A - - 375s foo 312895 C G - 375s foo 313889 C - - 375s foo 315109 A R + 375s foo 316083 C - - 375s foo 316466 A R + 375s foo 318040 G C - 375s foo 319446 T C - 375s foo 320236 C S + 375s foo 320652 A - - 375s foo 320716 T K + 375s foo 323644 A - - 375s foo 325359 G T - 375s foo 329476 - CA + 375s foo 329706 T G - 375s foo 330181 T Y + 375s foo 330703 C Y + 375s foo 331315 G S + 375s foo 332351 C A - 375s foo 333408 A R + 375s foo 333468 C S + 375s foo 336247 A G - 375s foo 336586 A M + 375s foo 337364 G K + 375s foo 337686 A T - 375s foo 338043 A - - 375s foo 338292 C G - 375s foo 338962 A C - 375s foo 339353 G K + 375s foo 340647 - A + 375s foo 341705 G R + 375s foo 344283 C M + 375s foo 345898 - AG - 375s foo 347959 T - - 375s foo 349162 C M + 375s foo 352072 T Y + 375s foo 354614 C Y + 375s foo 359304 T - - 375s foo 359312 - G + 375s foo 360972 C S + 375s foo 363857 C Y + 375s foo 366226 A C - 375s foo 367259 C M + 375s foo 372502 T Y + 375s foo 372747 A M + 375s foo 375140 C S + 375s foo 376298 T W + 375s foo 376313 C - - 375s foo 376760 T W + 375s foo 378494 A W + 375s foo 381137 T G - 375s foo 381186 A R + 375s foo 381701 A G - 375s foo 382614 A W + 375s foo 382761 C T - 375s foo 382854 T C - 375s foo 383201 C T - 375s foo 385104 G S + 375s foo 385233 - A + 375s foo 386138 C T - 375s foo 386316 A W + 375s foo 387072 A R + 375s foo 387642 - A + 375s foo 388232 T C - 375s foo 388890 GGG - - 375s foo 390508 C S + 375s foo 390625 C M + 375s foo 391921 C G - 375s foo 395256 G T - 375s foo 395542 G S + 375s foo 397015 A - - 375s foo 397516 C Y + 375s foo 397528 GC - - 375s foo 398152 C T - 375s foo 399802 A W + 375s foo 400972 T K + 375s foo 401419 - T + 375s foo 401477 T W + 375s foo 402437 A M + 375s foo 402722 G R + 375s foo 403452 C M + 375s foo 404234 - A + 375s foo 405344 A W + 375s foo 407040 G S + 375s foo 408483 G R + 375s foo 408586 A C - 375s foo 408721 A R + 375s foo 409494 A M + 375s foo 410078 A G - 375s foo 411170 C A - 375s foo 415342 T Y + 375s foo 416265 C G - 375s foo 417740 C A - 375s foo 418622 C S + 375s foo 420232 A W + 375s foo 420288 T Y + 375s foo 420908 A W + 375s foo 421109 T A - 375s foo 421357 A R + 375s foo 422799 G A - 375s foo 424383 C S + 375s foo 424871 - GCA + 375s foo 427273 T A - 375s foo 429822 C M + 375s foo 429846 T W + 375s foo 432015 A G - 375s foo 432414 G K + 375s foo 433606 C Y + 375s foo 433831 T Y + 375s foo 437721 - A - 375s foo 438402 G - - 375s foo 438799 A T - 375s foo 439422 C M + 375s foo 440734 C A - 375s foo 441840 T G - 375s foo 442021 - C + 375s foo 445021 T A - 375s foo 445591 G A - 375s foo 446138 T W + 375s foo 447757 A W + 375s foo 449156 T - - 375s foo 449161 G K + 375s foo 450114 A W + 375s foo 450688 A W + 375s foo 454421 C G - 375s foo 454718 T Y + 375s foo 455675 TC - - 375s foo 461721 G R + 375s foo 462526 G S + 375s foo 467296 G A - 375s foo 467510 G K + 375s foo 468267 T K + 375s foo 469118 G R + 375s foo 469830 C Y + 375s foo 471073 G T - 375s foo 472056 G A - 375s foo 472773 - A + 375s foo 473046 G R + 375s foo 473188 G A - 375s foo 473742 C - - 375s foo 474789 T A - 375s foo 477763 G R + 375s foo 478246 T W + 375s foo 478975 T G - 375s foo 479038 A R + 375s foo 480275 T Y + 375s foo 480317 G A - 375s foo 481512 T K + 375s foo 482069 G S + 375s foo 482534 A R + 375s foo 483760 C Y + 375s foo 485281 T W + 375s foo 486255 T C - 375s foo 487038 T K + 375s foo 487225 T A - 375s foo 488012 C Y + 375s foo 488795 T C - 375s foo 490241 A R + 375s foo 492595 - CGG + 375s foo 493224 C A - 375s foo 494284 A T - 375s foo 495990 - T - 375s foo 497306 A R + 375s foo 497403 T Y + 375s foo 499569 C Y + 375s foo 499651 T K + 375s foo 503139 T C - 375s foo 504660 A R + 375s foo 508679 C - - 375s foo 513643 G K + 375s foo 515668 CC - - 375s foo 515836 G R + 375s foo 516488 C S + 375s foo 517602 G R + 375s foo 517962 G K + 375s foo 517975 T K + 375s foo 519144 A T - 375s foo 520068 T K + 375s foo 520926 A W + 375s foo 521562 C S + 375s foo 522076 CG - - 375s foo 522838 T Y + 375s foo 523513 - C + 375s foo 523907 - TA + 375s foo 526271 T A - 375s foo 526533 AC - - 375s foo 526767 C Y + 375s foo 528217 C Y + 375s foo 531924 G S + 375s foo 532333 - TT + 375s foo 533132 C M + 375s foo 534689 A T - 375s foo 534779 A W + 375s foo 535594 C A - 375s foo 535795 G R + 375s foo 538368 A R + 375s foo 540879 G K + 375s foo 542530 A - - 375s foo 543620 G R + 375s foo 544733 - C - 375s foo 546300 - TT + 375s foo 548196 A T - 375s foo 548878 C M + 375s foo 548885 G R + 375s foo 549459 T K + 375s foo 550908 A G - 375s foo 551170 A - - 375s foo 553130 T Y + 375s foo 555293 T G - 375s foo 556198 G R + 375s foo 556355 A T - 375s foo 557688 G K + 375s foo 558415 G C - 375s foo 558461 - G + 375s foo 559287 T Y + 375s foo 559465 C M + 375s foo 560184 T W + 375s foo 560252 T W + 375s foo 562579 A M + 375s foo 562961 G A - 375s foo 566986 C A - 375s foo 568134 C A - 375s foo 569698 T C - 375s foo 570180 T K + 375s foo 570451 TG - - 375s foo 570832 - A - 375s foo 571589 A W + 375s foo 572208 C M + 375s foo 572871 C S + 375s foo 574334 G - - 375s foo 575673 T Y + 375s foo 576797 G S + 375s foo 578486 - C - 375s foo 578494 C S + 375s foo 579257 G A - 375s foo 580103 G T - 375s foo 580872 A W + 375s foo 580925 G S + 375s foo 580950 G C - 375s foo 581637 T Y + 375s foo 581654 A G - 375s foo 582538 A T - 375s foo 582691 C M + 375s foo 582938 A W + 375s foo 583104 T K + 375s foo 584763 T W + 375s foo 585723 T W + 375s foo 588253 T Y + 375s foo 588972 T C - 375s foo 589438 - C - 375s foo 591131 C Y + 375s foo 591950 G R + 375s foo 592194 T G - 375s foo 592310 G S + 375s foo 593892 G A - 375s foo 598556 A - - 375s foo 601660 G S + 375s foo 602112 G T - 375s foo 602412 T Y + 375s foo 607282 - C + 375s foo 607394 A M + 375s foo 608438 A T - 375s foo 609255 A W + 375s foo 609365 - T + 375s foo 611161 G K + 375s foo 612224 C G - 375s foo 614493 G R + 375s foo 614601 G A - 375s foo 614607 C Y + 375s foo 619507 C M + 375s foo 619798 T C - 375s foo 621872 C T - 375s foo 622375 C Y + 375s foo 623208 - G - 375s foo 624366 C A - 375s foo 625320 - ACA - 375s foo 626664 - G + 375s foo 627140 T C - 375s foo 627353 G T - 375s foo 628714 T Y + 375s foo 628744 A - - 375s foo 629152 A G - 375s foo 630110 T G - 375s foo 631744 G K + 375s foo 632763 C S + 375s foo 634419 G - - 375s foo 634459 A G - 375s foo 634571 G A - 375s foo 635366 - A + 375s foo 635604 G T - 375s foo 637057 T C - 375s foo 637525 A T - 375s foo 638412 A R + 375s foo 640547 A W + 375s foo 641514 T K + 375s foo 642219 A R + 375s foo 642427 A G - 375s foo 642612 A R + 375s foo 643553 T W + 375s foo 647316 - T + 375s foo 647598 C - - 375s foo 651093 G A - 375s foo 651718 G R + 375s foo 652235 A G - 375s foo 652579 A C - 375s foo 653355 A W + 375s foo 655174 C M + 375s foo 655487 A M + 375s foo 656849 G S + 375s foo 661081 T K + 375s foo 661134 G C - 375s foo 661935 A W + 375s foo 662010 A M + 375s foo 662040 G R + 375s foo 663030 A W + 375s foo 663268 - C + 375s foo 664991 T - - 375s foo 665489 T K + 375s foo 665555 C M + 375s foo 665965 C Y + 375s foo 668725 A C - 375s foo 668834 - G - 375s foo 668873 C S + 375s foo 669654 T W + 375s foo 671041 G S + 375s foo 671485 T W + 375s foo 671690 C M + 375s foo 673022 G R + 375s foo 674137 - T + 375s foo 674782 A C - 375s foo 676373 G T - 375s foo 676793 T C - 375s foo 677409 G S + 375s foo 677536 - AA - 375s foo 677620 G K + 375s foo 677686 C Y + 375s foo 678327 G S + 375s foo 678704 G S + 375s foo 678771 A C - 375s foo 678866 C T - 375s foo 679960 A W + 375s foo 680447 - C + 375s foo 682102 C T - 375s foo 685497 T A - 375s foo 686884 G S + 375s foo 687324 ACA - - 375s foo 687684 - AC + 375s foo 687823 T C - 375s foo 688590 G K + 375s foo 690802 C M + 375s foo 691388 T C - 375s foo 691403 T G - 375s foo 691790 G A - 375s foo 692973 C A - 375s foo 694058 G S + 375s foo 694550 G R + 375s foo 694968 T W + 375s foo 695898 A T - 375s foo 696721 C S + 375s foo 696787 C S + 375s foo 696935 A M + 375s foo 698024 - C + 375s foo 699813 A - - 375s foo 700179 G R + 375s foo 701421 A M + 375s foo 701989 T A - 375s foo 702862 C A - 375s foo 707020 G A - 375s foo 708420 A - - 375s foo 708669 C G - 375s foo 710521 T W + 375s foo 711801 G C - 375s foo 711913 T G - 375s foo 715830 C M + 375s foo 717664 TC - - 375s foo 718845 A W + 375s foo 719069 T Y + 375s foo 719565 A W + 375s foo 721136 T K + 375s foo 726116 T K + 375s foo 727809 T K + 375s foo 728864 G K + 375s foo 728918 G A - 375s foo 730296 - T + 375s foo 731988 C Y + 375s foo 734658 A M + 375s foo 734715 A W + 375s foo 736618 C G - 375s foo 737257 T Y + 375s foo 740864 C A - 375s foo 741640 G - - 375s foo 741859 - TA - 375s foo 742011 T K + 375s foo 742237 A R + 375s foo 742960 G K + 375s foo 743731 G R + 375s foo 743971 A W + 375s foo 744635 T K + 375s foo 746430 C G - 375s foo 746489 - GC - 375s foo 746881 C M + 375s foo 756997 TC - - 375s foo 757776 A M + 375s foo 759870 A T - 375s foo 760224 G K + 375s foo 760799 G C - 375s foo 761692 T C - 375s foo 762569 G S + 375s foo 763140 A G - 375s foo 763842 - T - 375s foo 764192 A M + 375s foo 764334 G A - 375s foo 764889 - AAT + 375s foo 766464 G S + 375s foo 768226 G A - 375s foo 770272 T G - 375s foo 771145 C Y + 375s foo 772209 T A - 375s foo 773672 T K + 375s foo 773932 G C - 375s foo 774658 C S + 375s foo 775969 A M + 375s foo 776816 T G - 375s foo 777591 C Y + 375s foo 777891 A M + 375s foo 778164 C M + 375s foo 778219 T W + 375s foo 779260 G T - 375s foo 779465 A W + 375s foo 779779 G S + 375s foo 780033 G K + 375s foo 783243 C M + 375s foo 783860 A R + 375s foo 788345 A M + 375s foo 789554 G - - 375s foo 790025 G K + 375s foo 791454 T K + 375s foo 792009 C A - 375s foo 792872 C G - 375s foo 794616 T W + 375s foo 795031 G R + 375s foo 796919 C M + 375s foo 797020 G S + 375s foo 797042 G C - 375s foo 797149 G A - 375s foo 797177 A C - 375s foo 799076 G C - 375s foo 799580 G S + 375s foo 800356 A R + 375s foo 802297 G T - 375s foo 802309 T Y + 375s foo 802343 - C + 375s foo 802769 A W + 375s foo 803104 C G - 375s foo 805819 C Y + 375s foo 805972 T Y + 375s foo 807503 T K + 375s foo 807950 C M + 375s foo 807994 - A - 375s foo 809167 A G - 375s foo 809658 A W + 375s foo 810152 A M + 375s foo 811506 G R + 375s foo 813494 A M + 375s foo 814035 G T - 375s foo 814476 A W + 375s foo 819399 T K + 375s foo 820171 T W + 375s foo 820445 G C - 375s foo 822178 C G - 375s foo 822504 C T - 375s foo 823378 C M + 375s foo 823591 CG - - 375s foo 824229 C M + 375s foo 824579 C T - 375s foo 824858 C M + 375s foo 826101 T K + 375s foo 827593 C G - 375s foo 827794 T Y + 375s foo 828228 A M + 375s foo 828367 T K + 375s foo 828788 C M + 375s foo 829002 C Y + 375s foo 830345 C M + 375s foo 831018 C A - 375s foo 831459 T K + 375s foo 832413 A T - 375s foo 832782 T Y + 375s foo 832908 T Y + 375s foo 833130 T - - 375s foo 833142 G S + 375s foo 833241 G A - 375s foo 836727 A T - 375s foo 836829 G S + 375s foo 838452 T G - 375s foo 838543 A T - 375s foo 838605 C M + 375s foo 838954 G C - 375s foo 841829 G K + 375s foo 842324 - TC + 375s foo 842996 - C + 375s foo 844390 C A - 375s foo 844793 A C - 375s foo 844925 C A - 375s foo 845082 G C - 375s foo 846202 G R + 375s foo 846707 A G - 375s foo 848713 G A - 375s foo 849372 C S + 375s foo 849742 G A - 375s foo 850499 C - - 375s foo 850927 GT - - 375s foo 851084 - G + 375s foo 852247 A R + 375s foo 852972 C A - 375s foo 854808 T W + 375s foo 855956 G K + 375s foo 856225 G A - 375s foo 856582 T K + 375s foo 857351 C M + 375s foo 857504 AC - - 375s foo 858324 A T - 375s foo 858858 T C - 375s foo 859488 T Y + 375s foo 862441 T Y + 375s foo 863827 C Y + 375s foo 864165 C A - 375s foo 865997 C M + 375s foo 866370 G S + 375s foo 867653 G S + 375s foo 867722 C Y + 375s foo 868696 C M + 375s foo 869005 T W + 375s foo 869791 T Y + 375s foo 875339 C Y + 375s foo 875347 C M + 375s foo 875584 T G - 375s foo 876780 C T - 375s foo 878368 A C - 375s foo 878916 - CAG + 375s foo 879005 A R + 375s foo 880112 G T - 375s foo 881021 - T - 375s foo 881175 T W + 375s foo 882168 - GGG + 375s foo 882223 - G - 375s foo 883033 TG - - 375s foo 883381 C G - 375s foo 884378 C - - 375s foo 885075 A M + 375s foo 885190 A W + 375s foo 885568 A W + 375s foo 885827 T Y + 375s foo 887610 TG - - 375s foo 889139 G R + 375s foo 890978 T - - 375s foo 891500 C Y + 375s foo 892257 G C - 375s foo 892642 G R + 375s foo 892644 T W + 375s foo 892757 C A - 375s foo 893222 T - - 375s foo 893348 T W + 375s foo 894161 - C - 375s foo 894447 A G - 375s foo 894614 A W + 375s foo 897817 T W + 375s foo 899408 C S + 375s foo 902450 A T - 375s foo 902970 AT - - 375s foo 905836 G K + 375s foo 906524 GA - - 375s foo 907484 A W + 375s foo 907537 C M + 375s foo 908515 G R + 375s foo 908642 C T - 375s foo 911145 T C - 375s foo 912220 T Y + 375s foo 912682 C Y + 375s foo 914260 C S + 375s foo 914757 T Y + 375s foo 916413 G C - 375s foo 916783 T G - 375s foo 917033 G C - 375s foo 917218 A - - 375s foo 918225 G - - 375s foo 918459 A - - 375s foo 918732 A M + 375s foo 919640 TC - - 375s foo 920824 T W + 375s foo 920836 G C - 375s foo 924560 G R + 375s foo 924659 GA - - 375s foo 925868 T A - 375s foo 928254 T G - 375s foo 928369 - A - 375s foo 928641 - AG + 375s foo 929857 C M + 375s foo 930211 T W + 375s foo 930935 C T - 375s foo 931986 A M + 375s foo 932852 G T - 375s foo 933965 T A - 375s foo 935564 A W + 375s foo 936034 T Y + 375s foo 936221 AC - - 375s foo 936670 C S + 375s foo 936704 T A - 375s foo 936786 T W + 375s foo 939218 C S + 375s foo 939312 A W + 375s foo 939467 A W + 375s foo 939934 C S + 375s foo 941603 C Y + 375s foo 942910 A W + 375s foo 944654 T Y + 375s foo 945301 A C - 375s foo 945770 C T - 375s foo 946078 G S + 375s foo 948833 G K + 375s foo 948999 A W + 375s foo 949193 A R + 375s foo 950276 C M + 375s foo 950414 A W + 375s foo 951285 G C - 375s foo 953158 G R + 375s foo 953287 A W + 375s foo 954150 C G - 375s foo 954258 G - - 375s foo 955396 CC - - 375s foo 956490 - AC + 375s foo 958129 A R + 375s foo 959027 T A - 375s foo 959964 A W + 375s foo 962042 A G - 375s foo 962742 C G - 375s foo 963306 T W + 375s foo 963422 G K + 375s foo 964082 G S + 375s foo 965561 C S + 375s foo 966531 T K + 375s foo 967324 T W + 375s foo 968419 - C - 375s foo 969054 G - - 375s foo 969158 G S + 375s foo 972658 C M + 375s foo 974266 T W + 375s foo 974629 G K + 375s foo 975034 A R + 375s foo 975636 T W + 375s foo 977078 - A - 375s foo 978321 G T - 375s foo 978595 C G - 375s foo 979090 C M + 375s foo 983855 TA - - 375s foo 985725 T A - 375s foo 988497 C Y + 375s foo 990171 C M + 375s foo 990804 - CA - 375s foo 990941 T W + 375s foo 991797 A W + 375s foo 992469 A M + 375s foo 994610 C Y + 375s foo 998107 - T + 375s foo 999725 G R + 375s [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.2580.smaltmap.smalt_index foo1.fasta 375s # Command line: smalt index -k 13 -s 2 out.bam.tmp.2580.smaltmap.smalt_index foo1.fasta 375s # Reading sequences ... 375s # Writing sequence set ... 375s # Setting up hash index with collisions ... 375s # word length = 13 bases, skip step = 2 bases ... 375s # number of bits for key = 18 with 0 perfect bits 375s # Counting keys ... 375s # Counting k-tuples ... 375s # Allocating k-tuple arrays ... 375s # Counting k-tuple occurrences ... 375s # Setting the k-tuple positions in index ... 375s # Hash table is set up. 375s # =-=-=-=-= Hash Index Stats =-=-=-=-= 375s # Hash index with collisions. 375s # Word length: 13 bases 375s # Skip step: 2 bases 375s # Number of hash keys: 262144 375s # Number of word positions: 499970 375s # Number of different words: 498076 375s # Maximum number of words per key: 11 375s # Number of keys without words: 39377 375s # =-=-= End of Hash Index Stats =-=-= 375s # Writing table to file ... 375s # smalt: Total elapsed wall clock time: 0 seconds 375s [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.2580.smaltmap.smalt_sample out.bam.tmp.2580.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 375s # Command line: smalt sample -u 1000 -o out.bam.tmp.2580.smaltmap.smalt_sample out.bam.tmp.2580.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 375s # Opening read files ... 375s # Reading reference sequences ... 375s # Reading hash table ... 375s # =-=-=-=-= Hash Index Stats =-=-=-=-= 375s # Hash index with collisions. 375s # Word length: 13 bases 375s # Skip step: 2 bases 375s # Number of hash keys: 262144 375s # Number of word positions: 499970 375s # Number of different words: 498076 375s # Maximum number of words per key: 11 375s # Number of keys without words: 39377 375s # =-=-= End of Hash Index Stats =-=-= 375s # Check of read pairs ok ... 375s # Mate names match ... 375s # Sampling insert size distribution ... 379s # Processed 9999 read pairs. 379s [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2580.smaltmap.smalt_sample -f samsoft out.bam.tmp.2580.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.2580.smaltmap.raw.bam 379s # smalt: Time spent setting up hash index:0 seconds 379s # smalt: Time spent mapping reads:4 seconds 379s # smalt: Total elapsed wall clock time: 4 seconds 379s # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2580.smaltmap.smalt_sample -f samsoft out.bam.tmp.2580.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 379s # Reading distribution of insert sizes from file ... 379s # Sampled histogram 379s # Smoothed histogram 379s # Opening read files ... 379s # Reading reference sequences ... 379s # Reading hash table ... 379s # =-=-=-=-= Hash Index Stats =-=-=-=-= 379s # Hash index with collisions. 379s # Word length: 13 bases 379s # Skip step: 2 bases 379s # Number of hash keys: 262144 379s # Number of word positions: 499970 379s # Number of different words: 498076 379s # Maximum number of words per key: 11 379s # Number of keys without words: 39377 379s # =-=-= End of Hash Index Stats =-=-= 379s # Processing query reads ... 397s # Processed 10000 read pairs. 397s # smalt: Time spent setting up hash index:0 seconds 397s # smalt: Time spent mapping reads:18 seconds 397s # smalt: Total elapsed wall clock time: 18 seconds 397s [REAPR smaltmap] Running: samtools sort out.bam.tmp.2580.smaltmap.raw.bam -O bam -o out.bam.tmp.2580.smaltmap.raw.bam.sort.bam 397s [bam_rmdup_core] processing reference foo... 397s [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.2580.smaltmap.raw.bam.sort.bam out.bam.tmp.2580.smaltmap.rmdup.bam 397s [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' 397s [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.2580.smaltmap.header 397s [REAPR smaltmap] Running: samtools view -H out.bam.tmp.2580.smaltmap.rmdup.bam >> out.bam.tmp.2580.smaltmap.header 397s [REAPR smaltmap] Running: samtools reheader out.bam.tmp.2580.smaltmap.header out.bam.tmp.2580.smaltmap.rmdup.bam > out.bam 397s [REAPR smaltmap] Running: samtools index out.bam 397s [REAPR smaltmap] Running: rm out.bam.tmp.2580.smaltmap.* 397s Running reapr version 1.0.18 pipeline: 397s reapr foo1.fasta out.bam result 397s [REAPR pipeline] Running facheck 397s [REAPR pipeline] Running preprocess 400s [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases 400s [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases 400s [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases 400s [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases 403s [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation 406s [REAPR pipeline] Running stats 425s [REAPR pipeline] Running fcdrate 428s [REAPR pipeline] Running score 434s [REAPR pipeline] Running break 434s [REAPR pipeline] Running summary 434s autopkgtest [15:55:49]: test test-example: -----------------------] 435s autopkgtest [15:55:50]: test test-example: - - - - - - - - - - results - - - - - - - - - - 435s test-example PASS 435s autopkgtest [15:55:50]: @@@@@@@@@@@@@@@@@@@@ summary 435s test-example PASS 487s Creating nova instance adt-noble-ppc64el-reapr-20240323-154835-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...