0s autopkgtest [12:23:40]: starting date and time: 2024-11-13 12:23:40+0000 0s autopkgtest [12:23:40]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [12:23:40]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2_68l77z/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade circlator --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-15.secgroup --name adt-plucky-i386-circlator-20241113-122340-juju-7f2275-prod-proposed-migration-environment-20-26ed46f0-b135-4bce-b37f-95b66c53ffa2 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 351s autopkgtest [12:29:31]: testbed dpkg architecture: amd64 351s autopkgtest [12:29:31]: testbed apt version: 2.9.8 352s autopkgtest [12:29:32]: test architecture: i386 352s autopkgtest [12:29:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 353s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 353s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 353s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 353s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 353s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 353s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.6 kB] 353s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [131 kB] 353s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 353s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [281 kB] 353s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [721 kB] 353s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [38.5 kB] 353s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.3 kB] 353s Fetched 2466 kB in 1s (2982 kB/s) 354s Reading package lists... 356s Reading package lists... 356s Building dependency tree... 356s Reading state information... 356s Calculating upgrade... 357s The following NEW packages will be installed: 357s python3.13-gdbm 357s The following packages will be upgraded: 357s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 357s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 357s Need to get 253 kB of archives. 357s After this operation, 147 kB of additional disk space will be used. 357s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 357s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 357s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 357s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 357s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 357s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 357s Fetched 253 kB in 0s (612 kB/s) 357s (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 ... 75541 files and directories currently installed.) 357s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 357s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 357s Setting up python3-minimal (3.12.7-1) ... 358s (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 ... 75541 files and directories currently installed.) 358s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 358s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 358s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 358s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 358s Selecting previously unselected package python3.13-gdbm. 358s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 358s Unpacking python3.13-gdbm (3.13.0-2) ... 358s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 358s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 358s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 358s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 358s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 358s Setting up python3.13-gdbm (3.13.0-2) ... 358s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 358s Setting up python3 (3.12.7-1) ... 358s Setting up python3-gdbm:amd64 (3.12.7-1) ... 358s Processing triggers for man-db (2.12.1-3) ... 359s Processing triggers for libc-bin (2.40-1ubuntu3) ... 359s Reading package lists... 359s Building dependency tree... 359s Reading state information... 359s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 359s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 360s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 360s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 360s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 360s Reading package lists... 360s Reading package lists... 361s Building dependency tree... 361s Reading state information... 361s Calculating upgrade... 361s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 361s Reading package lists... 361s Building dependency tree... 361s Reading state information... 361s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 364s autopkgtest [12:29:44]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 364s autopkgtest [12:29:44]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator 367s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (dsc) [1672 B] 367s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (tar) [5724 kB] 367s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (diff) [6152 B] 367s gpgv: Signature made Sat Dec 2 21:39:17 2023 UTC 367s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 367s gpgv: Can't check signature: No public key 367s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found 367s autopkgtest [12:29:47]: testing package circlator version 1.5.6-11 367s autopkgtest [12:29:47]: build not needed 368s autopkgtest [12:29:48]: test run-unit-test: preparing testbed 370s Note, using file '/tmp/autopkgtest.zwlDOt/1-autopkgtest-satdep.dsc' to get the build dependencies 370s Reading package lists... 371s Building dependency tree... 371s Reading state information... 371s Starting pkgProblemResolver with broken count: 0 371s Starting 2 pkgProblemResolver with broken count: 0 371s Done 371s The following NEW packages will be installed: 371s aglfn bamtools binfmt-support build-essential bwa ca-certificates-java canu 371s circlator cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 371s default-jre-headless fastaq fastjar fontconfig fontconfig-config 371s fonts-dejavu-core fonts-dejavu-mono g++ g++-14 g++-14-x86-64-linux-gnu 371s g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 371s gnuplot-data gnuplot-nox jaligner jarwrapper java-common libaom3 371s libapache-pom-java libasan8 libatinject-jsr330-api-java libbamtools2.5.2 371s libcairo2 libcc1-0 libcommons-codec-java libcommons-compress-java 371s libcommons-io-java libcommons-parent-java libdatrie1 libde265-0 libdeflate0 371s liberror-prone-java libfastutil-java libfilesys-df-perl libfontconfig1 371s libgcc-14-dev libgd3 libgomp1 libgraphite2-3 libguava-java libharfbuzz0b 371s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libhts3t64 371s libhtscodecs2 libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 371s libjpeg-turbo8 libjpeg8 libjsoncpp26 libjsr305-java liblcms2-2 liblerc4 371s liblsan0 liblua5.4-0 libmpc3 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 371s libpangoft2-1.0-0 libpcsclite1 libpixman-1-0 libpython3.13-minimal 371s libpython3.13-stdlib libquadmath0 libraqm0 libsharpyuv0 libsnappy1v5 371s libssw-java libssw0 libstdc++-14-dev libthai-data libthai0 libtiff6 libtsan2 371s libubsan1 libwebp7 libwebpmux3 libxcb-render0 libxcb-shm0 libxpm4 371s libxrender1 libxslt1.1 mhap mummer openjdk-21-jre-headless prodigal 371s python3-all python3-et-xmlfile python3-iniconfig python3-joblib python3-lxml 371s python3-openpyxl python3-packaging python3-pluggy python3-pymummer 371s python3-pysam python3-pytest python3.13 python3.13-minimal samtools spades 371s 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. 371s Need to get 177 MB of archives. 371s After this operation, 636 MB of additional disk space will be used. 371s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 binfmt-support amd64 2.2.2-7 [56.2 kB] 371s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 372s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 372s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB] 372s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libjsoncpp26 amd64 1.9.6-2 [89.9 kB] 372s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 bamtools amd64 2.5.2+dfsg-6build1 [178 kB] 372s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 372s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 372s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 373s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 373s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 373s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 373s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 373s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 373s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 373s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 373s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 373s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 373s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 373s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 373s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 373s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 374s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 374s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 374s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 374s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 374s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 374s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 375s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 375s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 375s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 375s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 375s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB] 375s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 375s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 375s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libfilesys-df-perl amd64 0.92-7build5 [11.4 kB] 375s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 375s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 375s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 375s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 375s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB] 375s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [46.4 MB] 376s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B] 376s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastjar amd64 2:0.98-7 [67.1 kB] 376s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 jarwrapper all 0.80 [9800 B] 376s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 376s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 376s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB] 376s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.17.0-1 [457 kB] 376s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB] 376s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfastutil-java all 8.5.15+dfsg-1 [20.2 MB] 377s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B] 377s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] 377s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB] 377s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 libguava-java all 32.0.1-1 [2692 kB] 377s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 jaligner all 1.0+dfsg-11 [136 kB] 377s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw-java amd64 1.1-15 [18.9 kB] 377s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 mhap all 2.1.3+dfsg-3 [160 kB] 377s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB] 377s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB] 377s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 377s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 377s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 377s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 377s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 377s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 377s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 377s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 377s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 377s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 377s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.11.0~rc1-1 [2762 kB] 377s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.18.1-2 [11.1 kB] 377s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB] 377s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.18.1-2 [8758 B] 377s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.18.1-2 [293 kB] 377s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 377s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 377s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 377s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 377s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 377s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 377s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 377s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 377s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 377s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 377s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 377s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.6-3build2 [166 kB] 377s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 377s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 377s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 377s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 377s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB] 377s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB] 377s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB] 377s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 377s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 gnuplot-nox amd64 6.0.0+dfsg1-1ubuntu3 [989 kB] 378s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 canu amd64 2.2+dfsg-5 [1536 kB] 378s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 378s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 378s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 378s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastaq all 3.17.0-8 [48.2 kB] 378s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-et-xmlfile all 2.0.0-1 [79.4 kB] 378s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 378s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 378s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openpyxl all 3.1.5+dfsg-1 [152 kB] 378s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 378s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB] 378s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymummer all 0.11.0-4 [17.1 kB] 378s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 379s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB] 379s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 circlator all 1.5.6-11 [4618 kB] 379s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 379s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw0 amd64 1.1-15 [22.5 kB] 379s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 379s Get:115 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 379s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 379s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 379s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 379s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 379s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-5ubuntu1 [183 kB] 379s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 spades amd64 3.15.5+dfsg-7 [9133 kB] 379s Fetched 177 MB in 8s (22.4 MB/s) 379s Selecting previously unselected package binfmt-support. 380s (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 ... 75548 files and directories currently installed.) 380s Preparing to unpack .../000-binfmt-support_2.2.2-7_amd64.deb ... 380s Unpacking binfmt-support (2.2.2-7) ... 380s Selecting previously unselected package libpython3.13-minimal:amd64. 380s Preparing to unpack .../001-libpython3.13-minimal_3.13.0-2_amd64.deb ... 380s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 380s Selecting previously unselected package python3.13-minimal. 380s Preparing to unpack .../002-python3.13-minimal_3.13.0-2_amd64.deb ... 380s Unpacking python3.13-minimal (3.13.0-2) ... 380s Selecting previously unselected package libbamtools2.5.2:amd64. 380s Preparing to unpack .../003-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ... 380s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 380s Selecting previously unselected package libjsoncpp26:amd64. 380s Preparing to unpack .../004-libjsoncpp26_1.9.6-2_amd64.deb ... 380s Unpacking libjsoncpp26:amd64 (1.9.6-2) ... 380s Selecting previously unselected package bamtools. 380s Preparing to unpack .../005-bamtools_2.5.2+dfsg-6build1_amd64.deb ... 380s Unpacking bamtools (2.5.2+dfsg-6build1) ... 380s Selecting previously unselected package libisl23:amd64. 380s Preparing to unpack .../006-libisl23_0.27-1_amd64.deb ... 380s Unpacking libisl23:amd64 (0.27-1) ... 380s Selecting previously unselected package libmpc3:amd64. 380s Preparing to unpack .../007-libmpc3_1.3.1-1build2_amd64.deb ... 380s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 380s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 380s Preparing to unpack .../008-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package cpp-14. 380s Preparing to unpack .../009-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package cpp-x86-64-linux-gnu. 380s Preparing to unpack .../010-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 380s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 380s Selecting previously unselected package cpp. 380s Preparing to unpack .../011-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 380s Unpacking cpp (4:14.1.0-2ubuntu1) ... 380s Selecting previously unselected package libcc1-0:amd64. 380s Preparing to unpack .../012-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libgomp1:amd64. 380s Preparing to unpack .../013-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libitm1:amd64. 380s Preparing to unpack .../014-libitm1_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libasan8:amd64. 380s Preparing to unpack .../015-libasan8_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package liblsan0:amd64. 380s Preparing to unpack .../016-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libtsan2:amd64. 380s Preparing to unpack .../017-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libubsan1:amd64. 380s Preparing to unpack .../018-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libhwasan0:amd64. 380s Preparing to unpack .../019-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libquadmath0:amd64. 380s Preparing to unpack .../020-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package libgcc-14-dev:amd64. 380s Preparing to unpack .../021-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 380s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 380s Preparing to unpack .../022-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 380s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 381s Selecting previously unselected package gcc-14. 381s Preparing to unpack .../023-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 381s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 381s Selecting previously unselected package gcc-x86-64-linux-gnu. 381s Preparing to unpack .../024-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 381s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 381s Selecting previously unselected package gcc. 381s Preparing to unpack .../025-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 381s Unpacking gcc (4:14.1.0-2ubuntu1) ... 381s Selecting previously unselected package libstdc++-14-dev:amd64. 381s Preparing to unpack .../026-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 381s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 381s Selecting previously unselected package g++-14-x86-64-linux-gnu. 381s Preparing to unpack .../027-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 381s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 381s Selecting previously unselected package g++-14. 381s Preparing to unpack .../028-g++-14_14.2.0-8ubuntu1_amd64.deb ... 381s Unpacking g++-14 (14.2.0-8ubuntu1) ... 381s Selecting previously unselected package g++-x86-64-linux-gnu. 381s Preparing to unpack .../029-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 381s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 381s Selecting previously unselected package g++. 381s Preparing to unpack .../030-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 381s Unpacking g++ (4:14.1.0-2ubuntu1) ... 381s Selecting previously unselected package build-essential. 381s Preparing to unpack .../031-build-essential_12.10ubuntu1_amd64.deb ... 381s Unpacking build-essential (12.10ubuntu1) ... 381s Selecting previously unselected package bwa. 381s Preparing to unpack .../032-bwa_0.7.18-1_amd64.deb ... 381s Unpacking bwa (0.7.18-1) ... 381s Selecting previously unselected package ca-certificates-java. 381s Preparing to unpack .../033-ca-certificates-java_20240118_all.deb ... 381s Unpacking ca-certificates-java (20240118) ... 381s Selecting previously unselected package libsnappy1v5:amd64. 381s Preparing to unpack .../034-libsnappy1v5_1.2.1-1_amd64.deb ... 381s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 381s Selecting previously unselected package libfilesys-df-perl. 381s Preparing to unpack .../035-libfilesys-df-perl_0.92-7build5_amd64.deb ... 381s Unpacking libfilesys-df-perl (0.92-7build5) ... 381s Selecting previously unselected package java-common. 381s Preparing to unpack .../036-java-common_0.76_all.deb ... 381s Unpacking java-common (0.76) ... 381s Selecting previously unselected package liblcms2-2:amd64. 381s Preparing to unpack .../037-liblcms2-2_2.16-2_amd64.deb ... 381s Unpacking liblcms2-2:amd64 (2.16-2) ... 381s Selecting previously unselected package libjpeg-turbo8:amd64. 381s Preparing to unpack .../038-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 381s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 381s Selecting previously unselected package libjpeg8:amd64. 381s Preparing to unpack .../039-libjpeg8_8c-2ubuntu11_amd64.deb ... 381s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 381s Selecting previously unselected package libpcsclite1:amd64. 381s Preparing to unpack .../040-libpcsclite1_2.3.0-1_amd64.deb ... 381s Unpacking libpcsclite1:amd64 (2.3.0-1) ... 381s Selecting previously unselected package openjdk-21-jre-headless:amd64. 381s Preparing to unpack .../041-openjdk-21-jre-headless_21.0.5+11-1_amd64.deb ... 381s Unpacking openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... 382s Selecting previously unselected package default-jre-headless. 382s Preparing to unpack .../042-default-jre-headless_2%3a1.21-76_amd64.deb ... 382s Unpacking default-jre-headless (2:1.21-76) ... 382s Selecting previously unselected package fastjar. 382s Preparing to unpack .../043-fastjar_2%3a0.98-7_amd64.deb ... 382s Unpacking fastjar (2:0.98-7) ... 382s Selecting previously unselected package jarwrapper. 382s Preparing to unpack .../044-jarwrapper_0.80_all.deb ... 382s Unpacking jarwrapper (0.80) ... 382s Selecting previously unselected package libapache-pom-java. 382s Preparing to unpack .../045-libapache-pom-java_33-2_all.deb ... 382s Unpacking libapache-pom-java (33-2) ... 382s Selecting previously unselected package libcommons-parent-java. 382s Preparing to unpack .../046-libcommons-parent-java_56-1_all.deb ... 382s Unpacking libcommons-parent-java (56-1) ... 382s Selecting previously unselected package libcommons-codec-java. 382s Preparing to unpack .../047-libcommons-codec-java_1.17.1-1_all.deb ... 382s Unpacking libcommons-codec-java (1.17.1-1) ... 382s Selecting previously unselected package libcommons-io-java. 382s Preparing to unpack .../048-libcommons-io-java_2.17.0-1_all.deb ... 382s Unpacking libcommons-io-java (2.17.0-1) ... 382s Selecting previously unselected package libcommons-compress-java. 382s Preparing to unpack .../049-libcommons-compress-java_1.27.1-2_all.deb ... 382s Unpacking libcommons-compress-java (1.27.1-2) ... 382s Selecting previously unselected package libfastutil-java. 382s Preparing to unpack .../050-libfastutil-java_8.5.15+dfsg-1_all.deb ... 382s Unpacking libfastutil-java (8.5.15+dfsg-1) ... 382s Selecting previously unselected package libatinject-jsr330-api-java. 382s Preparing to unpack .../051-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ... 382s Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ... 382s Selecting previously unselected package liberror-prone-java. 382s Preparing to unpack .../052-liberror-prone-java_2.18.0-1_all.deb ... 382s Unpacking liberror-prone-java (2.18.0-1) ... 382s Selecting previously unselected package libjsr305-java. 382s Preparing to unpack .../053-libjsr305-java_0.1~+svn49-11_all.deb ... 382s Unpacking libjsr305-java (0.1~+svn49-11) ... 383s Selecting previously unselected package libguava-java. 383s Preparing to unpack .../054-libguava-java_32.0.1-1_all.deb ... 383s Unpacking libguava-java (32.0.1-1) ... 383s Selecting previously unselected package jaligner. 383s Preparing to unpack .../055-jaligner_1.0+dfsg-11_all.deb ... 383s Unpacking jaligner (1.0+dfsg-11) ... 383s Selecting previously unselected package libssw-java. 383s Preparing to unpack .../056-libssw-java_1.1-15_amd64.deb ... 383s Unpacking libssw-java (1.1-15) ... 383s Selecting previously unselected package mhap. 383s Preparing to unpack .../057-mhap_2.1.3+dfsg-3_all.deb ... 383s Unpacking mhap (2.1.3+dfsg-3) ... 383s Selecting previously unselected package aglfn. 383s Preparing to unpack .../058-aglfn_1.7+git20191031.4036a9c-2_all.deb ... 383s Unpacking aglfn (1.7+git20191031.4036a9c-2) ... 383s Selecting previously unselected package gnuplot-data. 383s Preparing to unpack .../059-gnuplot-data_6.0.0+dfsg1-1ubuntu3_all.deb ... 383s Unpacking gnuplot-data (6.0.0+dfsg1-1ubuntu3) ... 383s Selecting previously unselected package fonts-dejavu-mono. 383s Preparing to unpack .../060-fonts-dejavu-mono_2.37-8_all.deb ... 383s Unpacking fonts-dejavu-mono (2.37-8) ... 383s Selecting previously unselected package fonts-dejavu-core. 383s Preparing to unpack .../061-fonts-dejavu-core_2.37-8_all.deb ... 383s Unpacking fonts-dejavu-core (2.37-8) ... 383s Selecting previously unselected package fontconfig-config. 383s Preparing to unpack .../062-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 383s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 383s Selecting previously unselected package libfontconfig1:amd64. 383s Preparing to unpack .../063-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 383s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 383s Selecting previously unselected package libpixman-1-0:amd64. 383s Preparing to unpack .../064-libpixman-1-0_0.44.0-3_amd64.deb ... 383s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 383s Selecting previously unselected package libxcb-render0:amd64. 383s Preparing to unpack .../065-libxcb-render0_1.17.0-2_amd64.deb ... 383s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 383s Selecting previously unselected package libxcb-shm0:amd64. 383s Preparing to unpack .../066-libxcb-shm0_1.17.0-2_amd64.deb ... 383s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 383s Selecting previously unselected package libxrender1:amd64. 383s Preparing to unpack .../067-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 383s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 383s Selecting previously unselected package libcairo2:amd64. 383s Preparing to unpack .../068-libcairo2_1.18.2-2_amd64.deb ... 383s Unpacking libcairo2:amd64 (1.18.2-2) ... 383s Selecting previously unselected package libsharpyuv0:amd64. 383s Preparing to unpack .../069-libsharpyuv0_1.4.0-0.1_amd64.deb ... 383s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 383s Selecting previously unselected package libaom3:amd64. 383s Preparing to unpack .../070-libaom3_3.11.0~rc1-1_amd64.deb ... 383s Unpacking libaom3:amd64 (3.11.0~rc1-1) ... 383s Selecting previously unselected package libheif-plugin-aomdec:amd64. 383s Preparing to unpack .../071-libheif-plugin-aomdec_1.18.1-2_amd64.deb ... 383s Unpacking libheif-plugin-aomdec:amd64 (1.18.1-2) ... 383s Selecting previously unselected package libde265-0:amd64. 383s Preparing to unpack .../072-libde265-0_1.0.15-1build4_amd64.deb ... 383s Unpacking libde265-0:amd64 (1.0.15-1build4) ... 383s Selecting previously unselected package libheif-plugin-libde265:amd64. 383s Preparing to unpack .../073-libheif-plugin-libde265_1.18.1-2_amd64.deb ... 383s Unpacking libheif-plugin-libde265:amd64 (1.18.1-2) ... 383s Selecting previously unselected package libheif1:amd64. 383s Preparing to unpack .../074-libheif1_1.18.1-2_amd64.deb ... 383s Unpacking libheif1:amd64 (1.18.1-2) ... 383s Selecting previously unselected package libimagequant0:amd64. 383s Preparing to unpack .../075-libimagequant0_2.18.0-1build1_amd64.deb ... 383s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 383s Selecting previously unselected package libgraphite2-3:amd64. 383s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 383s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 383s Selecting previously unselected package libharfbuzz0b:amd64. 383s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_amd64.deb ... 383s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 383s Selecting previously unselected package libraqm0:amd64. 383s Preparing to unpack .../078-libraqm0_0.10.1-1build1_amd64.deb ... 383s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 383s Selecting previously unselected package libdeflate0:amd64. 383s Preparing to unpack .../079-libdeflate0_1.22-1_amd64.deb ... 383s Unpacking libdeflate0:amd64 (1.22-1) ... 384s Selecting previously unselected package libjbig0:amd64. 384s Preparing to unpack .../080-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 384s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 384s Selecting previously unselected package liblerc4:amd64. 384s Preparing to unpack .../081-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 384s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 384s Selecting previously unselected package libwebp7:amd64. 384s Preparing to unpack .../082-libwebp7_1.4.0-0.1_amd64.deb ... 384s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 384s Selecting previously unselected package libtiff6:amd64. 384s Preparing to unpack .../083-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 384s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 384s Selecting previously unselected package libxpm4:amd64. 384s Preparing to unpack .../084-libxpm4_1%3a3.5.17-1build2_amd64.deb ... 384s Unpacking libxpm4:amd64 (1:3.5.17-1build2) ... 384s Selecting previously unselected package libgd3:amd64. 384s Preparing to unpack .../085-libgd3_2.3.3-12ubuntu3_amd64.deb ... 384s Unpacking libgd3:amd64 (2.3.3-12ubuntu3) ... 384s Selecting previously unselected package liblua5.4-0:amd64. 384s Preparing to unpack .../086-liblua5.4-0_5.4.6-3build2_amd64.deb ... 384s Unpacking liblua5.4-0:amd64 (5.4.6-3build2) ... 384s Selecting previously unselected package fontconfig. 384s Preparing to unpack .../087-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 384s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 384s Selecting previously unselected package libthai-data. 384s Preparing to unpack .../088-libthai-data_0.1.29-2build1_all.deb ... 384s Unpacking libthai-data (0.1.29-2build1) ... 384s Selecting previously unselected package libdatrie1:amd64. 384s Preparing to unpack .../089-libdatrie1_0.2.13-3build1_amd64.deb ... 384s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 384s Selecting previously unselected package libthai0:amd64. 384s Preparing to unpack .../090-libthai0_0.1.29-2build1_amd64.deb ... 384s Unpacking libthai0:amd64 (0.1.29-2build1) ... 384s Selecting previously unselected package libpango-1.0-0:amd64. 384s Preparing to unpack .../091-libpango-1.0-0_1.54.0+ds-3_amd64.deb ... 384s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-3) ... 384s Selecting previously unselected package libpangoft2-1.0-0:amd64. 384s Preparing to unpack .../092-libpangoft2-1.0-0_1.54.0+ds-3_amd64.deb ... 384s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 384s Selecting previously unselected package libpangocairo-1.0-0:amd64. 384s Preparing to unpack .../093-libpangocairo-1.0-0_1.54.0+ds-3_amd64.deb ... 384s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 384s Selecting previously unselected package libwebpmux3:amd64. 384s Preparing to unpack .../094-libwebpmux3_1.4.0-0.1_amd64.deb ... 384s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 384s Selecting previously unselected package gnuplot-nox. 384s Preparing to unpack .../095-gnuplot-nox_6.0.0+dfsg1-1ubuntu3_amd64.deb ... 384s Unpacking gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ... 384s Selecting previously unselected package canu. 384s Preparing to unpack .../096-canu_2.2+dfsg-5_amd64.deb ... 384s Unpacking canu (2.2+dfsg-5) ... 384s Selecting previously unselected package libhtscodecs2:amd64. 384s Preparing to unpack .../097-libhtscodecs2_1.6.1-1_amd64.deb ... 384s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 384s Selecting previously unselected package libhts3t64:amd64. 384s Preparing to unpack .../098-libhts3t64_1.20+ds-1_amd64.deb ... 384s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 384s Selecting previously unselected package samtools. 384s Preparing to unpack .../099-samtools_1.20-3_amd64.deb ... 384s Unpacking samtools (1.20-3) ... 384s Selecting previously unselected package fastaq. 384s Preparing to unpack .../100-fastaq_3.17.0-8_all.deb ... 384s Unpacking fastaq (3.17.0-8) ... 384s Selecting previously unselected package python3-et-xmlfile. 384s Preparing to unpack .../101-python3-et-xmlfile_2.0.0-1_all.deb ... 384s Unpacking python3-et-xmlfile (2.0.0-1) ... 384s Selecting previously unselected package libxslt1.1:amd64. 384s Preparing to unpack .../102-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 384s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 384s Selecting previously unselected package python3-lxml:amd64. 384s Preparing to unpack .../103-python3-lxml_5.3.0-1_amd64.deb ... 384s Unpacking python3-lxml:amd64 (5.3.0-1) ... 384s Selecting previously unselected package python3-openpyxl. 384s Preparing to unpack .../104-python3-openpyxl_3.1.5+dfsg-1_all.deb ... 384s Unpacking python3-openpyxl (3.1.5+dfsg-1) ... 384s Selecting previously unselected package python3-packaging. 384s Preparing to unpack .../105-python3-packaging_24.1-1_all.deb ... 384s Unpacking python3-packaging (24.1-1) ... 384s Selecting previously unselected package mummer. 384s Preparing to unpack .../106-mummer_3.23+dfsg-8_amd64.deb ... 384s Unpacking mummer (3.23+dfsg-8) ... 384s Selecting previously unselected package python3-pymummer. 384s Preparing to unpack .../107-python3-pymummer_0.11.0-4_all.deb ... 384s Unpacking python3-pymummer (0.11.0-4) ... 384s Selecting previously unselected package python3-pysam. 384s Preparing to unpack .../108-python3-pysam_0.22.1+ds-2_amd64.deb ... 384s Unpacking python3-pysam (0.22.1+ds-2) ... 384s Selecting previously unselected package prodigal. 384s Preparing to unpack .../109-prodigal_1%3a2.6.3-6_amd64.deb ... 384s Unpacking prodigal (1:2.6.3-6) ... 385s Selecting previously unselected package circlator. 385s Preparing to unpack .../110-circlator_1.5.6-11_all.deb ... 385s Unpacking circlator (1.5.6-11) ... 385s Selecting previously unselected package libpython3.13-stdlib:amd64. 385s Preparing to unpack .../111-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 385s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 385s Selecting previously unselected package libssw0:amd64. 385s Preparing to unpack .../112-libssw0_1.1-15_amd64.deb ... 385s Unpacking libssw0:amd64 (1.1-15) ... 385s Selecting previously unselected package python3.13. 385s Preparing to unpack .../113-python3.13_3.13.0-2_amd64.deb ... 385s Unpacking python3.13 (3.13.0-2) ... 385s Selecting previously unselected package python3-all. 385s Preparing to unpack .../114-python3-all_3.12.7-1_amd64.deb ... 385s Unpacking python3-all (3.12.7-1) ... 385s Selecting previously unselected package python3-iniconfig. 385s Preparing to unpack .../115-python3-iniconfig_1.1.1-2_all.deb ... 385s Unpacking python3-iniconfig (1.1.1-2) ... 385s Selecting previously unselected package python3-joblib. 385s Preparing to unpack .../116-python3-joblib_1.3.2-5_all.deb ... 385s Unpacking python3-joblib (1.3.2-5) ... 385s Selecting previously unselected package python3-pluggy. 385s Preparing to unpack .../117-python3-pluggy_1.5.0-1_all.deb ... 385s Unpacking python3-pluggy (1.5.0-1) ... 385s Selecting previously unselected package python3-pytest. 385s Preparing to unpack .../118-python3-pytest_8.3.3-1_all.deb ... 385s Unpacking python3-pytest (8.3.3-1) ... 385s Selecting previously unselected package libnlopt0:amd64. 385s Preparing to unpack .../119-libnlopt0_2.7.1-5ubuntu1_amd64.deb ... 385s Unpacking libnlopt0:amd64 (2.7.1-5ubuntu1) ... 385s Selecting previously unselected package spades. 385s Preparing to unpack .../120-spades_3.15.5+dfsg-7_amd64.deb ... 385s Unpacking spades (3.15.5+dfsg-7) ... 385s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 385s Setting up fastjar (2:0.98-7) ... 385s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 385s Setting up liblcms2-2:amd64 (2.16-2) ... 385s Setting up python3-iniconfig (1.1.1-2) ... 385s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 385s Setting up libfastutil-java (8.5.15+dfsg-1) ... 385s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 385s Setting up libaom3:amd64 (3.11.0~rc1-1) ... 385s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 385s Setting up libjsr305-java (0.1~+svn49-11) ... 385s Setting up libxpm4:amd64 (1:3.5.17-1build2) ... 385s Setting up java-common (0.76) ... 385s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 385s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 385s Setting up python3-joblib (1.3.2-5) ... 386s Setting up libxcb-render0:amd64 (1.17.0-2) ... 386s Setting up prodigal (1:2.6.3-6) ... 386s Setting up bwa (0.7.18-1) ... 386s Setting up libfilesys-df-perl (0.92-7build5) ... 386s Setting up libdeflate0:amd64 (1.22-1) ... 386s Setting up libnlopt0:amd64 (2.7.1-5ubuntu1) ... 386s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 386s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 386s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 386s Setting up libssw-java (1.1-15) ... 386s Setting up libsnappy1v5:amd64 (1.2.1-1) ... 386s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 386s Setting up python3-packaging (24.1-1) ... 386s Setting up libjsoncpp26:amd64 (1.9.6-2) ... 386s Setting up aglfn (1.7+git20191031.4036a9c-2) ... 386s Setting up libapache-pom-java (33-2) ... 386s Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... 386s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 386s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 386s Setting up fonts-dejavu-mono (2.37-8) ... 386s Setting up libmpc3:amd64 (1.3.1-1build2) ... 386s Setting up binfmt-support (2.2.2-7) ... 386s update-binfmts: warning: python3.12 already enabled in kernel. 386s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'. 387s Setting up fonts-dejavu-core (2.37-8) ... 387s Setting up libpcsclite1:amd64 (2.3.0-1) ... 387s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 387s Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 387s Setting up python3-pluggy (1.5.0-1) ... 387s Setting up libwebp7:amd64 (1.4.0-0.1) ... 387s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 387s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 387s Setting up bamtools (2.5.2+dfsg-6build1) ... 387s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 387s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 387s Setting up mummer (3.23+dfsg-8) ... 387s Setting up python3-et-xmlfile (2.0.0-1) ... 387s Setting up libhts3t64:amd64 (1.20+ds-1) ... 387s Setting up liblua5.4-0:amd64 (5.4.6-3build2) ... 387s Setting up python3.13-minimal (3.13.0-2) ... 388s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 388s Setting up libthai-data (0.1.29-2build1) ... 388s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 388s Setting up ca-certificates-java (20240118) ... 388s No JRE found. Skipping Java certificates setup. 388s Setting up libisl23:amd64 (0.27-1) ... 388s Setting up libde265-0:amd64 (1.0.15-1build4) ... 388s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 388s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 388s Setting up libssw0:amd64 (1.1-15) ... 388s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 388s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 388s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 388s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 388s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ... 388s Setting up python3-pysam (0.22.1+ds-2) ... 388s Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... 388s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 388s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 388s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 388s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 388s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 388s Setting up jarwrapper (0.80) ... 388s Setting up python3.13 (3.13.0-2) ... 389s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 389s Setting up python3-pytest (8.3.3-1) ... 389s Setting up libcommons-parent-java (56-1) ... 389s Setting up python3-all (3.12.7-1) ... 389s Setting up samtools (1.20-3) ... 389s Setting up libthai0:amd64 (0.1.29-2build1) ... 389s Setting up libraqm0:amd64 (0.10.1-1build1) ... 389s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 389s Setting up cpp-14 (14.2.0-8ubuntu1) ... 389s Setting up python3-lxml:amd64 (5.3.0-1) ... 390s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 390s Setting up spades (3.15.5+dfsg-7) ... 390s /usr/share/spades/spades_pipeline/support.py:531: SyntaxWarning: invalid escape sequence '\d' 390s return [atoi(c) for c in re.split("(\d+)", text)] 390s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 390s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 390s Setting up libcommons-codec-java (1.17.1-1) ... 390s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 390s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 390s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 392s Regenerating fonts cache... done. 392s Setting up libcommons-io-java (2.17.0-1) ... 392s Setting up fastaq (3.17.0-8) ... 392s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 392s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 392s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 392s gbk_regex = re.compile('^LOCUS\s+\S') 392s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 392s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 392s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 392s gbk_regex = re.compile('^LOCUS\s+\S') 392s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... 392s Setting up libcairo2:amd64 (1.18.2-2) ... 392s Setting up python3-pymummer (0.11.0-4) ... 392s Setting up python3-openpyxl (3.1.5+dfsg-1) ... 393s Setting up cpp (4:14.1.0-2ubuntu1) ... 393s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 393s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 393s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 393s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 393s Setting up libcommons-compress-java (1.27.1-2) ... 393s Setting up gcc-14 (14.2.0-8ubuntu1) ... 393s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 393s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 393s Setting up g++-14 (14.2.0-8ubuntu1) ... 393s Setting up gcc (4:14.1.0-2ubuntu1) ... 393s Setting up g++ (4:14.1.0-2ubuntu1) ... 393s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 393s Setting up build-essential (12.10ubuntu1) ... 393s Setting up libheif1:amd64 (1.18.1-2) ... 393s Setting up libguava-java (32.0.1-1) ... 393s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ... 393s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ... 393s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode 393s Setting up libheif-plugin-aomdec:amd64 (1.18.1-2) ... 393s Setting up libheif-plugin-libde265:amd64 (1.18.1-2) ... 393s Setting up liberror-prone-java (2.18.0-1) ... 393s Processing triggers for libc-bin (2.40-1ubuntu3) ... 393s Processing triggers for systemd (256.5-2ubuntu4) ... 393s Processing triggers for man-db (2.12.1-3) ... 394s Processing triggers for install-info (7.1.1-1) ... 394s Processing triggers for ca-certificates-java (20240118) ... 394s Adding debian:ACCVRAIZ1.pem 394s Adding debian:AC_RAIZ_FNMT-RCM.pem 394s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 394s Adding debian:ANF_Secure_Server_Root_CA.pem 394s Adding debian:Actalis_Authentication_Root_CA.pem 394s Adding debian:AffirmTrust_Commercial.pem 394s Adding debian:AffirmTrust_Networking.pem 394s Adding debian:AffirmTrust_Premium.pem 394s Adding debian:AffirmTrust_Premium_ECC.pem 394s Adding debian:Amazon_Root_CA_1.pem 394s Adding debian:Amazon_Root_CA_2.pem 394s Adding debian:Amazon_Root_CA_3.pem 394s Adding debian:Amazon_Root_CA_4.pem 394s Adding debian:Atos_TrustedRoot_2011.pem 394s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 394s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 394s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 394s Adding debian:BJCA_Global_Root_CA1.pem 394s Adding debian:BJCA_Global_Root_CA2.pem 394s Adding debian:Baltimore_CyberTrust_Root.pem 394s Adding debian:Buypass_Class_2_Root_CA.pem 394s Adding debian:Buypass_Class_3_Root_CA.pem 394s Adding debian:CA_Disig_Root_R2.pem 394s Adding debian:CFCA_EV_ROOT.pem 394s Adding debian:COMODO_Certification_Authority.pem 394s Adding debian:COMODO_ECC_Certification_Authority.pem 394s Adding debian:COMODO_RSA_Certification_Authority.pem 394s Adding debian:Certainly_Root_E1.pem 394s Adding debian:Certainly_Root_R1.pem 394s Adding debian:Certigna.pem 394s Adding debian:Certigna_Root_CA.pem 394s Adding debian:Certum_EC-384_CA.pem 394s Adding debian:Certum_Trusted_Network_CA.pem 394s Adding debian:Certum_Trusted_Network_CA_2.pem 394s Adding debian:Certum_Trusted_Root_CA.pem 394s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 394s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 394s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 394s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 394s Adding debian:Comodo_AAA_Services_root.pem 394s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 394s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 394s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 394s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 394s Adding debian:DigiCert_Assured_ID_Root_CA.pem 394s Adding debian:DigiCert_Assured_ID_Root_G2.pem 394s Adding debian:DigiCert_Assured_ID_Root_G3.pem 394s Adding debian:DigiCert_Global_Root_CA.pem 394s Adding debian:DigiCert_Global_Root_G2.pem 394s Adding debian:DigiCert_Global_Root_G3.pem 394s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 394s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 394s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 394s Adding debian:DigiCert_Trusted_Root_G4.pem 394s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 394s Adding debian:Entrust_Root_Certification_Authority.pem 394s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 394s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 394s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 394s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 394s Adding debian:GLOBALTRUST_2020.pem 394s Adding debian:GTS_Root_R1.pem 394s Adding debian:GTS_Root_R2.pem 394s Adding debian:GTS_Root_R3.pem 394s Adding debian:GTS_Root_R4.pem 394s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 394s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 394s Adding debian:GlobalSign_Root_CA.pem 394s Adding debian:GlobalSign_Root_CA_-_R3.pem 394s Adding debian:GlobalSign_Root_CA_-_R6.pem 394s Adding debian:GlobalSign_Root_E46.pem 394s Adding debian:GlobalSign_Root_R46.pem 394s Adding debian:Go_Daddy_Class_2_CA.pem 394s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 394s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 394s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 394s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 394s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 394s Adding debian:HiPKI_Root_CA_-_G1.pem 394s Adding debian:Hongkong_Post_Root_CA_3.pem 394s Adding debian:ISRG_Root_X1.pem 394s Adding debian:ISRG_Root_X2.pem 394s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 394s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 394s Adding debian:Izenpe.com.pem 394s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 394s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 394s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 394s Adding debian:NAVER_Global_Root_Certification_Authority.pem 394s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 394s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 394s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 394s Adding debian:QuoVadis_Root_CA_1_G3.pem 394s Adding debian:QuoVadis_Root_CA_2.pem 394s Adding debian:QuoVadis_Root_CA_2_G3.pem 394s Adding debian:QuoVadis_Root_CA_3.pem 394s Adding debian:QuoVadis_Root_CA_3_G3.pem 394s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 394s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 394s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 394s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 394s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 394s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 394s Adding debian:SZAFIR_ROOT_CA2.pem 394s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 394s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 394s Adding debian:SecureSign_RootCA11.pem 394s Adding debian:SecureTrust_CA.pem 394s Adding debian:Secure_Global_CA.pem 394s Adding debian:Security_Communication_ECC_RootCA1.pem 394s Adding debian:Security_Communication_RootCA2.pem 394s Adding debian:Security_Communication_RootCA3.pem 394s Adding debian:Security_Communication_Root_CA.pem 394s Adding debian:Starfield_Class_2_CA.pem 394s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 394s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 394s Adding debian:SwissSign_Gold_CA_-_G2.pem 394s Adding debian:SwissSign_Silver_CA_-_G2.pem 394s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 394s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 394s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 394s Adding debian:TWCA_Global_Root_CA.pem 394s Adding debian:TWCA_Root_Certification_Authority.pem 394s Adding debian:TeliaSonera_Root_CA_v1.pem 394s Adding debian:Telia_Root_CA_v2.pem 394s Adding debian:TrustAsia_Global_Root_CA_G3.pem 394s Adding debian:TrustAsia_Global_Root_CA_G4.pem 394s Adding debian:Trustwave_Global_Certification_Authority.pem 394s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 394s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 394s Adding debian:TunTrust_Root_CA.pem 394s Adding debian:UCA_Extended_Validation_Root.pem 394s Adding debian:UCA_Global_G2_Root.pem 394s Adding debian:USERTrust_ECC_Certification_Authority.pem 394s Adding debian:USERTrust_RSA_Certification_Authority.pem 394s Adding debian:XRamp_Global_CA_Root.pem 394s Adding debian:certSIGN_ROOT_CA.pem 394s Adding debian:certSIGN_Root_CA_G2.pem 394s Adding debian:e-Szigno_Root_CA_2017.pem 394s Adding debian:ePKI_Root_Certification_Authority.pem 394s Adding debian:emSign_ECC_Root_CA_-_C3.pem 394s Adding debian:emSign_ECC_Root_CA_-_G3.pem 394s Adding debian:emSign_Root_CA_-_C1.pem 394s Adding debian:emSign_Root_CA_-_G1.pem 394s Adding debian:vTrus_ECC_Root_CA.pem 394s Adding debian:vTrus_Root_CA.pem 394s done. 394s Setting up default-jre-headless (2:1.21-76) ... 394s Setting up jaligner (1.0+dfsg-11) ... 394s Setting up mhap (2.1.3+dfsg-3) ... 394s Setting up canu (2.2+dfsg-5) ... 394s Setting up circlator (1.5.6-11) ... 395s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s' 395s self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip()) 395s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s' 395s self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip()) 396s Reading package lists... 396s Building dependency tree... 396s Reading state information... 397s Starting pkgProblemResolver with broken count: 0 397s Starting 2 pkgProblemResolver with broken count: 0 397s Done 397s The following NEW packages will be installed: 397s autopkgtest-satdep 397s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 397s Need to get 0 B/704 B of archives. 397s After this operation, 0 B of additional disk space will be used. 397s Get:1 /tmp/autopkgtest.zwlDOt/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 397s Selecting previously unselected package autopkgtest-satdep. 397s (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 ... 80650 files and directories currently installed.) 397s Preparing to unpack .../2-autopkgtest-satdep.deb ... 397s Unpacking autopkgtest-satdep (0) ... 397s Setting up autopkgtest-satdep (0) ... 399s (Reading database ... 80650 files and directories currently installed.) 399s Removing autopkgtest-satdep (0) ... 400s autopkgtest [12:30:20]: test run-unit-test: [----------------------- 400s + pkg=circlator 400s + export LC_ALL=C.UTF-8 400s + LC_ALL=C.UTF-8 400s + '[' /tmp/autopkgtest.zwlDOt/autopkgtest_tmp = '' ']' 400s + cp -a /usr/share/doc/circlator/examples/assemble_test.py /usr/share/doc/circlator/examples/assembly_test.py /usr/share/doc/circlator/examples/bamfilter_test.py /usr/share/doc/circlator/examples/clean_test.py /usr/share/doc/circlator/examples/common_test.py /usr/share/doc/circlator/examples/data.tar.xz /usr/share/doc/circlator/examples/dnaa_test.py /usr/share/doc/circlator/examples/external_progs_test.py /usr/share/doc/circlator/examples/mapping_test.py /usr/share/doc/circlator/examples/merge_test.py /usr/share/doc/circlator/examples/minimus2_test.py /usr/share/doc/circlator/examples/start_fixer_test.py /tmp/autopkgtest.zwlDOt/autopkgtest_tmp 400s + cd /tmp/autopkgtest.zwlDOt/autopkgtest_tmp 400s + tar xaf data.tar.xz 400s + sed -i 's/data_dir = os.path.join(modules_dir, '\''tests'\'', '\''data'\'')/data_dir = os.path.join(os.getcwd(), '\''data'\'')/' ./assemble_test.py ./assembly_test.py ./bamfilter_test.py ./clean_test.py ./common_test.py ./dnaa_test.py ./external_progs_test.py ./mapping_test.py ./merge_test.py ./minimus2_test.py ./start_fixer_test.py 400s ++ py3versions --supported 400s + for py in $(py3versions --supported 2> /dev/null) 400s + eval dpkg-architecture --is amd64 400s ++ dpkg-architecture --is amd64 400s + python3.13 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)' 400s ============================= test session starts ============================== 400s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 400s cachedir: .pytest_cache 400s rootdir: /tmp/autopkgtest.zwlDOt/autopkgtest_tmp 400s plugins: typeguard-4.4.1 400s collecting ... collected 0 items / 11 errors 400s 400s ==================================== ERRORS ==================================== 400s ______________________ ERROR collecting assemble_test.py _______________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/assemble_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s assemble_test.py:6: in 400s from circlator import assemble 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ______________________ ERROR collecting assembly_test.py _______________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/assembly_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s assembly_test.py:7: in 400s from circlator import assembly 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ______________________ ERROR collecting bamfilter_test.py ______________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/bamfilter_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s bamfilter_test.py:5: in 400s from circlator import bamfilter 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ________________________ ERROR collecting clean_test.py ________________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/clean_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s clean_test.py:5: in 400s from circlator import clean 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s _______________________ ERROR collecting common_test.py ________________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/common_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s common_test.py:3: in 400s from circlator import common 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ________________________ ERROR collecting dnaa_test.py _________________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/dnaa_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s dnaa_test.py:5: in 400s from circlator import dnaa 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ___________________ ERROR collecting external_progs_test.py ____________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/external_progs_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s external_progs_test.py:2: in 400s from circlator import external_progs 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s _______________________ ERROR collecting mapping_test.py _______________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/mapping_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s mapping_test.py:5: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ________________________ ERROR collecting merge_test.py ________________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/merge_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s merge_test.py:8: in 400s from circlator import merge 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s ______________________ ERROR collecting minimus2_test.py _______________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/minimus2_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s minimus2_test.py:6: in 400s from circlator import minimus2 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s _____________________ ERROR collecting start_fixer_test.py _____________________ 400s ImportError while importing test module '/tmp/autopkgtest.zwlDOt/autopkgtest_tmp/start_fixer_test.py'. 400s Hint: make sure your test modules/packages have valid Python names. 400s Traceback: 400s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 400s return _bootstrap._gcd_import(name[level:], package, level) 400s start_fixer_test.py:9: in 400s from circlator import start_fixer 400s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in 400s from circlator import * 400s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in 400s import pysam 400s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in 400s from pysam.libchtslib import * 400s E ModuleNotFoundError: No module named 'pysam.libchtslib' 400s =============================== warnings summary =============================== 400s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3 400s /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'} 400s __version__ = Distribution().from_name('pyfastaq').version 400s 400s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1 400s /usr/lib/python3/dist-packages/circlator/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 400s from pkg_resources import get_distribution 400s 400s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 400s =========================== short test summary info ============================ 400s ERROR assemble_test.py 400s ERROR assembly_test.py 400s ERROR bamfilter_test.py 400s ERROR clean_test.py 400s ERROR common_test.py 400s ERROR dnaa_test.py 400s ERROR external_progs_test.py 400s ERROR mapping_test.py 400s ERROR merge_test.py 400s ERROR minimus2_test.py 400s ERROR start_fixer_test.py 400s !!!!!!!!!!!!!!!!!!! Interrupted: 11 errors during collection !!!!!!!!!!!!!!!!!!! 400s ======================== 2 warnings, 11 errors in 0.34s ======================== 401s autopkgtest [12:30:21]: test run-unit-test: -----------------------] 401s autopkgtest [12:30:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 401s run-unit-test FAIL non-zero exit status 2 401s autopkgtest [12:30:21]: @@@@@@@@@@@@@@@@@@@@ summary 401s run-unit-test FAIL non-zero exit status 2 407s nova [W] Skipping flock for amd64 407s Creating nova instance adt-plucky-i386-circlator-20241113-122340-juju-7f2275-prod-proposed-migration-environment-20-26ed46f0-b135-4bce-b37f-95b66c53ffa2 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)... 407s nova [W] nova quota exceeded (attempt #0)