0s autopkgtest [18:22:21]: starting date and time: 2024-03-18 18:22:21+0000 0s autopkgtest [18:22:21]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [18:22:21]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j9so498d/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@bos01-ppc64el-12.secgroup --name adt-noble-ppc64el-presto-20240318-182220-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 163s autopkgtest [18:25:04]: testbed dpkg architecture: ppc64el 163s autopkgtest [18:25:04]: testbed apt version: 2.7.12 163s autopkgtest [18:25:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 164s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 164s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3720 kB] 166s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 166s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 166s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 167s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [643 kB] 167s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 167s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 167s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 167s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4012 kB] 167s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 167s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [48.4 kB] 167s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 170s Fetched 9098 kB in 4s (2234 kB/s) 171s Reading package lists... 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Calculating upgrade... 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s sh: Attempting to set up Debian/Ubuntu apt sources automatically 176s sh: Distribution appears to be Ubuntu 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s eatmydata is already the newest version (131-1). 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s dbus is already the newest version (1.14.10-4ubuntu1). 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s rng-tools-debian is already the newest version (2.4). 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s The following packages will be REMOVED: 178s cloud-init* python3-configobj* python3-debconf* 179s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 179s After this operation, 3252 kB disk space will be freed. 179s (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 ... 70095 files and directories currently installed.) 179s Removing cloud-init (24.1.1-0ubuntu1) ... 180s Removing python3-configobj (5.0.8-3) ... 180s Removing python3-debconf (1.5.86) ... 180s Processing triggers for man-db (2.12.0-3) ... 180s (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 ... 69706 files and directories currently installed.) 180s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 181s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 181s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 181s invoke-rc.d: policy-rc.d denied execution of try-restart. 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s linux-generic is already the newest version (6.8.0-11.11+1). 182s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 182s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 182s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 185s Reading package lists... 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 185s Calculating upgrade... 186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s autopkgtest [18:25:27]: rebooting testbed after setup commands that affected boot 360s autopkgtest [18:28:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 363s autopkgtest [18:28:24]: @@@@@@@@@@@@@@@@@@@@ apt-source presto 365s Get:1 http://ftpmaster.internal/ubuntu noble/universe presto 0.7.2-1 (dsc) [2233 B] 365s Get:2 http://ftpmaster.internal/ubuntu noble/universe presto 0.7.2-1 (tar) [362 kB] 365s Get:3 http://ftpmaster.internal/ubuntu noble/universe presto 0.7.2-1 (diff) [20.8 kB] 365s gpgv: Signature made Mon Feb 19 12:51:18 2024 UTC 365s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 365s gpgv: Can't check signature: No public key 365s dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-1.dsc: no acceptable signature found 366s autopkgtest [18:28:27]: testing package presto version 0.7.2-1 366s autopkgtest [18:28:27]: build not needed 374s autopkgtest [18:28:35]: test pybuild-autopkgtest: preparing testbed 376s Reading package lists... 376s Building dependency tree... 376s Reading state information... 376s Starting pkgProblemResolver with broken count: 0 376s Starting 2 pkgProblemResolver with broken count: 0 376s Done 377s The following additional packages will be installed: 377s autoconf automake autopoint autotools-dev build-essential cd-hit cpp cpp-13 377s cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper debugedit 377s dh-autoreconf dh-python dh-strip-nondeterminism dwz fontconfig-config 377s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 g++ 377s g++-13 g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 377s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 377s intltool-debian libarchive-zip-perl libasan8 libatomic1 libblas3 377s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl 377s libdeflate0 libdw1 libfile-stripnondeterminism-perl libfontconfig1 377s libfontenc1 libgcc-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 377s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 377s liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmbedcrypto7 libmbedtls14 377s libmbedx509-1 libmpc3 libnsl-dev libopenjp2-7 libpixman-1-0 libquadmath0 377s libraqm0 libsharpyuv0 libstdc++-13-dev libsub-override-perl libtiff6 377s libtirpc-dev libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 377s libxcb-render0 libxcb-shm0 libxrender1 linux-libc-dev m4 ncbi-blast+ 377s ncbi-data po-debconf presto pybuild-plugin-autopkgtest python3-all 377s python3-biopython python3-cairo python3-dateutil python3-decorator 377s python3-freetype python3-numpy python3-packaging python3-pandas 377s python3-pandas-lib python3-pil python3-presto python3-reportlab 377s python3-rlpycairo python3-scipy rpcsvc-proto sgml-base vsearch w3c-sgml-lib 377s x11-common xfonts-encodings xfonts-utils xml-core 377s Suggested packages: 377s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 377s cpp-13-doc dh-make flit python3-build python3-installer python3-wheel 377s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-13-doc 377s gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-powerpc64le-linux-gnu 377s gettext-doc libasprintf-dev libgettextpo-dev glibc-doc liblcms2-utils 377s libstdc++-13-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 377s libmail-box-perl python3-tk bwa clustalo clustalw dialign dssp emboss 377s fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb 377s python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 raxml 377s samtools t-coffee wise gfortran python3-dev python3-pytest python-pandas-doc 377s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 377s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc sgml-base-doc 377s Recommended packages: 377s manpages manpages-dev libc-devtools libarchive-cpio-perl libltdl-dev 377s libmail-sendmail-perl python-biopython-doc python3-matplotlib 377s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 377s python3-html5lib python3-lxml python3-tables python3-olefile 377s The following NEW packages will be installed: 377s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 377s cd-hit cpp cpp-13 cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu 377s debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz 377s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 377s fonts-urw-base35 g++ g++-13 g++-13-powerpc64le-linux-gnu 377s g++-powerpc64le-linux-gnu gcc gcc-13 gcc-13-powerpc64le-linux-gnu 377s gcc-powerpc64le-linux-gnu gettext intltool-debian libarchive-zip-perl 377s libasan8 libatomic1 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 377s libcrypt-dev libdebhelper-perl libdeflate0 libdw1 377s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libgcc-13-dev 377s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libisl23 377s libitm1 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 377s liblerc4 liblsan0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmpc3 377s libnsl-dev libopenjp2-7 libpixman-1-0 libquadmath0 libraqm0 libsharpyuv0 377s libstdc++-13-dev libsub-override-perl libtiff6 libtirpc-dev libtool libtsan2 377s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 377s libxrender1 linux-libc-dev m4 ncbi-blast+ ncbi-data po-debconf presto 377s pybuild-plugin-autopkgtest python3-all python3-biopython python3-cairo 377s python3-dateutil python3-decorator python3-freetype python3-numpy 377s python3-packaging python3-pandas python3-pandas-lib python3-pil 377s python3-presto python3-reportlab python3-rlpycairo python3-scipy 377s rpcsvc-proto sgml-base vsearch w3c-sgml-lib x11-common xfonts-encodings 377s xfonts-utils xml-core 377s 0 upgraded, 116 newly installed, 0 to remove and 0 not upgraded. 377s Need to get 151 MB/151 MB of archives. 377s After this operation, 651 MB of additional disk space will be used. 377s Get:1 /tmp/autopkgtest.WRhFYi/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [828 B] 377s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] 377s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el m4 ppc64el 1.4.19-4 [275 kB] 377s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el autoconf all 2.71-3 [339 kB] 377s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 377s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 377s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el autopoint all 0.21-14ubuntu1 [422 kB] 377s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu2 [21.3 kB] 377s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 377s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 377s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1build1 [262 kB] 377s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libnsl-dev ppc64el 1.3.0-3 [79.2 kB] 377s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 377s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu2 [2102 kB] 378s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 378s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 378s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 378s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 378s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 378s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 378s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 378s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 378s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 378s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 378s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 378s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 378s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 378s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 378s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 378s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 378s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 379s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 379s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 379s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 379s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 379s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 380s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 380s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 380s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 380s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 380s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el cd-hit ppc64el 4.8.1-4 [547 kB] 380s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libdebhelper-perl all 13.14.1ubuntu1 [89.5 kB] 380s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtool all 2.4.7-7 [166 kB] 380s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-autoreconf all 20 [16.1 kB] 380s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 380s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] 380s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 380s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] 380s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libdw1 ppc64el 0.190-1 [294 kB] 380s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] 380s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el dwz ppc64el 0.15-1 [139 kB] 380s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] 380s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 380s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 380s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el debhelper all 13.14.1ubuntu1 [869 kB] 380s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el dh-python all 6.20231223ubuntu2 [111 kB] 380s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 380s Get:58 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 380s Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB] 380s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 380s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 380s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB] 380s Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 381s Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 381s Get:65 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-extra all 2.37-8 [1947 kB] 381s Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 381s Get:67 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 381s Get:68 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 381s Get:69 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 381s Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 381s Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 381s Get:72 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 381s Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 381s Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 381s Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 381s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 381s Get:77 http://ftpmaster.internal/ubuntu noble/main ppc64el libimagequant0 ppc64el 2.18.0-1 [42.5 kB] 381s Get:78 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 381s Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 381s Get:80 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 381s Get:81 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 381s Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 381s Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 381s Get:84 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedcrypto7 ppc64el 2.28.7-1ubuntu1 [262 kB] 381s Get:85 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedx509-1 ppc64el 2.28.7-1ubuntu1 [51.4 kB] 381s Get:86 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedtls14 ppc64el 2.28.7-1ubuntu1 [89.7 kB] 381s Get:87 http://ftpmaster.internal/ubuntu noble/main ppc64el libraqm0 ppc64el 0.10.1-1 [18.9 kB] 381s Get:88 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 381s Get:89 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 381s Get:90 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 381s Get:91 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 381s Get:92 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4 [14.4 kB] 381s Get:93 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4 [31.2 kB] 381s Get:94 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 382s Get:95 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4 [13.4 MB] 382s Get:96 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 382s Get:97 http://ftpmaster.internal/ubuntu noble/main ppc64el libopenjp2-7 ppc64el 2.5.0-2 [233 kB] 382s Get:98 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pil ppc64el 10.2.0-1 [526 kB] 382s Get:99 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-cairo ppc64el 1.25.1-2 [162 kB] 382s Get:100 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB] 382s Get:101 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 382s Get:102 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-reportlab all 4.1.0-1 [683 kB] 382s Get:103 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] 382s Get:104 http://ftpmaster.internal/ubuntu noble/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 383s Get:105 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biopython ppc64el 1.81+dfsg-3 [1738 kB] 383s Get:106 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 383s Get:107 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 383s Get:108 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 383s Get:109 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 383s Get:110 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 384s Get:111 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] 384s Get:112 http://ftpmaster.internal/ubuntu noble/universe ppc64el vsearch ppc64el 2.27.0-1 [444 kB] 384s Get:113 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-presto ppc64el 0.7.2-1 [80.7 kB] 384s Get:114 http://ftpmaster.internal/ubuntu noble/universe ppc64el presto all 0.7.2-1 [240 kB] 385s Get:115 http://ftpmaster.internal/ubuntu noble/universe ppc64el pybuild-plugin-autopkgtest all 6.20231223ubuntu2 [1760 B] 385s Get:116 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B] 385s Fetched 151 MB in 8s (19.5 MB/s) 385s Selecting previously unselected package sgml-base. 385s (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 ... 69651 files and directories currently installed.) 385s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 385s Unpacking sgml-base (1.31) ... 385s Selecting previously unselected package m4. 385s Preparing to unpack .../001-m4_1.4.19-4_ppc64el.deb ... 385s Unpacking m4 (1.4.19-4) ... 385s Selecting previously unselected package autoconf. 385s Preparing to unpack .../002-autoconf_2.71-3_all.deb ... 385s Unpacking autoconf (2.71-3) ... 385s Selecting previously unselected package autotools-dev. 385s Preparing to unpack .../003-autotools-dev_20220109.1_all.deb ... 385s Unpacking autotools-dev (20220109.1) ... 385s Selecting previously unselected package automake. 385s Preparing to unpack .../004-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 385s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 385s Selecting previously unselected package autopoint. 385s Preparing to unpack .../005-autopoint_0.21-14ubuntu1_all.deb ... 385s Unpacking autopoint (0.21-14ubuntu1) ... 385s Selecting previously unselected package libc-dev-bin. 385s Preparing to unpack .../006-libc-dev-bin_2.39-0ubuntu2_ppc64el.deb ... 385s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 385s Selecting previously unselected package linux-libc-dev:ppc64el. 385s Preparing to unpack .../007-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 385s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 385s Selecting previously unselected package libcrypt-dev:ppc64el. 385s Preparing to unpack .../008-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 385s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 386s Selecting previously unselected package libtirpc-dev:ppc64el. 386s Preparing to unpack .../009-libtirpc-dev_1.3.4+ds-1build1_ppc64el.deb ... 386s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 386s Selecting previously unselected package libnsl-dev:ppc64el. 386s Preparing to unpack .../010-libnsl-dev_1.3.0-3_ppc64el.deb ... 386s Unpacking libnsl-dev:ppc64el (1.3.0-3) ... 386s Selecting previously unselected package rpcsvc-proto. 386s Preparing to unpack .../011-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 386s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 386s Selecting previously unselected package libc6-dev:ppc64el. 386s Preparing to unpack .../012-libc6-dev_2.39-0ubuntu2_ppc64el.deb ... 386s Unpacking libc6-dev:ppc64el (2.39-0ubuntu2) ... 386s Selecting previously unselected package libisl23:ppc64el. 386s Preparing to unpack .../013-libisl23_0.26-3_ppc64el.deb ... 386s Unpacking libisl23:ppc64el (0.26-3) ... 386s Selecting previously unselected package libmpc3:ppc64el. 386s Preparing to unpack .../014-libmpc3_1.3.1-1_ppc64el.deb ... 386s Unpacking libmpc3:ppc64el (1.3.1-1) ... 386s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 386s Preparing to unpack .../015-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 386s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 386s Selecting previously unselected package cpp-13. 386s Preparing to unpack .../016-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 386s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 386s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 386s Preparing to unpack .../017-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 386s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 386s Selecting previously unselected package cpp. 386s Preparing to unpack .../018-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 386s Unpacking cpp (4:13.2.0-7ubuntu1) ... 386s Selecting previously unselected package libcc1-0:ppc64el. 386s Preparing to unpack .../019-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libgomp1:ppc64el. 386s Preparing to unpack .../020-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libitm1:ppc64el. 386s Preparing to unpack .../021-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libatomic1:ppc64el. 386s Preparing to unpack .../022-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libasan8:ppc64el. 386s Preparing to unpack .../023-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package liblsan0:ppc64el. 386s Preparing to unpack .../024-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libtsan2:ppc64el. 386s Preparing to unpack .../025-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libubsan1:ppc64el. 386s Preparing to unpack .../026-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libquadmath0:ppc64el. 386s Preparing to unpack .../027-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 386s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 386s Selecting previously unselected package libgcc-13-dev:ppc64el. 386s Preparing to unpack .../028-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 386s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 387s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 387s Preparing to unpack .../029-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 387s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 387s Selecting previously unselected package gcc-13. 387s Preparing to unpack .../030-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 387s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 387s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 387s Preparing to unpack .../031-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 387s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 387s Selecting previously unselected package gcc. 387s Preparing to unpack .../032-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 387s Unpacking gcc (4:13.2.0-7ubuntu1) ... 387s Selecting previously unselected package libstdc++-13-dev:ppc64el. 387s Preparing to unpack .../033-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 387s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 387s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 387s Preparing to unpack .../034-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 387s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 388s Selecting previously unselected package g++-13. 388s Preparing to unpack .../035-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 388s Unpacking g++-13 (13.2.0-17ubuntu2) ... 388s Selecting previously unselected package g++-powerpc64le-linux-gnu. 388s Preparing to unpack .../036-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 388s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 388s Selecting previously unselected package g++. 388s Preparing to unpack .../037-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 388s Unpacking g++ (4:13.2.0-7ubuntu1) ... 388s Selecting previously unselected package build-essential. 388s Preparing to unpack .../038-build-essential_12.10ubuntu1_ppc64el.deb ... 388s Unpacking build-essential (12.10ubuntu1) ... 388s Selecting previously unselected package cd-hit. 388s Preparing to unpack .../039-cd-hit_4.8.1-4_ppc64el.deb ... 388s Unpacking cd-hit (4.8.1-4) ... 388s Selecting previously unselected package libdebhelper-perl. 388s Preparing to unpack .../040-libdebhelper-perl_13.14.1ubuntu1_all.deb ... 388s Unpacking libdebhelper-perl (13.14.1ubuntu1) ... 388s Selecting previously unselected package libtool. 388s Preparing to unpack .../041-libtool_2.4.7-7_all.deb ... 388s Unpacking libtool (2.4.7-7) ... 388s Selecting previously unselected package dh-autoreconf. 388s Preparing to unpack .../042-dh-autoreconf_20_all.deb ... 388s Unpacking dh-autoreconf (20) ... 388s Selecting previously unselected package libarchive-zip-perl. 388s Preparing to unpack .../043-libarchive-zip-perl_1.68-1_all.deb ... 388s Unpacking libarchive-zip-perl (1.68-1) ... 388s Selecting previously unselected package libsub-override-perl. 388s Preparing to unpack .../044-libsub-override-perl_0.10-1_all.deb ... 388s Unpacking libsub-override-perl (0.10-1) ... 388s Selecting previously unselected package libfile-stripnondeterminism-perl. 388s Preparing to unpack .../045-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 388s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 388s Selecting previously unselected package dh-strip-nondeterminism. 388s Preparing to unpack .../046-dh-strip-nondeterminism_1.13.1-1_all.deb ... 388s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 388s Selecting previously unselected package libdw1:ppc64el. 388s Preparing to unpack .../047-libdw1_0.190-1_ppc64el.deb ... 388s Unpacking libdw1:ppc64el (0.190-1) ... 388s Selecting previously unselected package debugedit. 388s Preparing to unpack .../048-debugedit_1%3a5.0-5_ppc64el.deb ... 388s Unpacking debugedit (1:5.0-5) ... 388s Selecting previously unselected package dwz. 388s Preparing to unpack .../049-dwz_0.15-1_ppc64el.deb ... 388s Unpacking dwz (0.15-1) ... 388s Selecting previously unselected package gettext. 388s Preparing to unpack .../050-gettext_0.21-14ubuntu1_ppc64el.deb ... 388s Unpacking gettext (0.21-14ubuntu1) ... 388s Selecting previously unselected package intltool-debian. 388s Preparing to unpack .../051-intltool-debian_0.35.0+20060710.6_all.deb ... 388s Unpacking intltool-debian (0.35.0+20060710.6) ... 388s Selecting previously unselected package po-debconf. 388s Preparing to unpack .../052-po-debconf_1.0.21+nmu1_all.deb ... 388s Unpacking po-debconf (1.0.21+nmu1) ... 388s Selecting previously unselected package debhelper. 388s Preparing to unpack .../053-debhelper_13.14.1ubuntu1_all.deb ... 388s Unpacking debhelper (13.14.1ubuntu1) ... 388s Selecting previously unselected package dh-python. 388s Preparing to unpack .../054-dh-python_6.20231223ubuntu2_all.deb ... 388s Unpacking dh-python (6.20231223ubuntu2) ... 388s Selecting previously unselected package fonts-dejavu-mono. 388s Preparing to unpack .../055-fonts-dejavu-mono_2.37-8_all.deb ... 388s Unpacking fonts-dejavu-mono (2.37-8) ... 388s Selecting previously unselected package fonts-dejavu-core. 388s Preparing to unpack .../056-fonts-dejavu-core_2.37-8_all.deb ... 388s Unpacking fonts-dejavu-core (2.37-8) ... 388s Selecting previously unselected package libfontenc1:ppc64el. 388s Preparing to unpack .../057-libfontenc1_1%3a1.1.8-1_ppc64el.deb ... 388s Unpacking libfontenc1:ppc64el (1:1.1.8-1) ... 388s Selecting previously unselected package x11-common. 388s Preparing to unpack .../058-x11-common_1%3a7.7+23ubuntu2_all.deb ... 388s Unpacking x11-common (1:7.7+23ubuntu2) ... 388s Selecting previously unselected package xfonts-encodings. 388s Preparing to unpack .../059-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 388s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 388s Selecting previously unselected package xfonts-utils. 388s Preparing to unpack .../060-xfonts-utils_1%3a7.7+6build2_ppc64el.deb ... 388s Unpacking xfonts-utils (1:7.7+6build2) ... 388s Selecting previously unselected package fonts-urw-base35. 388s Preparing to unpack .../061-fonts-urw-base35_20200910-8_all.deb ... 388s Unpacking fonts-urw-base35 (20200910-8) ... 389s Selecting previously unselected package fontconfig-config. 389s Preparing to unpack .../062-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 389s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 389s Selecting previously unselected package fonts-dejavu-extra. 389s Preparing to unpack .../063-fonts-dejavu-extra_2.37-8_all.deb ... 389s Unpacking fonts-dejavu-extra (2.37-8) ... 389s Selecting previously unselected package libblas3:ppc64el. 389s Preparing to unpack .../064-libblas3_3.12.0-3_ppc64el.deb ... 389s Unpacking libblas3:ppc64el (3.12.0-3) ... 389s Selecting previously unselected package libfontconfig1:ppc64el. 389s Preparing to unpack .../065-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 389s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 389s Selecting previously unselected package libpixman-1-0:ppc64el. 389s Preparing to unpack .../066-libpixman-1-0_0.42.2-1_ppc64el.deb ... 389s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 389s Selecting previously unselected package libxcb-render0:ppc64el. 389s Preparing to unpack .../067-libxcb-render0_1.15-1_ppc64el.deb ... 389s Unpacking libxcb-render0:ppc64el (1.15-1) ... 389s Selecting previously unselected package libxcb-shm0:ppc64el. 389s Preparing to unpack .../068-libxcb-shm0_1.15-1_ppc64el.deb ... 389s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 389s Selecting previously unselected package libxrender1:ppc64el. 389s Preparing to unpack .../069-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 389s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 389s Selecting previously unselected package libcairo2:ppc64el. 389s Preparing to unpack .../070-libcairo2_1.18.0-1_ppc64el.deb ... 389s Unpacking libcairo2:ppc64el (1.18.0-1) ... 389s Selecting previously unselected package libdeflate0:ppc64el. 389s Preparing to unpack .../071-libdeflate0_1.19-1_ppc64el.deb ... 389s Unpacking libdeflate0:ppc64el (1.19-1) ... 389s Selecting previously unselected package libgfortran5:ppc64el. 389s Preparing to unpack .../072-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 389s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 389s Selecting previously unselected package libgraphite2-3:ppc64el. 389s Preparing to unpack .../073-libgraphite2-3_1.3.14-2_ppc64el.deb ... 389s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 389s Selecting previously unselected package libharfbuzz0b:ppc64el. 389s Preparing to unpack .../074-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 389s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 389s Selecting previously unselected package libimagequant0:ppc64el. 389s Preparing to unpack .../075-libimagequant0_2.18.0-1_ppc64el.deb ... 389s Unpacking libimagequant0:ppc64el (2.18.0-1) ... 389s Selecting previously unselected package libjpeg-turbo8:ppc64el. 389s Preparing to unpack .../076-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 389s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 389s Selecting previously unselected package libjpeg8:ppc64el. 389s Preparing to unpack .../077-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 389s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 389s Selecting previously unselected package liblapack3:ppc64el. 389s Preparing to unpack .../078-liblapack3_3.12.0-3_ppc64el.deb ... 389s Unpacking liblapack3:ppc64el (3.12.0-3) ... 389s Selecting previously unselected package liblbfgsb0:ppc64el. 389s Preparing to unpack .../079-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 389s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 389s Selecting previously unselected package liblcms2-2:ppc64el. 389s Preparing to unpack .../080-liblcms2-2_2.14-2_ppc64el.deb ... 389s Unpacking liblcms2-2:ppc64el (2.14-2) ... 389s Selecting previously unselected package liblerc4:ppc64el. 389s Preparing to unpack .../081-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 389s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 389s Selecting previously unselected package libmbedcrypto7:ppc64el. 389s Preparing to unpack .../082-libmbedcrypto7_2.28.7-1ubuntu1_ppc64el.deb ... 389s Unpacking libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 389s Selecting previously unselected package libmbedx509-1:ppc64el. 389s Preparing to unpack .../083-libmbedx509-1_2.28.7-1ubuntu1_ppc64el.deb ... 389s Unpacking libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 389s Selecting previously unselected package libmbedtls14:ppc64el. 389s Preparing to unpack .../084-libmbedtls14_2.28.7-1ubuntu1_ppc64el.deb ... 389s Unpacking libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 389s Selecting previously unselected package libraqm0:ppc64el. 389s Preparing to unpack .../085-libraqm0_0.10.1-1_ppc64el.deb ... 389s Unpacking libraqm0:ppc64el (0.10.1-1) ... 389s Selecting previously unselected package libsharpyuv0:ppc64el. 389s Preparing to unpack .../086-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 389s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 389s Selecting previously unselected package libjbig0:ppc64el. 389s Preparing to unpack .../087-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 389s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 389s Selecting previously unselected package libwebp7:ppc64el. 389s Preparing to unpack .../088-libwebp7_1.3.2-0.4_ppc64el.deb ... 389s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 389s Selecting previously unselected package libtiff6:ppc64el. 389s Preparing to unpack .../089-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 389s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 389s Selecting previously unselected package libwebpdemux2:ppc64el. 389s Preparing to unpack .../090-libwebpdemux2_1.3.2-0.4_ppc64el.deb ... 389s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4) ... 389s Selecting previously unselected package libwebpmux3:ppc64el. 389s Preparing to unpack .../091-libwebpmux3_1.3.2-0.4_ppc64el.deb ... 389s Unpacking libwebpmux3:ppc64el (1.3.2-0.4) ... 389s Selecting previously unselected package ncbi-data. 389s Preparing to unpack .../092-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 389s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 390s Selecting previously unselected package ncbi-blast+. 390s Preparing to unpack .../093-ncbi-blast+_2.12.0+ds-4_ppc64el.deb ... 390s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 390s Selecting previously unselected package python3-numpy. 390s Preparing to unpack .../094-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 390s Unpacking python3-numpy (1:1.24.2-2) ... 390s Selecting previously unselected package libopenjp2-7:ppc64el. 390s Preparing to unpack .../095-libopenjp2-7_2.5.0-2_ppc64el.deb ... 390s Unpacking libopenjp2-7:ppc64el (2.5.0-2) ... 390s Selecting previously unselected package python3-pil:ppc64el. 390s Preparing to unpack .../096-python3-pil_10.2.0-1_ppc64el.deb ... 390s Unpacking python3-pil:ppc64el (10.2.0-1) ... 390s Selecting previously unselected package python3-cairo. 390s Preparing to unpack .../097-python3-cairo_1.25.1-2_ppc64el.deb ... 390s Unpacking python3-cairo (1.25.1-2) ... 390s Selecting previously unselected package python3-freetype. 390s Preparing to unpack .../098-python3-freetype_2.4.0-1_all.deb ... 390s Unpacking python3-freetype (2.4.0-1) ... 390s Selecting previously unselected package python3-rlpycairo. 390s Preparing to unpack .../099-python3-rlpycairo_0.3.0-3_all.deb ... 390s Unpacking python3-rlpycairo (0.3.0-3) ... 390s Selecting previously unselected package python3-reportlab. 390s Preparing to unpack .../100-python3-reportlab_4.1.0-1_all.deb ... 390s Unpacking python3-reportlab (4.1.0-1) ... 390s Selecting previously unselected package xml-core. 390s Preparing to unpack .../101-xml-core_0.19_all.deb ... 390s Unpacking xml-core (0.19) ... 391s Selecting previously unselected package w3c-sgml-lib. 391s Preparing to unpack .../102-w3c-sgml-lib_1.3-3_all.deb ... 391s Unpacking w3c-sgml-lib (1.3-3) ... 391s Selecting previously unselected package python3-biopython. 391s Preparing to unpack .../103-python3-biopython_1.81+dfsg-3_ppc64el.deb ... 391s Unpacking python3-biopython (1.81+dfsg-3) ... 391s Selecting previously unselected package python3-dateutil. 391s Preparing to unpack .../104-python3-dateutil_2.8.2-3_all.deb ... 391s Unpacking python3-dateutil (2.8.2-3) ... 391s Selecting previously unselected package python3-pandas-lib:ppc64el. 391s Preparing to unpack .../105-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 391s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 391s Selecting previously unselected package python3-pandas. 391s Preparing to unpack .../106-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 391s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 391s Selecting previously unselected package python3-decorator. 391s Preparing to unpack .../107-python3-decorator_5.1.1-5_all.deb ... 391s Unpacking python3-decorator (5.1.1-5) ... 392s Selecting previously unselected package python3-scipy. 392s Preparing to unpack .../108-python3-scipy_1.11.4-6_ppc64el.deb ... 392s Unpacking python3-scipy (1.11.4-6) ... 393s Selecting previously unselected package python3-packaging. 393s Preparing to unpack .../109-python3-packaging_23.2-1_all.deb ... 393s Unpacking python3-packaging (23.2-1) ... 393s Selecting previously unselected package vsearch. 393s Preparing to unpack .../110-vsearch_2.27.0-1_ppc64el.deb ... 393s Unpacking vsearch (2.27.0-1) ... 393s Selecting previously unselected package python3-presto. 393s Preparing to unpack .../111-python3-presto_0.7.2-1_ppc64el.deb ... 393s Unpacking python3-presto (0.7.2-1) ... 393s Selecting previously unselected package presto. 393s Preparing to unpack .../112-presto_0.7.2-1_all.deb ... 393s Unpacking presto (0.7.2-1) ... 393s Selecting previously unselected package pybuild-plugin-autopkgtest. 393s Preparing to unpack .../113-pybuild-plugin-autopkgtest_6.20231223ubuntu2_all.deb ... 393s Unpacking pybuild-plugin-autopkgtest (6.20231223ubuntu2) ... 393s Selecting previously unselected package python3-all. 393s Preparing to unpack .../114-python3-all_3.12.1-0ubuntu2_ppc64el.deb ... 393s Unpacking python3-all (3.12.1-0ubuntu2) ... 393s Selecting previously unselected package autopkgtest-satdep. 393s Preparing to unpack .../115-1-autopkgtest-satdep.deb ... 393s Unpacking autopkgtest-satdep (0) ... 393s Setting up dh-python (6.20231223ubuntu2) ... 393s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 393s Setting up liblcms2-2:ppc64el (2.14-2) ... 393s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 393s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 393s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 393s Setting up libdw1:ppc64el (0.190-1) ... 393s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 393s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 393s Setting up libxcb-render0:ppc64el (1.15-1) ... 393s Setting up libarchive-zip-perl (1.68-1) ... 393s Setting up vsearch (2.27.0-1) ... 393s Setting up libdebhelper-perl (13.14.1ubuntu1) ... 393s Setting up x11-common (1:7.7+23ubuntu2) ... 393s Setting up libdeflate0:ppc64el (1.19-1) ... 393s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 393s Setting up m4 (1.4.19-4) ... 393s Setting up python3-all (3.12.1-0ubuntu2) ... 393s Setting up libxcb-shm0:ppc64el (1.15-1) ... 393s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 393s Setting up python3-freetype (2.4.0-1) ... 394s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 394s Setting up python3-decorator (5.1.1-5) ... 394s Setting up libfontenc1:ppc64el (1:1.1.8-1) ... 394s Setting up autotools-dev (20220109.1) ... 394s Setting up libblas3:ppc64el (3.12.0-3) ... 394s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 394s Setting up python3-packaging (23.2-1) ... 394s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 394s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 394s Setting up libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 394s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 394s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up libimagequant0:ppc64el (2.18.0-1) ... 394s Setting up fonts-dejavu-mono (2.37-8) ... 394s Setting up libmpc3:ppc64el (1.3.1-1) ... 394s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up autopoint (0.21-14ubuntu1) ... 394s Setting up fonts-dejavu-core (2.37-8) ... 394s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 394s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up autoconf (2.71-3) ... 394s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 394s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up fonts-dejavu-extra (2.37-8) ... 394s Setting up dwz (0.15-1) ... 394s Setting up libnsl-dev:ppc64el (1.3.0-3) ... 394s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 394s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up debugedit (1:5.0-5) ... 394s Setting up libopenjp2-7:ppc64el (2.5.0-2) ... 394s Setting up libsub-override-perl (0.10-1) ... 394s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 394s Setting up python3-dateutil (2.8.2-3) ... 394s Setting up sgml-base (1.31) ... 394s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up libisl23:ppc64el (0.26-3) ... 394s Setting up libc-dev-bin (2.39-0ubuntu2) ... 394s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 394s Setting up libwebpmux3:ppc64el (1.3.2-0.4) ... 394s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 394s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 394s Setting up cd-hit (4.8.1-4) ... 394s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 394s Setting up automake (1:1.16.5-1.3ubuntu1) ... 394s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 394s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 394s Setting up liblapack3:ppc64el (3.12.0-3) ... 394s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 394s Setting up gettext (0.21-14ubuntu1) ... 394s Setting up libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 394s Setting up libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 394s Setting up cpp-13 (13.2.0-17ubuntu2) ... 394s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 394s Setting up libwebpdemux2:ppc64el (1.3.2-0.4) ... 394s Setting up xfonts-utils (1:7.7+6build2) ... 394s Setting up intltool-debian (0.35.0+20060710.6) ... 394s Setting up ncbi-blast+ (2.12.0+ds-4) ... 394s Setting up libraqm0:ppc64el (0.10.1-1) ... 394s Setting up python3-numpy (1:1.24.2-2) ... 396s Setting up dh-strip-nondeterminism (1.13.1-1) ... 396s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 396s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 396s Setting up cpp (4:13.2.0-7ubuntu1) ... 396s Setting up xml-core (0.19) ... 397s Setting up libc6-dev:ppc64el (2.39-0ubuntu2) ... 397s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 397s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 397s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 397s Setting up python3-scipy (1.11.4-6) ... 400s Setting up po-debconf (1.0.21+nmu1) ... 400s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 400s Setting up fonts-urw-base35 (20200910-8) ... 400s Setting up libcairo2:ppc64el (1.18.0-1) ... 400s Setting up python3-pil:ppc64el (10.2.0-1) ... 400s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 405s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 405s Setting up gcc-13 (13.2.0-17ubuntu2) ... 405s Setting up python3-cairo (1.25.1-2) ... 405s Setting up libtool (2.4.7-7) ... 405s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 405s Setting up dh-autoreconf (20) ... 405s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 405s Setting up python3-rlpycairo (0.3.0-3) ... 405s Setting up python3-reportlab (4.1.0-1) ... 406s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 406s Setting up g++-13 (13.2.0-17ubuntu2) ... 406s Setting up debhelper (13.14.1ubuntu1) ... 406s Setting up gcc (4:13.2.0-7ubuntu1) ... 406s Setting up g++ (4:13.2.0-7ubuntu1) ... 406s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 406s Setting up build-essential (12.10ubuntu1) ... 406s Setting up pybuild-plugin-autopkgtest (6.20231223ubuntu2) ... 406s Processing triggers for libc-bin (2.39-0ubuntu2) ... 406s Processing triggers for man-db (2.12.0-3) ... 408s Processing triggers for install-info (7.1-3) ... 408s Processing triggers for sgml-base (1.31) ... 408s Setting up w3c-sgml-lib (1.3-3) ... 437s Setting up python3-biopython (1.81+dfsg-3) ... 438s Setting up python3-presto (0.7.2-1) ... 438s /usr/lib/python3/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' 438s sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) 438s /usr/lib/python3/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' 438s sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) 438s /usr/lib/python3/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' 438s header['SPECIES'] = re.sub('\s', '_', fields[2]) 438s /usr/lib/python3/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' 438s header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) 438s /usr/lib/python3/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' 438s header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' 438s /usr/lib/python3/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' 438s version = re.sub('\.linux.*$','',version) 438s /usr/lib/python3/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' 438s id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') 438s /usr/lib/python3/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' 438s if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) 438s Setting up presto (0.7.2-1) ... 438s Setting up autopkgtest-satdep (0) ... 441s (Reading database ... 80648 files and directories currently installed.) 441s Removing autopkgtest-satdep (0) ... 442s autopkgtest [18:29:43]: test pybuild-autopkgtest: pybuild-autopkgtest 442s autopkgtest [18:29:43]: test pybuild-autopkgtest: [----------------------- 442s pybuild-autopkgtest 443s I: pybuild pybuild:310: cp -r /tmp/autopkgtest.WRhFYi/build.nrF/src/bin /tmp/autopkgtest.WRhFYi/autopkgtest_tmp/build; rm /tmp/autopkgtest.WRhFYi/build.nrF/src/tests/test_ClusterSets.py || echo "Test file already removed or moved"; 443s I: pybuild base:305: cd /tmp/autopkgtest.WRhFYi/autopkgtest_tmp/build; python3.12 -m unittest discover -v 444s test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok 444s test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok 444s test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok 444s test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok 444s test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' 444s test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' 444s test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' 444s test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' 444s test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' 444s test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' 444s test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok 444s test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok 444s test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok 444s test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok 444s test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok 444s test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok 444s test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok 444s test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok 444s test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok 444s test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok 444s test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok 444s test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok 444s test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... ok 444s test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok 444s test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok 444s test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok 444s test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok 444s test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... ok 444s test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok 444s test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok 444s test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok 444s test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok 444s test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok 444s test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok 444s test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... ok 444s -> test_collapseAnnotation() 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) 444s <- test_collapseAnnotation() 0.000 444s -> test_getCoordKey() 444s ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] 444s ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] 444s ['000034_0199_0169', 'GXGJ56Z01AE06X'] 444s <- test_getCoordKey() 0.000 444s -> test_mergeAnnotation() 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) 444s <- test_mergeAnnotation() 0.000 444s -> test_renameAnnotation() 444s OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) 444s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) 444s <- test_renameAnnotation() 0.000 444s -> test_calculateSetError() 444s Frequency consensus error> 444s REF> CGGCGTAA 444s SEQ1> CGGCGTAA 444s SEQ2> CCNNGTAA 444s SEQ3> CGGC--TA 444s SEQ4> CGNN--TA 444s SEQ5> CGGC--AA 444s ERROR> 0.250000 444s Quality consensus error> 444s REF> CGGCNNAA 444s SEQ1> CGGCGTAA 444s SEQ2> CCNNGTAA 444s SEQ3> CGGC--TA 444s SEQ4> CGNN--TA 444s SEQ5> CGGC--AA 444s ERROR> 0.233333 444s <- test_calculateSetError() 0.000 444s -> test_deleteSeqPositions() 444s MAX_GAP=0.4> CGGCAA 444s MAX_GAP=0.8> CGGCGTAA 444s <- test_deleteSeqPositions() 0.000 444s -> test_findGapPositions() 444s MAX_GAP=0.4> [4, 5] 444s MAX_GAP=0.8> [] 444s <- test_findGapPositions() 0.000 444s -> test_frequencyConsensus() 444s MIN_FREQ=0.2> CGGCGTAA 444s MIN_FREQ=0.8> CGGCGTNA 444s <- test_frequencyConsensus() 0.000 444s -> test_qualityConsensus() 444s MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] 444s MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] 444s MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] 444s <- test_qualityConsensus() 0.000 444s -> test_checkSeqEqual() 444s DNA Equality> 444s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 444s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 444s EQUAL> True 444s 444s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 444s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 444s EQUAL> False 444s 444s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 444s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 444s EQUAL> True 444s 444s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 444s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 444s EQUAL> False 444s 444s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 444s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 444s EQUAL> True 444s 444s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 444s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 444s EQUAL> True 444s 444s <- test_checkSeqEqual() 0.000 444s -> test_convert454Header() 444s OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) 444s OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) 444s <- test_convert454Header() 0.000 444s -> test_convertGenbankHeader() 444s OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 444s OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) 444s <- test_convertGenbankHeader() 0.000 444s -> test_convertGenericHeader() 444s OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 444s OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 444s OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) 444s 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'_"}) 444s 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_'}) 444s OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) 444s <- test_convertGenericHeader() 0.000 444s -> test_convertIMGTHeader() 444s OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) 444s OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) 444s OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) 444s OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) 444s OrderedDict({'ID': 'IGHV1-18*01'}) 444s OrderedDict({'ID': 'IGHV1-69*07'}) 444s OrderedDict({'ID': 'IGHV(III)-22-2*01'}) 444s OrderedDict({'ID': 'TRAV11*01'}) 444s <- test_convertIMGTHeader() 0.000 444s -> test_convertIlluminaHeader() 444s OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) 444s OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) 444s OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) 444s <- test_convertIlluminaHeader() 0.000 444s -> test_convertSRAHeader() 444s OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) 444s OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) 444s OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) 444s OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) 444s OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) 444s <- test_convertSRAHeader() 0.000 444s -> test_calculateDistances() 444s <- test_calculateDistances() 0.001 444s -> test_countMismatches() 444s <- test_countMismatches() 0.002 444s -> test_initializeMismatchDictionary() 444s <- test_initializeMismatchDictionary() 0.000 444s -> test_getFileType() 444s <- test_getFileType() 0.000 444s -> test_extractAlignment() 444s SEQ1> 444s SEQ> CCACGTTTTAGTAATTAATA 444s ALN-SEQ> CCACGTTTTAGT 444s ALN-PR> ----GTTTTAGT 444s PRIMER> GTTTTAGT 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ2> 444s SEQ> CCNCGTTTTAGTAATTAATA 444s ALN-SEQ> CCNCGTTTTAGT 444s ALN-PR> ----GTTTTAGT 444s PRIMER> GTTTTAGT 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ3> 444s SEQ> GGGCGTTTTAGTAATTAATA 444s ALN-SEQ> GGGCGTTTTAGT 444s ALN-PR> ----GTTTTAGT 444s PRIMER> GTTTTAGT 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ4> 444s SEQ> GGNNGTTTTACTAATTAATA 444s ALN-SEQ> GGNNGTTTTACT 444s ALN-PR> ----GTTTTACT 444s PRIMER> GTTTTACT 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ5> 444s SEQ> NNGCNNNNNACTAATTAATA 444s ALN-SEQ> NNGCNNNNNACT 444s ALN-PR> ----NNNNNACT 444s PRIMER> NNNNNACT 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ6> 444s SEQ> GGGATANNNACTAATTAATA 444s ALN-SEQ> GGGATANNNACT 444s ALN-PR> ----TANNNACT 444s PRIMER> TANNNACT 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ7> 444s SEQ> NNNNNNNNNNNNNNNNNNNN 444s ALN-SEQ> NNNNNNNNNNNN 444s ALN-PR> ----NNNNNNNN 444s PRIMER> NNNNNNNN 444s START> 4 444s END> 12 444s GAPS> 0 444s ERROR> 0.000000 444s 444s <- test_extractAlignment() 0.000 444s -> test_localAlignment() 444s TEST Ns> 444s SEQ1> 444s SEQ> CCACGTTTTAGTAATTAATA 444s ALN-SEQ> CCACGTTTTAGTAATTAATA 444s ALN-PR> -CACGTTTT----------- 444s PRIMER> PR1 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ2> 444s SEQ> CCNCGTTTTAGTAATTAATA 444s ALN-SEQ> CCNCGTTTTAGTAATTAATA 444s ALN-PR> -CACGTTTT----------- 444s PRIMER> PR1 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.125000 444s 444s SEQ3> 444s SEQ> GGGCGTTTTAGTAATTAATA 444s ALN-SEQ> GGGCGTTTTAGTAATTAATA 444s ALN-PR> -GGCGTTTT----------- 444s PRIMER> PR2 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ4> 444s SEQ> GGNNGTTTTACTAATTAATA 444s ALN-SEQ> GGNNGTTTTACTAATTAATA 444s ALN-PR> GGC-GTTTT----------- 444s PRIMER> PR2 444s START> 0 444s END> 9 444s GAPS> 1 444s test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok 444s test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok 444s test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok 444s 444s ---------------------------------------------------------------------- 444s Ran 38 tests in 0.062s 444s 444s OK (skipped=6) 444s ERROR> 0.250000 444s 444s SEQ5> 444s SEQ> NNGCNNNNNACTAATTAATA 444s ALN-SEQ> NNGCNNNNNACTAATTAATA 444s ALN-PR> ------------ANATAA-- 444s PRIMER> PR3 444s START> 12 444s END> 18 444s GAPS> 0 444s ERROR> 0.375000 444s 444s SEQ6> 444s SEQ> GGGATANNNACTAATTAATA 444s ALN-SEQ> GGGATANNNACTAATTAATA 444s ALN-PR> -GGANA-------------- 444s PRIMER> PR3 444s START> 1 444s END> 6 444s GAPS> 0 444s ERROR> 0.375000 444s 444s SEQ7> 444s SEQ> NNNNNNNNNNNNNNNNNNNN 444s ALN-SEQ> None 444s ALN-PR> None 444s PRIMER> None 444s START> None 444s END> None 444s GAPS> 0 444s ERROR> 1.000000 444s 444s TEST INDELS> 444s SEQ1> 444s SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG 444s ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG 444s ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ 444s PRIMER> PR1 444s START> 15 444s END> 38 444s GAPS> 0 444s ERROR> 0.083333 444s 444s SEQ2> 444s SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG 444s ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG 444s ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ 444s PRIMER> PR1 444s START> 14 444s END> 38 444s GAPS> 2 444s ERROR> 0.208333 444s 444s SEQ3> 444s SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG 444s ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG 444s ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ 444s PRIMER> PR1 444s START> 15 444s END> 38 444s GAPS> 1 444s ERROR> 0.125000 444s 444s SEQ4> 444s SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT 444s ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT 444s ALN-PR> ------CATCT-TCCTCTA------------------------------------------- 444s PRIMER> PR2 444s START> 6 444s END> 19 444s GAPS> 1 444s ERROR> 0.250000 444s 444s SEQ5> 444s SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG 444s ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG 444s ALN-PR> ------CATCTTCCTCTA-------------------------------------------- 444s PRIMER> PR2 444s START> 6 444s END> 18 444s GAPS> 0 444s ERROR> 0.166667 444s 444s SEQ6> 444s SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA 444s ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA 444s ALN-PR> TCT-TCCTCTA--------------------------------------------------- 444s PRIMER> PR2 444s START> 0 444s END> 11 444s GAPS> 1 444s ERROR> 0.250000 444s 444s SEQ7> 444s SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 444s ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 444s ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- 444s PRIMER> PR3 444s START> 2 444s END> 15 444s GAPS> 1 444s ERROR> 0.083333 444s 444s SEQ8> 444s SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 444s ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 444s ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- 444s PRIMER> PR3 444s START> 3 444s END> 15 444s GAPS> 1 444s ERROR> 0.166667 444s 444s SEQ9> 444s SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 444s ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 444s ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- 444s PRIMER> PR3 444s START> 3 444s END> 15 444s GAPS> 1 444s ERROR> 0.333333 444s 444s SEQ10> 444s SEQ> -------------------------------------------------------------- 444s ALN-SEQ> None 444s ALN-PR> None 444s PRIMER> None 444s START> None 444s END> None 444s GAPS> 0 444s ERROR> 1.000000 444s 444s <- test_localAlignment() 0.031 444s -> test_maskSeq() 444s TEST CUT> 444s ID> SEQ|PRIMER=A|BARCODE=CCA 444s SEQ> AGTAATTAATA 444s 444s TEST MASK> 444s ID> SEQ|PRIMER=A|BARCODE=CCA 444s SEQ> NNNNNNAGTAATTAATA 444s 444s TEST TRIM> 444s ID> SEQ|PRIMER=A|BARCODE=CCA 444s SEQ> CGTTTTAGTAATTAATA 444s 444s TEST TAG> 444s ID> SEQ|PRIMER=A|BARCODE=CCA 444s SEQ> CCACGTTTTAGTAATTAATA 444s 444s <- test_maskSeq() 0.002 444s -> test_scoreAlignment() 444s SEQ1> 444s SEQ> CCACGTTTTAGTAATTAATA 444s ALN-SEQ> CCACGTTTT 444s ALN-PR> -CACGTTTT 444s PRIMER> PR1 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ2> 444s SEQ> CCNCGTTTTAGTAATTAATA 444s ALN-SEQ> CCNCGTTTT 444s ALN-PR> -CACGTTTT 444s PRIMER> PR1 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.125000 444s 444s SEQ3> 444s SEQ> GGGCGTTTTAGTAATTAATA 444s ALN-SEQ> GGGCGTTTT 444s ALN-PR> -GGCGTTTT 444s PRIMER> PR2 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.000000 444s 444s SEQ4> 444s SEQ> GGNNGTTTTACTAATTAATA 444s ALN-SEQ> GGNNGTTTT 444s ALN-PR> -GGCGTTTT 444s PRIMER> PR2 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.250000 444s 444s SEQ5> 444s SEQ> NNGCNNNNNACTAATTAATA 444s ALN-SEQ> NNGCNNNNN 444s ALN-PR> -GGCGTTTT 444s PRIMER> PR2 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.750000 444s 444s SEQ6> 444s SEQ> GGGATANNNACTAATTAATA 444s ALN-SEQ> GGGATANNN 444s ALN-PR> -GGANATAA 444s PRIMER> PR3 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 0.375000 444s 444s SEQ7> 444s SEQ> NNNNNNNNNNNNNNNNNNNN 444s ALN-SEQ> NNNNNNNNN 444s ALN-PR> -CACGTTTT 444s PRIMER> None 444s START> 1 444s END> 9 444s GAPS> 0 444s ERROR> 1.000000 444s 444s <- test_scoreAlignment() 0.010 444s -> test_calculateSetError() 444s REF> CGGCGTAA 0.4347826086956522 444s REF> NNNNNNNN 1.0 444s <- test_calculateSetError() 0.000 444s -> test_filterQuality() 444s RESULT> True 25 444s RESULT> False 5 444s RESULT> False 0 444s <- test_filterQuality() 0.000 444s -> test_meanQuality() 444s RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] 444s RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] 444s RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] 444s <- test_meanQuality() 0.000 444s -> test_scoreDNA() 444s Default DNA Scores> 444s A==A> 1 444s A==T> 0 444s A==R> 1 444s U==T> 1 444s A==N> 1 444s N==A> 1 444s A==-> 0 444s -==A> 0 444s Symmetric DNA Scores> 444s A==A> 1 444s A==T> 0 444s A==R> 1 444s U==T> 1 444s A==N> 1 444s N==A> 1 444s A==-> 1 444s -==A> 1 444s Asymmetric DNA Scores> 444s A==A> 1 444s A==T> 0 444s A==R> 1 444s U==T> 1 444s A==N> 1 444s N==A> 0 444s A==-> 1 444s -==A> 0 444s <- test_scoreDNA() 0.000 444s -> test_scoreSeqPair() 444s Default DNA Scores> 444s SEQ1> CGGCGTAA 444s SEQ2> CGNNGTAG 444s SCORE> 7 444s WEIGHT> 8 444s ERROR> 0.125000 444s 444s SEQ1> CGGCGTAA 444s SEQ3> CGGC--AA 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ1> CGGCGTAA 444s SEQ4> CGNN--AG 444s SCORE> 5 444s WEIGHT> 8 444s ERROR> 0.375000 444s 444s SEQ1> CGGCGTAA 444s SEQ5> NNNNNNNN 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ6> NNNNNNAA 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ2> CGNNGTAG 444s SEQ3> CGGC--AA 444s SCORE> 5 444s WEIGHT> 8 444s ERROR> 0.375000 444s 444s SEQ2> CGNNGTAG 444s SEQ4> CGNN--AG 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ2> CGNNGTAG 444s SEQ5> NNNNNNNN 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ2> CGNNGTAG 444s SEQ6> NNNNNNAA 444s SCORE> 7 444s WEIGHT> 8 444s ERROR> 0.125000 444s 444s SEQ2> CGNNGTAG 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ2> CGNNGTAG 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ3> CGGC--AA 444s SEQ4> CGNN--AG 444s SCORE> 7 444s WEIGHT> 8 444s ERROR> 0.125000 444s 444s SEQ3> CGGC--AA 444s SEQ5> NNNNNNNN 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ3> CGGC--AA 444s SEQ6> NNNNNNAA 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ3> CGGC--AA 444s SEQ7> -------- 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ3> CGGC--AA 444s SEQ8> CG------ 444s SCORE> 4 444s WEIGHT> 8 444s ERROR> 0.500000 444s 444s SEQ4> CGNN--AG 444s SEQ5> NNNNNNNN 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ4> CGNN--AG 444s SEQ6> NNNNNNAA 444s SCORE> 5 444s WEIGHT> 8 444s ERROR> 0.375000 444s 444s SEQ4> CGNN--AG 444s SEQ7> -------- 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ4> CGNN--AG 444s SEQ8> CG------ 444s SCORE> 4 444s WEIGHT> 8 444s ERROR> 0.500000 444s 444s SEQ5> NNNNNNNN 444s SEQ6> NNNNNNAA 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ5> NNNNNNNN 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ5> NNNNNNNN 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ6> NNNNNNAA 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ6> NNNNNNAA 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ7> -------- 444s SEQ8> CG------ 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s Asymmetric DNA Scores> 444s SEQ1> CGGCGTAA 444s SEQ2> CGNNGTAG 444s SCORE> 7 444s WEIGHT> 8 444s ERROR> 0.125000 444s 444s SEQ1> CGGCGTAA 444s SEQ3> CGGC--AA 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ4> CGNN--AG 444s SCORE> 7 444s WEIGHT> 8 444s ERROR> 0.125000 444s 444s SEQ1> CGGCGTAA 444s SEQ5> NNNNNNNN 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ6> NNNNNNAA 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ7> -------- 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ8> CG------ 444s SCORE> 8 444s WEIGHT> 8 444s ERROR> 0.000000 444s 444s SEQ2> CGNNGTAG 444s SEQ3> CGGC--AA 444s SCORE> 5 444s WEIGHT> 8 444s ERROR> 0.375000 444s 444s SEQ2> CGNNGTAG 444s SEQ4> CGNN--AG 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ2> CGNNGTAG 444s SEQ5> NNNNNNNN 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ2> CGNNGTAG 444s SEQ6> NNNNNNAA 444s SCORE> 5 444s WEIGHT> 8 444s ERROR> 0.375000 444s 444s SEQ2> CGNNGTAG 444s SEQ7> -------- 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ2> CGNNGTAG 444s SEQ8> CG------ 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ3> CGGC--AA 444s SEQ4> CGNN--AG 444s SCORE> 5 444s WEIGHT> 8 444s ERROR> 0.375000 444s 444s SEQ3> CGGC--AA 444s SEQ5> NNNNNNNN 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ3> CGGC--AA 444s SEQ6> NNNNNNAA 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ3> CGGC--AA 444s SEQ7> -------- 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ3> CGGC--AA 444s SEQ8> CG------ 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ4> CGNN--AG 444s SEQ5> NNNNNNNN 444s SCORE> 4 444s WEIGHT> 8 444s ERROR> 0.500000 444s 444s SEQ4> CGNN--AG 444s SEQ6> NNNNNNAA 444s SCORE> 3 444s WEIGHT> 8 444s ERROR> 0.625000 444s 444s SEQ4> CGNN--AG 444s SEQ7> -------- 444s SCORE> 4 444s WEIGHT> 8 444s ERROR> 0.500000 444s 444s SEQ4> CGNN--AG 444s SEQ8> CG------ 444s SCORE> 4 444s WEIGHT> 8 444s ERROR> 0.500000 444s 444s SEQ5> NNNNNNNN 444s SEQ6> NNNNNNAA 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ5> NNNNNNNN 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ5> NNNNNNNN 444s SEQ8> CG------ 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ6> NNNNNNAA 444s SEQ7> -------- 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ6> NNNNNNAA 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ7> -------- 444s SEQ8> CG------ 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s Masked DNA Scores> 444s SEQ1> CGGCGTAA 444s SEQ2> CGNNGTAG 444s SCORE> 5 444s WEIGHT> 6 444s ERROR> 0.166667 444s 444s SEQ1> CGGCGTAA 444s SEQ3> CGGC--AA 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s SEQ1> CGGCGTAA 444s SEQ4> CGNN--AG 444s SCORE> 3 444s WEIGHT> 6 444s ERROR> 0.500000 444s 444s SEQ1> CGGCGTAA 444s SEQ5> NNNNNNNN 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ6> NNNNNNAA 444s SCORE> 2 444s WEIGHT> 2 444s ERROR> 0.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 8 444s ERROR> 1.000000 444s 444s SEQ1> CGGCGTAA 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ2> CGNNGTAG 444s SEQ3> CGGC--AA 444s SCORE> 3 444s WEIGHT> 6 444s ERROR> 0.500000 444s 444s SEQ2> CGNNGTAG 444s SEQ4> CGNN--AG 444s SCORE> 4 444s WEIGHT> 6 444s ERROR> 0.333333 444s 444s SEQ2> CGNNGTAG 444s SEQ5> NNNNNNNN 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ2> CGNNGTAG 444s SEQ6> NNNNNNAA 444s SCORE> 1 444s WEIGHT> 2 444s ERROR> 0.500000 444s 444s SEQ2> CGNNGTAG 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 6 444s ERROR> 1.000000 444s 444s SEQ2> CGNNGTAG 444s SEQ8> CG------ 444s SCORE> 2 444s WEIGHT> 6 444s ERROR> 0.666667 444s 444s SEQ3> CGGC--AA 444s SEQ4> CGNN--AG 444s SCORE> 5 444s WEIGHT> 6 444s ERROR> 0.166667 444s 444s SEQ3> CGGC--AA 444s SEQ5> NNNNNNNN 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ3> CGGC--AA 444s SEQ6> NNNNNNAA 444s SCORE> 2 444s WEIGHT> 2 444s ERROR> 0.000000 444s 444s SEQ3> CGGC--AA 444s SEQ7> -------- 444s SCORE> 2 444s WEIGHT> 8 444s ERROR> 0.750000 444s 444s SEQ3> CGGC--AA 444s SEQ8> CG------ 444s SCORE> 4 444s WEIGHT> 8 444s ERROR> 0.500000 444s 444s SEQ4> CGNN--AG 444s SEQ5> NNNNNNNN 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ4> CGNN--AG 444s SEQ6> NNNNNNAA 444s SCORE> 1 444s WEIGHT> 2 444s ERROR> 0.500000 444s 444s SEQ4> CGNN--AG 444s SEQ7> -------- 444s SCORE> 2 444s WEIGHT> 6 444s ERROR> 0.666667 444s 444s SEQ4> CGNN--AG 444s SEQ8> CG------ 444s SCORE> 4 444s WEIGHT> 6 444s ERROR> 0.333333 444s 444s SEQ5> NNNNNNNN 444s SEQ6> NNNNNNAA 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ5> NNNNNNNN 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ5> NNNNNNNN 444s SEQ8> CG------ 444s SCORE> 0 444s WEIGHT> 0 444s ERROR> 1.000000 444s 444s SEQ6> NNNNNNAA 444s SEQ7> -------- 444s SCORE> 0 444s WEIGHT> 2 444s ERROR> 1.000000 444s 444s SEQ6> NNNNNNAA 444s SEQ8> CG------ 444s SCORE> 0 444s WEIGHT> 2 444s ERROR> 1.000000 444s 444s SEQ7> -------- 444s SEQ8> CG------ 444s SCORE> 6 444s WEIGHT> 8 444s ERROR> 0.250000 444s 444s <- test_scoreSeqPair() 0.007 444s -> test_weightDNA() 444s DNA Weight> 444s SEQ1> 8 444s SEQ2> 6 444s SEQ3> 8 444s SEQ4> 6 444s SEQ5> 0 444s SEQ6> 2 444s SEQ7> 8 444s SEQ8> 8 444s AA Weight> 444s SEQ1> 8 444s SEQ2> 6 444s SEQ3> 8 444s SEQ4> 6 444s <- test_weightDNA() 0.000 444s -> test_consensusUnify() 444s ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 444s ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 444s ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 444s ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 444s ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 444s ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 444s ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 444s ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 444s <- test_consensusUnify() 0.001 444s -> test_deletionUnify() 444s ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False 444s ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False 444s ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False 444s ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False 444s ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False 444s ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False 444s ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True 444s ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True 444s <- test_deletionUnify() 0.000 444s autopkgtest [18:29:45]: test pybuild-autopkgtest: -----------------------] 445s autopkgtest [18:29:46]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 445s pybuild-autopkgtest PASS 445s autopkgtest [18:29:46]: @@@@@@@@@@@@@@@@@@@@ summary 445s pybuild-autopkgtest PASS 459s Creating nova instance adt-noble-ppc64el-presto-20240318-182220-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240316.img (UUID 1492b190-05c5-462d-b1de-84bc330afe32)...