0s autopkgtest [02:03:39]: starting date and time: 2024-03-18 02:03:39+0000 0s autopkgtest [02:03:39]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [02:03:39]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sxvi2xg9/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:ncbi-blast+,src:mbedtls --apt-upgrade presto --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-12.secgroup --name adt-noble-arm64-presto-20240318-020339-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 74s autopkgtest [02:04:53]: testbed dpkg architecture: arm64 75s autopkgtest [02:04:54]: testbed apt version: 2.7.12 75s autopkgtest [02:04:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 75s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 76s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 76s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 76s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 76s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 76s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 76s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 76s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 76s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 76s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 76s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 76s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 78s Fetched 9189 kB in 2s (5191 kB/s) 78s Reading package lists... 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s Calculating upgrade... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s sh: Attempting to set up Debian/Ubuntu apt sources automatically 86s sh: Distribution appears to be Ubuntu 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s eatmydata is already the newest version (131-1). 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s dbus is already the newest version (1.14.10-4ubuntu1). 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s rng-tools-debian is already the newest version (2.4). 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s The following packages will be REMOVED: 91s cloud-init* python3-configobj* python3-debconf* 92s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 92s After this operation, 3252 kB disk space will be freed. 92s (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 ... 74758 files and directories currently installed.) 92s Removing cloud-init (24.1.1-0ubuntu1) ... 92s Removing python3-configobj (5.0.8-3) ... 92s Removing python3-debconf (1.5.86) ... 93s Processing triggers for man-db (2.12.0-3) ... 93s (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 ... 74369 files and directories currently installed.) 93s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 94s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 94s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 94s invoke-rc.d: policy-rc.d denied execution of try-restart. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s linux-generic is already the newest version (6.8.0-11.11+1). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 95s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 95s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 97s Reading package lists... 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Calculating upgrade... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [02:05:19]: rebooting testbed after setup commands that affected boot 308s autopkgtest [02:08:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 311s autopkgtest [02:08:50]: @@@@@@@@@@@@@@@@@@@@ apt-source presto 314s Get:1 http://ftpmaster.internal/ubuntu noble/universe presto 0.7.2-1 (dsc) [2233 B] 314s Get:2 http://ftpmaster.internal/ubuntu noble/universe presto 0.7.2-1 (tar) [362 kB] 314s Get:3 http://ftpmaster.internal/ubuntu noble/universe presto 0.7.2-1 (diff) [20.8 kB] 314s gpgv: Signature made Mon Feb 19 12:51:18 2024 UTC 314s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 314s gpgv: Can't check signature: No public key 314s dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-1.dsc: no acceptable signature found 314s autopkgtest [02:08:53]: testing package presto version 0.7.2-1 315s autopkgtest [02:08:54]: build not needed 315s autopkgtest [02:08:54]: test pybuild-autopkgtest: preparing testbed 317s Reading package lists... 317s Building dependency tree... 317s Reading state information... 317s Starting pkgProblemResolver with broken count: 0 317s Starting 2 pkgProblemResolver with broken count: 0 317s Done 318s The following additional packages will be installed: 318s autoconf automake autopoint autotools-dev build-essential cd-hit cpp cpp-13 318s cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 318s dh-autoreconf dh-python dh-strip-nondeterminism dwz fontconfig-config 318s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 g++ 318s g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 318s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 318s libarchive-zip-perl libasan8 libatomic1 libblas3 libc-dev-bin libc6-dev 318s libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl libdeflate0 libdw1 318s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libgcc-13-dev 318s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libimagequant0 318s libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 318s liblcms2-2 liblerc4 liblsan0 libmbedcrypto7 libmbedtls14 libmbedx509-1 318s libmpc3 libnsl-dev libopenjp2-7 libpixman-1-0 libpython3.11-minimal 318s libpython3.11-stdlib libraqm0 libsharpyuv0 libstdc++-13-dev 318s libsub-override-perl libtiff6 libtirpc-dev libtool libtsan2 libubsan1 318s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 318s linux-libc-dev m4 ncbi-blast+ ncbi-data po-debconf presto 318s pybuild-plugin-autopkgtest python3-all python3-biopython python3-cairo 318s python3-dateutil python3-decorator python3-distutils python3-freetype 318s python3-lib2to3 python3-numpy python3-packaging python3-pandas 318s python3-pandas-lib python3-pil python3-presto python3-reportlab 318s python3-rlpycairo python3-scipy python3-setuptools python3.11 318s python3.11-minimal rpcsvc-proto sgml-base vsearch w3c-sgml-lib x11-common 318s xfonts-encodings xfonts-utils xml-core 318s Suggested packages: 318s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 318s cpp-13-doc dh-make flit python3-build python3-installer python3-wheel 318s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-13-doc 318s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-aarch64-linux-gnu 318s gettext-doc libasprintf-dev libgettextpo-dev glibc-doc liblcms2-utils 318s libstdc++-13-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 318s libmail-box-perl python3-tk bwa clustalo clustalw dialign dssp emboss 318s fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb 318s python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 raxml 318s samtools t-coffee wise gfortran python3-dev python3-pytest python-pandas-doc 318s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 318s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 318s python-setuptools-doc python3.11-venv python3.11-doc binfmt-support 318s sgml-base-doc 318s Recommended packages: 318s manpages manpages-dev libc-devtools libarchive-cpio-perl libltdl-dev 318s libmail-sendmail-perl python-biopython-doc python3-matplotlib 318s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 318s python3-html5lib python3-lxml python3-tables python3-olefile 318s The following NEW packages will be installed: 318s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 318s cd-hit cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 318s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz 318s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 318s fonts-urw-base35 g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu 318s gcc gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext 318s intltool-debian libarchive-zip-perl libasan8 libatomic1 libblas3 318s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl 318s libdeflate0 libdw1 libfile-stripnondeterminism-perl libfontconfig1 318s libfontenc1 libgcc-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 318s libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 318s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmbedcrypto7 318s libmbedtls14 libmbedx509-1 libmpc3 libnsl-dev libopenjp2-7 libpixman-1-0 318s libpython3.11-minimal libpython3.11-stdlib libraqm0 libsharpyuv0 318s libstdc++-13-dev libsub-override-perl libtiff6 libtirpc-dev libtool libtsan2 318s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 318s libxrender1 linux-libc-dev m4 ncbi-blast+ ncbi-data po-debconf presto 318s pybuild-plugin-autopkgtest python3-all python3-biopython python3-cairo 318s python3-dateutil python3-decorator python3-distutils python3-freetype 318s python3-lib2to3 python3-numpy python3-packaging python3-pandas 318s python3-pandas-lib python3-pil python3-presto python3-reportlab 318s python3-rlpycairo python3-scipy python3-setuptools python3.11 318s python3.11-minimal rpcsvc-proto sgml-base vsearch w3c-sgml-lib x11-common 318s xfonts-encodings xfonts-utils xml-core 318s 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. 318s Need to get 148 MB/148 MB of archives. 318s After this operation, 594 MB of additional disk space will be used. 318s Get:1 /tmp/autopkgtest.ZyRcv5/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [824 B] 318s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 318s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 319s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 319s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 319s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 319s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] 319s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] 319s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] 319s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 319s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] 319s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 319s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 319s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 319s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] 319s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 319s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 319s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 319s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 319s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 319s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 319s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 319s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 319s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 319s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 319s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 319s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 319s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 319s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 319s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 319s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 319s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 319s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 319s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 319s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 320s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 320s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 320s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 320s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 320s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 320s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 320s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 320s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 320s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 320s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 cd-hit arm64 4.8.1-4 [522 kB] 320s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 320s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] 320s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] 320s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 320s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] 320s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 320s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] 320s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libdw1 arm64 0.190-1 [254 kB] 320s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] 320s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 dwz arm64 0.15-1 [110 kB] 320s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] 320s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 320s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 320s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 debhelper all 13.14.1ubuntu1 [869 kB] 320s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 320s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 320s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] 320s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 dh-python all 6.20231223ubuntu2 [111 kB] 320s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 320s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 320s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 320s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 320s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 320s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 320s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 321s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 321s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 321s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 321s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 321s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 321s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 321s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 321s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 321s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 321s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 321s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 321s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 321s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 321s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 321s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 321s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 321s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 321s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 321s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 321s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 321s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 321s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 321s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 321s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 321s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 321s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 321s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 321s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 321s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 321s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 321s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 321s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 322s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 322s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 322s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 322s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 322s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 322s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 322s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 322s Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 322s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 322s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 322s Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 322s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 323s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 323s Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 323s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 324s Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 324s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 vsearch arm64 2.27.0-1 [401 kB] 324s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-presto arm64 0.7.2-1 [80.7 kB] 324s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 presto all 0.7.2-1 [240 kB] 324s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 pybuild-plugin-autopkgtest all 6.20231223ubuntu2 [1760 B] 324s Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 324s Fetched 148 MB in 6s (25.7 MB/s) 324s Selecting previously unselected package libpython3.11-minimal:arm64. 325s (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 ... 74314 files and directories currently installed.) 325s Preparing to unpack .../000-libpython3.11-minimal_3.11.8-1_arm64.deb ... 325s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 325s Selecting previously unselected package python3.11-minimal. 325s Preparing to unpack .../001-python3.11-minimal_3.11.8-1_arm64.deb ... 325s Unpacking python3.11-minimal (3.11.8-1) ... 325s Selecting previously unselected package sgml-base. 325s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 325s Unpacking sgml-base (1.31) ... 325s Selecting previously unselected package libpython3.11-stdlib:arm64. 325s Preparing to unpack .../003-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 325s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 325s Selecting previously unselected package python3.11. 325s Preparing to unpack .../004-python3.11_3.11.8-1_arm64.deb ... 325s Unpacking python3.11 (3.11.8-1) ... 325s Selecting previously unselected package m4. 325s Preparing to unpack .../005-m4_1.4.19-4_arm64.deb ... 325s Unpacking m4 (1.4.19-4) ... 325s Selecting previously unselected package autoconf. 325s Preparing to unpack .../006-autoconf_2.71-3_all.deb ... 325s Unpacking autoconf (2.71-3) ... 325s Selecting previously unselected package autotools-dev. 325s Preparing to unpack .../007-autotools-dev_20220109.1_all.deb ... 325s Unpacking autotools-dev (20220109.1) ... 325s Selecting previously unselected package automake. 325s Preparing to unpack .../008-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 325s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 325s Selecting previously unselected package autopoint. 325s Preparing to unpack .../009-autopoint_0.21-14ubuntu1_all.deb ... 325s Unpacking autopoint (0.21-14ubuntu1) ... 325s Selecting previously unselected package libc-dev-bin. 325s Preparing to unpack .../010-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 325s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 326s Selecting previously unselected package linux-libc-dev:arm64. 326s Preparing to unpack .../011-linux-libc-dev_6.8.0-11.11_arm64.deb ... 326s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 326s Selecting previously unselected package libcrypt-dev:arm64. 326s Preparing to unpack .../012-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 326s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 326s Selecting previously unselected package libtirpc-dev:arm64. 326s Preparing to unpack .../013-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ... 326s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 326s Selecting previously unselected package libnsl-dev:arm64. 326s Preparing to unpack .../014-libnsl-dev_1.3.0-3_arm64.deb ... 326s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 326s Selecting previously unselected package rpcsvc-proto. 326s Preparing to unpack .../015-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 326s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 326s Selecting previously unselected package libc6-dev:arm64. 326s Preparing to unpack .../016-libc6-dev_2.39-0ubuntu2_arm64.deb ... 326s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 326s Selecting previously unselected package libisl23:arm64. 326s Preparing to unpack .../017-libisl23_0.26-3_arm64.deb ... 326s Unpacking libisl23:arm64 (0.26-3) ... 326s Selecting previously unselected package libmpc3:arm64. 326s Preparing to unpack .../018-libmpc3_1.3.1-1_arm64.deb ... 326s Unpacking libmpc3:arm64 (1.3.1-1) ... 326s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 326s Preparing to unpack .../019-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 326s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 326s Selecting previously unselected package cpp-13. 326s Preparing to unpack .../020-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 326s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 326s Selecting previously unselected package cpp-aarch64-linux-gnu. 326s Preparing to unpack .../021-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 326s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 326s Selecting previously unselected package cpp. 326s Preparing to unpack .../022-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 326s Unpacking cpp (4:13.2.0-7ubuntu1) ... 326s Selecting previously unselected package libcc1-0:arm64. 326s Preparing to unpack .../023-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libgomp1:arm64. 326s Preparing to unpack .../024-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libitm1:arm64. 326s Preparing to unpack .../025-libitm1_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libatomic1:arm64. 326s Preparing to unpack .../026-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libasan8:arm64. 326s Preparing to unpack .../027-libasan8_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package liblsan0:arm64. 326s Preparing to unpack .../028-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libtsan2:arm64. 326s Preparing to unpack .../029-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libubsan1:arm64. 326s Preparing to unpack .../030-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libhwasan0:arm64. 326s Preparing to unpack .../031-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 326s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 326s Selecting previously unselected package libgcc-13-dev:arm64. 326s Preparing to unpack .../032-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 326s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 326s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 326s Preparing to unpack .../033-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 326s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 327s Selecting previously unselected package gcc-13. 327s Preparing to unpack .../034-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 327s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 327s Selecting previously unselected package gcc-aarch64-linux-gnu. 327s Preparing to unpack .../035-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 327s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 327s Selecting previously unselected package gcc. 327s Preparing to unpack .../036-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 327s Unpacking gcc (4:13.2.0-7ubuntu1) ... 327s Selecting previously unselected package libstdc++-13-dev:arm64. 327s Preparing to unpack .../037-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 327s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 327s Selecting previously unselected package g++-13-aarch64-linux-gnu. 327s Preparing to unpack .../038-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 327s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 327s Selecting previously unselected package g++-13. 327s Preparing to unpack .../039-g++-13_13.2.0-17ubuntu2_arm64.deb ... 327s Unpacking g++-13 (13.2.0-17ubuntu2) ... 327s Selecting previously unselected package g++-aarch64-linux-gnu. 327s Preparing to unpack .../040-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 327s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 327s Selecting previously unselected package g++. 327s Preparing to unpack .../041-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 327s Unpacking g++ (4:13.2.0-7ubuntu1) ... 327s Selecting previously unselected package build-essential. 327s Preparing to unpack .../042-build-essential_12.10ubuntu1_arm64.deb ... 327s Unpacking build-essential (12.10ubuntu1) ... 327s Selecting previously unselected package cd-hit. 327s Preparing to unpack .../043-cd-hit_4.8.1-4_arm64.deb ... 327s Unpacking cd-hit (4.8.1-4) ... 327s Selecting previously unselected package libdebhelper-perl. 327s Preparing to unpack .../044-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 327s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 327s Selecting previously unselected package libtool. 327s Preparing to unpack .../045-libtool_2.4.7-7_all.deb ... 327s Unpacking libtool (2.4.7-7) ... 327s Selecting previously unselected package dh-autoreconf. 327s Preparing to unpack .../046-dh-autoreconf_20_all.deb ... 327s Unpacking dh-autoreconf (20) ... 327s Selecting previously unselected package libarchive-zip-perl. 327s Preparing to unpack .../047-libarchive-zip-perl_1.68-1_all.deb ... 327s Unpacking libarchive-zip-perl (1.68-1) ... 327s Selecting previously unselected package libsub-override-perl. 327s Preparing to unpack .../048-libsub-override-perl_0.10-1_all.deb ... 327s Unpacking libsub-override-perl (0.10-1) ... 327s Selecting previously unselected package libfile-stripnondeterminism-perl. 327s Preparing to unpack .../049-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 327s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 327s Selecting previously unselected package dh-strip-nondeterminism. 327s Preparing to unpack .../050-dh-strip-nondeterminism_1.13.1-1_all.deb ... 327s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 327s Selecting previously unselected package libdw1:arm64. 327s Preparing to unpack .../051-libdw1_0.190-1_arm64.deb ... 327s Unpacking libdw1:arm64 (0.190-1) ... 327s Selecting previously unselected package debugedit. 327s Preparing to unpack .../052-debugedit_1%3a5.0-5_arm64.deb ... 327s Unpacking debugedit (1:5.0-5) ... 327s Selecting previously unselected package dwz. 327s Preparing to unpack .../053-dwz_0.15-1_arm64.deb ... 327s Unpacking dwz (0.15-1) ... 328s Selecting previously unselected package gettext. 328s Preparing to unpack .../054-gettext_0.21-14ubuntu1_arm64.deb ... 328s Unpacking gettext (0.21-14ubuntu1) ... 328s Selecting previously unselected package intltool-debian. 328s Preparing to unpack .../055-intltool-debian_0.35.0+20060710.6_all.deb ... 328s Unpacking intltool-debian (0.35.0+20060710.6) ... 328s Selecting previously unselected package po-debconf. 328s Preparing to unpack .../056-po-debconf_1.0.21+nmu1_all.deb ... 328s Unpacking po-debconf (1.0.21+nmu1) ... 328s Selecting previously unselected package debhelper. 328s Preparing to unpack .../057-debhelper_13.14.1ubuntu1_all.deb ... 328s Unpacking debhelper (13.14.1ubuntu1) ... 328s Selecting previously unselected package python3-lib2to3. 328s Preparing to unpack .../058-python3-lib2to3_3.11.5-1_all.deb ... 328s Unpacking python3-lib2to3 (3.11.5-1) ... 328s Selecting previously unselected package python3-distutils. 328s Preparing to unpack .../059-python3-distutils_3.11.5-1_all.deb ... 328s Unpacking python3-distutils (3.11.5-1) ... 328s Selecting previously unselected package python3-setuptools. 328s Preparing to unpack .../060-python3-setuptools_68.1.2-2_all.deb ... 328s Unpacking python3-setuptools (68.1.2-2) ... 328s Selecting previously unselected package dh-python. 328s Preparing to unpack .../061-dh-python_6.20231223ubuntu2_all.deb ... 328s Unpacking dh-python (6.20231223ubuntu2) ... 328s Selecting previously unselected package fonts-dejavu-mono. 328s Preparing to unpack .../062-fonts-dejavu-mono_2.37-8_all.deb ... 328s Unpacking fonts-dejavu-mono (2.37-8) ... 328s Selecting previously unselected package fonts-dejavu-core. 328s Preparing to unpack .../063-fonts-dejavu-core_2.37-8_all.deb ... 328s Unpacking fonts-dejavu-core (2.37-8) ... 328s Selecting previously unselected package libfontenc1:arm64. 328s Preparing to unpack .../064-libfontenc1_1%3a1.1.8-1_arm64.deb ... 328s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 328s Selecting previously unselected package x11-common. 328s Preparing to unpack .../065-x11-common_1%3a7.7+23ubuntu2_all.deb ... 328s Unpacking x11-common (1:7.7+23ubuntu2) ... 328s Selecting previously unselected package xfonts-encodings. 328s Preparing to unpack .../066-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 328s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 328s Selecting previously unselected package xfonts-utils. 328s Preparing to unpack .../067-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 328s Unpacking xfonts-utils (1:7.7+6build2) ... 328s Selecting previously unselected package fonts-urw-base35. 328s Preparing to unpack .../068-fonts-urw-base35_20200910-8_all.deb ... 328s Unpacking fonts-urw-base35 (20200910-8) ... 328s Selecting previously unselected package fontconfig-config. 328s Preparing to unpack .../069-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 328s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 328s Selecting previously unselected package fonts-dejavu-extra. 328s Preparing to unpack .../070-fonts-dejavu-extra_2.37-8_all.deb ... 328s Unpacking fonts-dejavu-extra (2.37-8) ... 328s Selecting previously unselected package libblas3:arm64. 328s Preparing to unpack .../071-libblas3_3.12.0-3_arm64.deb ... 328s Unpacking libblas3:arm64 (3.12.0-3) ... 329s Selecting previously unselected package libfontconfig1:arm64. 329s Preparing to unpack .../072-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 329s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 329s Selecting previously unselected package libpixman-1-0:arm64. 329s Preparing to unpack .../073-libpixman-1-0_0.42.2-1_arm64.deb ... 329s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 329s Selecting previously unselected package libxcb-render0:arm64. 329s Preparing to unpack .../074-libxcb-render0_1.15-1_arm64.deb ... 329s Unpacking libxcb-render0:arm64 (1.15-1) ... 329s Selecting previously unselected package libxcb-shm0:arm64. 329s Preparing to unpack .../075-libxcb-shm0_1.15-1_arm64.deb ... 329s Unpacking libxcb-shm0:arm64 (1.15-1) ... 329s Selecting previously unselected package libxrender1:arm64. 329s Preparing to unpack .../076-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 329s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 329s Selecting previously unselected package libcairo2:arm64. 329s Preparing to unpack .../077-libcairo2_1.18.0-1_arm64.deb ... 329s Unpacking libcairo2:arm64 (1.18.0-1) ... 329s Selecting previously unselected package libdeflate0:arm64. 329s Preparing to unpack .../078-libdeflate0_1.19-1_arm64.deb ... 329s Unpacking libdeflate0:arm64 (1.19-1) ... 329s Selecting previously unselected package libgfortran5:arm64. 329s Preparing to unpack .../079-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 329s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 329s Selecting previously unselected package libgraphite2-3:arm64. 329s Preparing to unpack .../080-libgraphite2-3_1.3.14-2_arm64.deb ... 329s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 329s Selecting previously unselected package libharfbuzz0b:arm64. 329s Preparing to unpack .../081-libharfbuzz0b_8.3.0-2_arm64.deb ... 329s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 329s Selecting previously unselected package libimagequant0:arm64. 329s Preparing to unpack .../082-libimagequant0_2.18.0-1_arm64.deb ... 329s Unpacking libimagequant0:arm64 (2.18.0-1) ... 329s Selecting previously unselected package libjpeg-turbo8:arm64. 329s Preparing to unpack .../083-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 329s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 329s Selecting previously unselected package libjpeg8:arm64. 329s Preparing to unpack .../084-libjpeg8_8c-2ubuntu11_arm64.deb ... 329s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 329s Selecting previously unselected package liblapack3:arm64. 329s Preparing to unpack .../085-liblapack3_3.12.0-3_arm64.deb ... 329s Unpacking liblapack3:arm64 (3.12.0-3) ... 329s Selecting previously unselected package liblbfgsb0:arm64. 329s Preparing to unpack .../086-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 329s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 329s Selecting previously unselected package liblcms2-2:arm64. 329s Preparing to unpack .../087-liblcms2-2_2.14-2_arm64.deb ... 329s Unpacking liblcms2-2:arm64 (2.14-2) ... 329s Selecting previously unselected package liblerc4:arm64. 329s Preparing to unpack .../088-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 329s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 329s Selecting previously unselected package libmbedcrypto7:arm64. 329s Preparing to unpack .../089-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 329s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 329s Selecting previously unselected package libmbedx509-1:arm64. 329s Preparing to unpack .../090-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 329s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 329s Selecting previously unselected package libmbedtls14:arm64. 329s Preparing to unpack .../091-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 329s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 329s Selecting previously unselected package libraqm0:arm64. 329s Preparing to unpack .../092-libraqm0_0.10.1-1_arm64.deb ... 329s Unpacking libraqm0:arm64 (0.10.1-1) ... 329s Selecting previously unselected package libsharpyuv0:arm64. 329s Preparing to unpack .../093-libsharpyuv0_1.3.2-0.4_arm64.deb ... 329s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package libjbig0:arm64. 329s Preparing to unpack .../094-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 329s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 329s Selecting previously unselected package libwebp7:arm64. 329s Preparing to unpack .../095-libwebp7_1.3.2-0.4_arm64.deb ... 329s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package libtiff6:arm64. 329s Preparing to unpack .../096-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 329s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 329s Selecting previously unselected package libwebpdemux2:arm64. 329s Preparing to unpack .../097-libwebpdemux2_1.3.2-0.4_arm64.deb ... 329s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package libwebpmux3:arm64. 329s Preparing to unpack .../098-libwebpmux3_1.3.2-0.4_arm64.deb ... 329s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 329s Selecting previously unselected package ncbi-data. 329s Preparing to unpack .../099-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 329s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 330s Selecting previously unselected package ncbi-blast+. 330s Preparing to unpack .../100-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 330s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 330s Selecting previously unselected package python3-numpy. 330s Preparing to unpack .../101-python3-numpy_1%3a1.24.2-2_arm64.deb ... 330s Unpacking python3-numpy (1:1.24.2-2) ... 330s Selecting previously unselected package libopenjp2-7:arm64. 330s Preparing to unpack .../102-libopenjp2-7_2.5.0-2_arm64.deb ... 330s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 330s Selecting previously unselected package python3-pil:arm64. 330s Preparing to unpack .../103-python3-pil_10.2.0-1_arm64.deb ... 330s Unpacking python3-pil:arm64 (10.2.0-1) ... 330s Selecting previously unselected package python3-cairo. 330s Preparing to unpack .../104-python3-cairo_1.25.1-2_arm64.deb ... 330s Unpacking python3-cairo (1.25.1-2) ... 330s Selecting previously unselected package python3-freetype. 330s Preparing to unpack .../105-python3-freetype_2.4.0-1_all.deb ... 330s Unpacking python3-freetype (2.4.0-1) ... 330s Selecting previously unselected package python3-rlpycairo. 330s Preparing to unpack .../106-python3-rlpycairo_0.3.0-3_all.deb ... 330s Unpacking python3-rlpycairo (0.3.0-3) ... 330s Selecting previously unselected package python3-reportlab. 330s Preparing to unpack .../107-python3-reportlab_4.1.0-1_all.deb ... 330s Unpacking python3-reportlab (4.1.0-1) ... 330s Selecting previously unselected package xml-core. 330s Preparing to unpack .../108-xml-core_0.19_all.deb ... 330s Unpacking xml-core (0.19) ... 330s Selecting previously unselected package w3c-sgml-lib. 330s Preparing to unpack .../109-w3c-sgml-lib_1.3-3_all.deb ... 330s Unpacking w3c-sgml-lib (1.3-3) ... 330s Selecting previously unselected package python3-biopython. 330s Preparing to unpack .../110-python3-biopython_1.81+dfsg-3_arm64.deb ... 330s Unpacking python3-biopython (1.81+dfsg-3) ... 331s Selecting previously unselected package python3-dateutil. 331s Preparing to unpack .../111-python3-dateutil_2.8.2-3_all.deb ... 331s Unpacking python3-dateutil (2.8.2-3) ... 331s Selecting previously unselected package python3-pandas-lib:arm64. 331s Preparing to unpack .../112-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 331s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 331s Selecting previously unselected package python3-pandas. 331s Preparing to unpack .../113-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 331s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 331s Selecting previously unselected package python3-decorator. 331s Preparing to unpack .../114-python3-decorator_5.1.1-5_all.deb ... 331s Unpacking python3-decorator (5.1.1-5) ... 331s Selecting previously unselected package python3-scipy. 331s Preparing to unpack .../115-python3-scipy_1.11.4-6_arm64.deb ... 331s Unpacking python3-scipy (1.11.4-6) ... 332s Selecting previously unselected package python3-packaging. 332s Preparing to unpack .../116-python3-packaging_23.2-1_all.deb ... 332s Unpacking python3-packaging (23.2-1) ... 332s Selecting previously unselected package vsearch. 332s Preparing to unpack .../117-vsearch_2.27.0-1_arm64.deb ... 332s Unpacking vsearch (2.27.0-1) ... 332s Selecting previously unselected package python3-presto. 332s Preparing to unpack .../118-python3-presto_0.7.2-1_arm64.deb ... 332s Unpacking python3-presto (0.7.2-1) ... 332s Selecting previously unselected package presto. 332s Preparing to unpack .../119-presto_0.7.2-1_all.deb ... 332s Unpacking presto (0.7.2-1) ... 332s Selecting previously unselected package pybuild-plugin-autopkgtest. 332s Preparing to unpack .../120-pybuild-plugin-autopkgtest_6.20231223ubuntu2_all.deb ... 332s Unpacking pybuild-plugin-autopkgtest (6.20231223ubuntu2) ... 332s Selecting previously unselected package python3-all. 332s Preparing to unpack .../121-python3-all_3.12.1-0ubuntu2_arm64.deb ... 332s Unpacking python3-all (3.12.1-0ubuntu2) ... 332s Selecting previously unselected package autopkgtest-satdep. 332s Preparing to unpack .../122-1-autopkgtest-satdep.deb ... 332s Unpacking autopkgtest-satdep (0) ... 332s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 332s Setting up liblcms2-2:arm64 (2.14-2) ... 332s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 332s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 332s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 332s Setting up libdw1:arm64 (0.190-1) ... 332s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 332s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 332s Setting up libxcb-render0:arm64 (1.15-1) ... 332s Setting up libarchive-zip-perl (1.68-1) ... 332s Setting up vsearch (2.27.0-1) ... 332s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 332s Setting up x11-common (1:7.7+23ubuntu2) ... 332s Setting up libdeflate0:arm64 (1.19-1) ... 332s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 332s Setting up m4 (1.4.19-4) ... 332s Setting up libxcb-shm0:arm64 (1.15-1) ... 332s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 332s Setting up python3-freetype (2.4.0-1) ... 332s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 332s Setting up python3-decorator (5.1.1-5) ... 332s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 332s Setting up autotools-dev (20220109.1) ... 332s Setting up libblas3:arm64 (3.12.0-3) ... 332s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 332s Setting up python3-packaging (23.2-1) ... 333s Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 333s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 333s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 333s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 333s Setting up libimagequant0:arm64 (2.18.0-1) ... 333s Setting up fonts-dejavu-mono (2.37-8) ... 333s Setting up libmpc3:arm64 (1.3.1-1) ... 333s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 333s Setting up autopoint (0.21-14ubuntu1) ... 333s Setting up fonts-dejavu-core (2.37-8) ... 333s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 333s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 333s Setting up autoconf (2.71-3) ... 333s Setting up libwebp7:arm64 (1.3.2-0.4) ... 333s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 333s Setting up fonts-dejavu-extra (2.37-8) ... 333s Setting up dwz (0.15-1) ... 333s Setting up libnsl-dev:arm64 (1.3.0-3) ... 333s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 333s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 333s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 333s Setting up debugedit (1:5.0-5) ... 333s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 333s Setting up libsub-override-perl (0.10-1) ... 333s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 333s Setting up python3-dateutil (2.8.2-3) ... 333s Setting up sgml-base (1.31) ... 333s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 333s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 333s Setting up libisl23:arm64 (0.26-3) ... 333s Setting up libc-dev-bin (2.39-0ubuntu2) ... 333s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 333s Setting up python3-lib2to3 (3.11.5-1) ... 333s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 333s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 333s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 333s Setting up cd-hit (4.8.1-4) ... 333s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 333s Setting up automake (1:1.16.5-1.3ubuntu1) ... 333s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 333s Setting up python3-distutils (3.11.5-1) ... 333s python3.12: can't get files for byte-compilation 333s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 333s Setting up python3.11-minimal (3.11.8-1) ... 334s Setting up liblapack3:arm64 (3.12.0-3) ... 334s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 334s Setting up gettext (0.21-14ubuntu1) ... 334s Setting up python3-setuptools (68.1.2-2) ... 334s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 334s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 334s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 335s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 335s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 335s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 335s Setting up python3-all (3.12.1-0ubuntu2) ... 335s Setting up xfonts-utils (1:7.7+6build2) ... 335s Setting up intltool-debian (0.35.0+20060710.6) ... 335s Setting up ncbi-blast+ (2.12.0+ds-4) ... 335s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 335s Setting up libraqm0:arm64 (0.10.1-1) ... 335s Setting up dh-strip-nondeterminism (1.13.1-1) ... 335s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 335s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 335s Setting up xml-core (0.19) ... 335s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 335s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 335s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 335s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 335s Setting up dh-python (6.20231223ubuntu2) ... 335s Setting up python3.11 (3.11.8-1) ... 336s Setting up cpp-13 (13.2.0-17ubuntu2) ... 336s Setting up po-debconf (1.0.21+nmu1) ... 336s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 336s Setting up fonts-urw-base35 (20200910-8) ... 336s Setting up libcairo2:arm64 (1.18.0-1) ... 336s Setting up python3-pil:arm64 (10.2.0-1) ... 336s Setting up gcc-13 (13.2.0-17ubuntu2) ... 336s Setting up python3-numpy (1:1.24.2-2) ... 338s Setting up cpp (4:13.2.0-7ubuntu1) ... 338s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 338s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 338s Setting up g++-13 (13.2.0-17ubuntu2) ... 338s Setting up python3-scipy (1.11.4-6) ... 340s Setting up python3-cairo (1.25.1-2) ... 340s Setting up libtool (2.4.7-7) ... 340s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 340s Setting up gcc (4:13.2.0-7ubuntu1) ... 340s Setting up dh-autoreconf (20) ... 340s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 345s Setting up python3-rlpycairo (0.3.0-3) ... 345s Setting up python3-reportlab (4.1.0-1) ... 345s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 345s Setting up debhelper (13.14.1ubuntu1) ... 345s Setting up g++ (4:13.2.0-7ubuntu1) ... 345s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 345s Setting up build-essential (12.10ubuntu1) ... 345s Setting up pybuild-plugin-autopkgtest (6.20231223ubuntu2) ... 345s Processing triggers for libc-bin (2.39-0ubuntu2) ... 345s Processing triggers for systemd (255.2-3ubuntu2) ... 345s Processing triggers for man-db (2.12.0-3) ... 347s Processing triggers for install-info (7.1-3) ... 347s Processing triggers for sgml-base (1.31) ... 347s Setting up w3c-sgml-lib (1.3-3) ... 369s Setting up python3-biopython (1.81+dfsg-3) ... 371s Setting up python3-presto (0.7.2-1) ... 371s /usr/lib/python3/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' 371s sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) 371s /usr/lib/python3/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' 371s sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) 371s /usr/lib/python3/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' 371s header['SPECIES'] = re.sub('\s', '_', fields[2]) 371s /usr/lib/python3/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' 371s header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) 371s /usr/lib/python3/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' 371s header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' 371s /usr/lib/python3/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' 371s version = re.sub('\.linux.*$','',version) 371s /usr/lib/python3/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' 371s id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') 371s /usr/lib/python3/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' 371s if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) 371s Setting up presto (0.7.2-1) ... 371s Setting up autopkgtest-satdep (0) ... 375s (Reading database ... 86396 files and directories currently installed.) 375s Removing autopkgtest-satdep (0) ... 376s autopkgtest [02:09:55]: test pybuild-autopkgtest: pybuild-autopkgtest 376s autopkgtest [02:09:55]: test pybuild-autopkgtest: [----------------------- 377s pybuild-autopkgtest 377s I: pybuild pybuild:310: cp -r /tmp/autopkgtest.ZyRcv5/build.64S/src/bin /tmp/autopkgtest.ZyRcv5/autopkgtest_tmp/build; rm /tmp/autopkgtest.ZyRcv5/build.64S/src/tests/test_ClusterSets.py || echo "Test file already removed or moved"; 377s I: pybuild base:305: cd /tmp/autopkgtest.ZyRcv5/autopkgtest_tmp/build; python3.12 -m unittest discover -v 378s test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok 378s test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok 378s test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok 378s test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok 378s test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' 378s test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' 378s test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' 378s test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' 378s test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' 378s test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' 378s test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok 378s test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok 378s test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok 378s test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok 378s test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok 378s test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok 378s test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok 378s test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok 378s test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok 378s test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok 378s test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok 378s test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok 378s test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... ok 378s test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok 378s test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok 378s test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok 378s test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok 378s -> test_collapseAnnotation() 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) 378s <- test_collapseAnnotation() 0.000 378s -> test_getCoordKey() 378s ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] 378s ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] 378s ['000034_0199_0169', 'GXGJ56Z01AE06X'] 378s <- test_getCoordKey() 0.000 378s -> test_mergeAnnotation() 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) 378s <- test_mergeAnnotation() 0.000 378s -> test_renameAnnotation() 378s OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) 378s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) 378s <- test_renameAnnotation() 0.000 378s -> test_calculateSetError() 378s Frequency consensus error> 378s REF> CGGCGTAA 378s SEQ1> CGGCGTAA 378s SEQ2> CCNNGTAA 378s SEQ3> CGGC--TA 378s SEQ4> CGNN--TA 378s SEQ5> CGGC--AA 378s ERROR> 0.250000 378s Quality consensus error> 378s REF> CGGCNNAA 378s SEQ1> CGGCGTAA 378s SEQ2> CCNNGTAA 378s SEQ3> CGGC--TA 378s SEQ4> CGNN--TA 378s SEQ5> CGGC--AA 378s ERROR> 0.233333 378s <- test_calculateSetError() 0.000 378s -> test_deleteSeqPositions() 378s MAX_GAP=0.4> CGGCAA 378s MAX_GAP=0.8> CGGCGTAA 378s <- test_deleteSeqPositions() 0.000 378s -> test_findGapPositions() 378s MAX_GAP=0.4> [4, 5] 378s MAX_GAP=0.8> [] 378s <- test_findGapPositions() 0.000 378s -> test_frequencyConsensus() 378s MIN_FREQ=0.2> CGGCGTAA 378s MIN_FREQ=0.8> CGGCGTNA 378s <- test_frequencyConsensus() 0.000 378s -> test_qualityConsensus() 378s MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] 378s MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] 378s MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] 378s <- test_qualityConsensus() 0.000 378s -> test_checkSeqEqual() 378s DNA Equality> 378s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 378s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 378s EQUAL> True 378s 378s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 378s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 378s EQUAL> False 378s 378s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 378s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 378s EQUAL> True 378s 378s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 378s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 378s EQUAL> False 378s 378s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 378s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 378s EQUAL> True 378s 378s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 378s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 378s EQUAL> True 378s 378s <- test_checkSeqEqual() 0.000 378s -> test_convert454Header() 378s OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) 378s OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) 378s <- test_convert454Header() 0.000 378s -> test_convertGenbankHeader() 378s OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 378s OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) 378s <- test_convertGenbankHeader() 0.000 378s -> test_convertGenericHeader() 378s OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 378s OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 378s OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) 378s OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) 378s OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) 378s OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) 378s <- test_convertGenericHeader() 0.000 378s -> test_convertIMGTHeader() 378s OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) 378s OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) 378s OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) 378s OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) 378s OrderedDict({'ID': 'IGHV1-18*01'}) 378s OrderedDict({'ID': 'IGHV1-69*07'}) 378s OrderedDict({'ID': 'IGHV(III)-22-2*01'}) 378s OrderedDict({'ID': 'TRAV11*01'}) 378s <- test_convertIMGTHeader() 0.000 378s -> test_convertIlluminaHeader() 378s OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) 378s OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) 378s OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) 378s <- test_convertIlluminaHeader() 0.000 378s -> test_convertSRAHeader() 378s OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) 378s OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) 378s OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) 378s OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) 378s OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) 378s <- test_convertSRAHeader() 0.000 378s -> test_calculateDistances() 378s <- test_calculateDistances() 0.006 378s -> test_countMismatches() 378s <- test_countMismatches() 0.001 378s -> test_initializeMismatchDictionary() 378s <- test_initializeMismatchDictionary() 0.000 378s -> test_getFileType() 378s <- test_getFileType() 0.000 378s -> test_extractAlignment() 378s SEQ1> 378s SEQ> CCACGTTTTAGTAATTAATA 378s ALN-SEQ> CCACGTTTTAGT 378s ALN-PR> ----GTTTTAGT 378s PRIMER> GTTTTAGT 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ2> 378s SEQ> CCNCGTTTTAGTAATTAATA 378s ALN-SEQ> CCNCGTTTTAGT 378s ALN-PR> ----GTTTTAGT 378s PRIMER> GTTTTAGT 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ3> 378s SEQ> GGGCGTTTTAGTAATTAATA 378s ALN-SEQ> GGGCGTTTTAGT 378s ALN-PR> ----GTTTTAGT 378s PRIMER> GTTTTAGT 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ4> 378s SEQ> GGNNGTTTTACTAATTAATA 378s ALN-SEQ> GGNNGTTTTACT 378s ALN-PR> ----GTTTTACT 378s PRIMER> GTTTTACT 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ5> 378s SEQ> NNGCNNNNNACTAATTAATA 378s ALN-SEQ> NNGCNNNNNACT 378s ALN-PR> ----NNNNNACT 378s PRIMER> NNNNNACT 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ6> 378s SEQ> GGGATANNNACTAATTAATA 378s ALN-SEQ> GGGATANNNACT 378s ALN-PR> ----TANNNACT 378s PRIMER> TANNNACT 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ7> 378s SEQ> NNNNNNNNNNNNNNNNNNNN 378s ALN-SEQ> NNNNNNNNNNNN 378s ALN-PR> ----NNNNNNNN 378s PRIMER> NNNNNNNN 378s START> 4 378s END> 12 378s GAPS> 0 378s ERROR> 0.000000 378s 378s <- test_extractAlignment() 0.000 378s -> test_localAlignment() 378s TEST Ns> 378s SEQ1> 378s SEQ> CCACGTTTTAGTAATTAATA 378s ALN-SEQ> CCACGTTTTAGTAATTAATA 378s ALN-PR> -CACGTTTT----------- 378s PRIMER> PR1 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ2> 378s SEQ> CCNCGTTTTAGTAATTAATA 378s ALN-SEQ> CCNCGTTTTAGTAATTAATA 378s ALN-PR> -CACGTTTT----------- 378s PRIMER> PR1 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.125000 378s 378s SEQ3> 378s SEQ> GGGCGTTTTAGTAATTAATA 378s ALN-SEQ> GGGCGTTTTAGTAATTAATA 378s ALN-PR> -GGCGTTTT----------- 378s PRIMER> PR2 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ4> 378s SEQ> GGNNGTTTTACTAATTAATA 378s ALN-SEQ> GGNNGTTTTACTAATTAATA 378s ALN-PR> GGC-GTTTT----------- 378s PRIMER> PR2 378s START> 0 378s END> 9 378s GAPS> 1 378s test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... ok 378s test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok 378s test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok 378s test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok 378s test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok 378s test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok 378s test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok 378s test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... ERROR> 0.250000 378s 378s SEQ5> 378s SEQ> NNGCNNNNNACTAATTAATA 378s ALN-SEQ> NNGCNNNNNACTAATTAATA 378s ALN-PR> ------------ANATAA-- 378s PRIMER> PR3 378s START> 12 378s END> 18 378s GAPS> 0 378s ERROR> 0.375000 378s 378s SEQ6> 378s SEQ> GGGATANNNACTAATTAATA 378s ALN-SEQ> GGGATANNNACTAATTAATA 378s ALN-PR> -GGANA-------------- 378s PRIMER> PR3 378s START> 1 378s END> 6 378s GAPS> 0 378s ERROR> 0.375000 378s 378s SEQ7> 378s SEQ> NNNNNNNNNNNNNNNNNNNN 378s ALN-SEQ> None 378s ALN-PR> None 378s PRIMER> None 378s START> None 378s END> None 378s GAPS> 0 378s ERROR> 1.000000 378s 378s TEST INDELS> 378s SEQ1> 378s SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG 378s ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG 378s ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ 378s PRIMER> PR1 378s START> 15 378s END> 38 378s GAPS> 0 378s ERROR> 0.083333 378s 378s SEQ2> 378s SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG 378s ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG 378s ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ 378s PRIMER> PR1 378s START> 14 378s END> 38 378s GAPS> 2 378s ERROR> 0.208333 378s 378s SEQ3> 378s SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG 378s ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG 378s ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ 378s PRIMER> PR1 378s START> 15 378s END> 38 378s GAPS> 1 378s ERROR> 0.125000 378s 378s SEQ4> 378s SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT 378s ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT 378s ALN-PR> ------CATCT-TCCTCTA------------------------------------------- 378s PRIMER> PR2 378s START> 6 378s END> 19 378s GAPS> 1 378s ERROR> 0.250000 378s 378s SEQ5> 378s SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG 378s ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG 378s ALN-PR> ------CATCTTCCTCTA-------------------------------------------- 378s PRIMER> PR2 378s START> 6 378s END> 18 378s GAPS> 0 378s ERROR> 0.166667 378s 378s SEQ6> 378s SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA 378s ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA 378s ALN-PR> TCT-TCCTCTA--------------------------------------------------- 378s PRIMER> PR2 378s START> 0 378s END> 11 378s GAPS> 1 378s ERROR> 0.250000 378s 378s SEQ7> 378s SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 378s ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 378s ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- 378s PRIMER> PR3 378s START> 2 378s END> 15 378s GAPS> 1 378s ERROR> 0.083333 378s 378s SEQ8> 378s SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 378s ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 378s ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- 378s PRIMER> PR3 378s START> 3 378s END> 15 378s GAPS> 1 378s ERROR> 0.166667 378s 378s SEQ9> 378s SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 378s ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 378s ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- 378s PRIMER> PR3 378s START> 3 378s END> 15 378s GAPS> 1 378s ERROR> 0.333333 378s 378s SEQ10> 378s SEQ> -------------------------------------------------------------- 378s ALN-SEQ> None 378s ALN-PR> None 378s PRIMER> None 378s START> None 378s END> None 378s GAPS> 0 378s ERROR> 1.000000 378s 378s <- test_localAlignment() 0.020 378s -> test_maskSeq() 378s TEST CUT> 378s ID> SEQ|PRIMER=A|BARCODE=CCA 378s SEQ> AGTAATTAATA 378s 378s TEST MASK> 378s ID> SEQ|PRIMER=A|BARCODE=CCA 378s SEQ> NNNNNNAGTAATTAATA 378s 378s TEST TRIM> 378s ID> SEQ|PRIMER=A|BARCODE=CCA 378s SEQ> CGTTTTAGTAATTAATA 378s 378s TEST TAG> 378s ID> SEQ|PRIMER=A|BARCODE=CCA 378s SEQ> CCACGTTTTAGTAATTAATA 378s 378s <- test_maskSeq() 0.001 378s -> test_scoreAlignment() 378s SEQ1> 378s SEQ> CCACGTTTTAGTAATTAATA 378s ALN-SEQ> CCACGTTTT 378s ALN-PR> -CACGTTTT 378s PRIMER> PR1 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ2> 378s SEQ> CCNCGTTTTAGTAATTAATA 378s ALN-SEQ> CCNCGTTTT 378s ALN-PR> -CACGTTTT 378s PRIMER> PR1 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.125000 378s 378s SEQ3> 378s SEQ> GGGCGTTTTAGTAATTAATA 378s ALN-SEQ> GGGCGTTTT 378s ALN-PR> -GGCGTTTT 378s PRIMER> PR2 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.000000 378s 378s SEQ4> 378s SEQ> GGNNGTTTTACTAATTAATA 378s ALN-SEQ> GGNNGTTTT 378s ALN-PR> -GGCGTTTT 378s PRIMER> PR2 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.250000 378s 378s SEQ5> 378s SEQ> NNGCNNNNNACTAATTAATA 378s ALN-SEQ> NNGCNNNNN 378s ALN-PR> -GGCGTTTT 378s PRIMER> PR2 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.750000 378s 378s SEQ6> 378s SEQ> GGGATANNNACTAATTAATA 378s ALN-SEQ> GGGATANNN 378s ALN-PR> -GGANATAA 378s PRIMER> PR3 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 0.375000 378s 378s SEQ7> 378s SEQ> NNNNNNNNNNNNNNNNNNNN 378s ALN-SEQ> NNNNNNNNN 378s ALN-PR> -CACGTTTT 378s PRIMER> None 378s START> 1 378s END> 9 378s GAPS> 0 378s ERROR> 1.000000 378s 378s <- test_scoreAlignment() 0.006 378s -> test_calculateSetError() 378s REF> CGGCGTAA 0.4347826086956522 378s REF> NNNNNNNN 1.0 378s <- test_calculateSetError() 0.000 378s -> test_filterQuality() 378s RESULT> True 25 378s RESULT> False 5 378s RESULT> False 0 378s <- test_filterQuality() 0.000 378s -> test_meanQuality() 378s RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] 378s RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] 378s RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] 378s <- test_meanQuality() 0.000 378s -> test_scoreDNA() 378s Default DNA Scores> 378s A==A> 1 378s A==T> 0 378s A==R> 1 378s U==T> 1 378s A==N> 1 378s N==A> 1 378s A==-> 0 378s -==A> 0 378s Symmetric DNA Scores> 378s A==A> 1 378s A==T> 0 378s A==R> 1 378s U==T> 1 378s A==N> 1 378s N==A> 1 378s A==-> 1 378s -==A> 1 378s Asymmetric DNA Scores> 378s A==A> 1 378s A==T> 0 378s A==R> 1 378s U==T> 1 378s A==N> 1 378s N==A> 0 378s A==-> 1 378s -==A> 0 378s <- test_scoreDNA() 0.000 378s -> test_scoreSeqPair() 378s Default DNA Scores> 378s SEQ1> CGGCGTAA 378s SEQ2> CGNNGTAG 378s SCORE> 7 378s WEIGHT> 8 378s ERROR> 0.125000 378s 378s SEQ1> CGGCGTAA 378s SEQ3> CGGC--AA 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ1> CGGCGTAA 378s SEQ4> CGNN--AG 378s SCORE> 5 378s WEIGHT> 8 378s ERROR> 0.375000 378s 378s SEQ1> CGGCGTAA 378s SEQ5> NNNNNNNN 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ6> NNNNNNAA 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ2> CGNNGTAG 378s SEQ3> CGGC--AA 378s SCORE> 5 378s WEIGHT> 8 378s ERROR> 0.375000 378s 378s SEQ2> CGNNGTAG 378s SEQ4> CGNN--AG 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ2> CGNNGTAG 378s SEQ5> NNNNNNNN 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ2> CGNNGTAG 378s SEQ6> NNNNNNAA 378s SCORE> 7 378s WEIGHT> 8 378s ERROR> 0.125000 378s 378s SEQ2> CGNNGTAG 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ2> CGNNGTAG 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ3> CGGC--AA 378s SEQ4> CGNN--AG 378s SCORE> 7 378s WEIGHT> 8 378s ERROR> 0.125000 378s 378s SEQ3> CGGC--AA 378s SEQ5> NNNNNNNN 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ3> CGGC--AA 378s SEQ6> NNNNNNAA 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ3> CGGC--AA 378s SEQ7> -------- 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ3> CGGC--AA 378s SEQ8> CG------ 378s SCORE> 4 378s WEIGHT> 8 378s ERROR> 0.500000 378s 378s SEQ4> CGNN--AG 378s SEQ5> NNNNNNNN 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ4> CGNN--AG 378s SEQ6> NNNNNNAA 378s SCORE> 5 378s WEIGHT> 8 378s ERROR> 0.375000 378s 378s SEQ4> CGNN--AG 378s SEQ7> -------- 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ4> CGNN--AG 378s SEQ8> CG------ 378s SCORE> 4 378s WEIGHT> 8 378s ERROR> 0.500000 378s 378s SEQ5> NNNNNNNN 378s SEQ6> NNNNNNAA 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ5> NNNNNNNN 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ5> NNNNNNNN 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ6> NNNNNNAA 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ6> NNNNNNAA 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ7> -------- 378s SEQ8> CG------ 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s Asymmetric DNA Scores> 378s SEQ1> CGGCGTAA 378s SEQ2> CGNNGTAG 378s SCORE> 7 378s WEIGHT> 8 378s ERROR> 0.125000 378s 378s SEQ1> CGGCGTAA 378s SEQ3> CGGC--AA 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ4> CGNN--AG 378s SCORE> 7 378s WEIGHT> 8 378s ERROR> 0.125000 378s 378s SEQ1> CGGCGTAA 378s SEQ5> NNNNNNNN 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ6> NNNNNNAA 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ7> -------- 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ8> CG------ 378s SCORE> 8 378s WEIGHT> 8 378s ERROR> 0.000000 378s 378s SEQ2> CGNNGTAG 378s SEQ3> CGGC--AA 378s SCORE> 5 378s WEIGHT> 8 378s ERROR> 0.375000 378s 378s SEQ2> CGNNGTAG 378s SEQ4> CGNN--AG 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ2> CGNNGTAG 378s SEQ5> NNNNNNNN 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ2> CGNNGTAG 378s SEQ6> NNNNNNAA 378s SCORE> 5 378s WEIGHT> 8 378s ERROR> 0.375000 378s 378s SEQ2> CGNNGTAG 378s SEQ7> -------- 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ2> CGNNGTAG 378s SEQ8> CG------ 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ3> CGGC--AA 378s SEQ4> CGNN--AG 378s SCORE> 5 378s WEIGHT> 8 378s ERROR> 0.375000 378s 378s SEQ3> CGGC--AA 378s SEQ5> NNNNNNNN 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ3> CGGC--AA 378s SEQ6> NNNNNNAA 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ3> CGGC--AA 378s SEQ7> -------- 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ3> CGGC--AA 378s SEQ8> CG------ 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ4> CGNN--AG 378s SEQ5> NNNNNNNN 378s SCORE> 4 378s WEIGHT> 8 378s ERROR> 0.500000 378s 378s SEQ4> CGNN--AG 378s SEQ6> NNNNNNAA 378s SCORE> 3 378s WEIGHT> 8 378s ERROR> 0.625000 378s 378s SEQ4> CGNN--AG 378s SEQ7> -------- 378s SCORE> 4 378s WEIGHT> 8 378s ERROR> 0.500000 378s 378s SEQ4> CGNN--AG 378s SEQ8> CG------ 378s SCORE> 4 378s WEIGHT> 8 378s ERROR> 0.500000 378s 378s SEQ5> NNNNNNNN 378s SEQ6> NNNNNNAA 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ5> NNNNNNNN 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ5> NNNNNNNN 378s SEQ8> CG------ 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ6> NNNNNNAA 378s SEQ7> -------- 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ6> NNNNNNAA 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ7> -------- 378s SEQ8> CG------ 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s Masked DNA Scores> 378s SEQ1> CGGCGTAA 378s SEQ2> CGNNGTAG 378s SCORE> 5 378s WEIGHT> 6 378s ERROR> 0.166667 378s 378s SEQ1> CGGCGTAA 378s SEQ3> CGGC--AA 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s SEQ1> CGGCGTAA 378s SEQ4> CGNN--AG 378s SCORE> 3 378s WEIGHT> 6 378s ERROR> 0.500000 378s 378s SEQ1> CGGCGTAA 378s SEQ5> NNNNNNNN 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ6> NNNNNNAA 378s SCORE> 2 378s WEIGHT> 2 378s ERROR> 0.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 8 378s ERROR> 1.000000 378s 378s SEQ1> CGGCGTAA 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ2> CGNNGTAG 378s SEQ3> CGGC--AA 378s SCORE> 3 378s WEIGHT> 6 378s ERROR> 0.500000 378s 378s SEQ2> CGNNGTAG 378s SEQ4> CGNN--AG 378s SCORE> 4 378s WEIGHT> 6 378s ERROR> 0.333333 378s 378s SEQ2> CGNNGTAG 378s SEQ5> NNNNNNNN 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ2> CGNNGTAG 378s SEQ6> NNNNNNAA 378s SCORE> 1 378s WEIGHT> 2 378s ERROR> 0.500000 378s 378s SEQ2> CGNNGTAG 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 6 378s ERROR> 1.000000 378s 378s SEQ2> CGNNGTAG 378s SEQ8> CG------ 378s SCORE> 2 378s WEIGHT> 6 378s ERROR> 0.666667 378s 378s SEQ3> CGGC--AA 378s SEQ4> CGNN--AG 378s SCORE> 5 378s WEIGHT> 6 378s ERROR> 0.166667 378s 378s SEQ3> CGGC--AA 378s SEQ5> NNNNNNNN 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ3> CGGC--AA 378s SEQ6> NNNNNNAA 378s SCORE> 2 378s WEIGHT> 2 378s ERROR> 0.000000 378s 378s SEQ3> CGGC--AA 378s SEQ7> -------- 378s SCORE> 2 378s WEIGHT> 8 378s ERROR> 0.750000 378s 378s SEQ3> CGGC--AA 378s SEQ8> CG------ 378s SCORE> 4 378s WEIGHT> 8 378s ERROR> 0.500000 378s 378s SEQ4> CGNN--AG 378s SEQ5> NNNNNNNN 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ4> CGNN--AG 378s SEQ6> NNNNNNAA 378s SCORE> 1 378s WEIGHT> 2 378s ERROR> 0.500000 378s 378s SEQ4> CGNN--AG 378s SEQ7> -------- 378s SCORE> 2 378s WEIGHT> 6 378s ERROR> 0.666667 378s 378s SEQ4> CGNN--AG 378s SEQ8> CG------ 378s SCORE> 4 378s WEIGHT> 6 378s ERROR> 0.333333 378s 378s SEQ5> NNNNNNNN 378s SEQ6> NNNNNNAA 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ5> NNNNNNNN 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ5> NNNNNNNN 378s SEQ8> CG------ 378s SCORE> 0 378s WEIGHT> 0 378s ERROR> 1.000000 378s 378s SEQ6> NNNNNNAA 378s SEQ7> -------- 378s SCORE> 0 378s WEIGHT> 2 378s ERROR> 1.000000 378s 378s SEQ6> NNNNNNAA 378s SEQ8> CG------ 378s SCORE> 0 378s WEIGHT> 2 378s ERROR> 1.000000 378s 378s SEQ7> -------- 378s SEQ8> CG------ 378s SCORE> 6 378s WEIGHT> 8 378s ERROR> 0.250000 378s 378s <- test_scoreSeqPair() 0.005 378s -> test_weightDNA() 378s DNA Weight> 378s SEQ1> 8 378s SEQ2> 6 378s SEQ3> 8 378s SEQ4> 6 378s SEQ5> 0 378s SEQ6> 2 378s SEQ7> 8 378s SEQ8> 8 378s AA Weight> 378s SEQ1> 8 378s SEQ2> 6 378s SEQ3> 8 378s SEQ4> 6 378s <- test_weightDNA() 0.000 378s -> test_consensusUnify() 378s ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 378s ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 378s ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 378s ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 378s ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 378s ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 378s ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 378s ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 378s <- test_consensusUnify() 0.000 378s -> test_deletionUnify() 378s ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False 378s ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False 378s ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False 378s ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False 378s ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False 378s ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False 378s ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True 378s ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True 378s <- test_deletionUnify() 0.000 378s ok 378s test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok 378s test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok 378s test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok 378s 378s ---------------------------------------------------------------------- 378s Ran 38 tests in 0.045s 378s 378s OK (skipped=6) 379s autopkgtest [02:09:58]: test pybuild-autopkgtest: -----------------------] 380s autopkgtest [02:09:59]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 380s pybuild-autopkgtest PASS 380s autopkgtest [02:09:59]: @@@@@@@@@@@@@@@@@@@@ summary 380s pybuild-autopkgtest PASS 399s Creating nova instance adt-noble-arm64-presto-20240318-020339-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...