0s autopkgtest [10:36:22]: starting date and time: 2025-11-01 10:36:22+0000 0s autopkgtest [10:36:22]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [10:36:22]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dm2r5paw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scipy --apt-upgrade presto --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scipy/1.16.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-2.secgroup --name adt-resolute-s390x-presto-20251101-103622-juju-7f2275-prod-proposed-migration-environment-15-af6e60bd-1653-4c5e-aa03-4334b8519f08 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-presto-20251101-103622-juju-7f2275-prod-proposed-migration-environment-15-af6e60bd-1653-4c5e-aa03-4334b8519f08 from image adt/ubuntu-resolute-s390x-server-20251031.img (UUID 0c045c9f-9f12-44be-973b-1d1fecbe207a)... 46s autopkgtest [10:37:08]: testbed dpkg architecture: s390x 46s autopkgtest [10:37:08]: testbed apt version: 3.1.11 46s autopkgtest [10:37:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [10:37:09]: testbed release detected to be: None 47s autopkgtest [10:37:09]: updating testbed package index (apt update) 48s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 48s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 48s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2408 kB] 49s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [50.0 kB] 49s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 49s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [198 kB] 49s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 49s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1727 kB] 49s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [28.9 kB] 49s Fetched 4647 kB in 2s (2875 kB/s) 50s Reading package lists... 51s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 51s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 51s Reading package lists... 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s The following packages will be upgraded: 52s gcc-15-base libatomic1 libfribidi0 libgcc-s1 libstdc++6 publicsuffix 52s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 1174 kB of archives. 52s After this operation, 14.3 kB of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libatomic1 s390x 15.2.0-7ubuntu1 [9488 B] 52s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++6 s390x 15.2.0-7ubuntu1 [907 kB] 53s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-base s390x 15.2.0-7ubuntu1 [58.4 kB] 53s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-s1 s390x 15.2.0-7ubuntu1 [35.7 kB] 53s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libfribidi0 s390x 1.0.16-3 [27.6 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x publicsuffix all 20251016.1743-0.1 [136 kB] 54s dpkg-preconfigure: unable to re-open stdin: No such file or directory 54s Fetched 1174 kB in 2s (728 kB/s) 54s (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 ... 56953 files and directories currently installed.) 54s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_s390x.deb ... 54s Unpacking libatomic1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 54s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_s390x.deb ... 54s Unpacking libstdc++6:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 54s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_s390x.deb ... 54s Unpacking gcc-15-base:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 54s Setting up gcc-15-base:s390x (15.2.0-7ubuntu1) ... 54s (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 ... 56953 files and directories currently installed.) 54s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_s390x.deb ... 54s Unpacking libgcc-s1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 54s Setting up libgcc-s1:s390x (15.2.0-7ubuntu1) ... 54s (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 ... 56953 files and directories currently installed.) 54s Preparing to unpack .../libfribidi0_1.0.16-3_s390x.deb ... 54s Unpacking libfribidi0:s390x (1.0.16-3) over (1.0.16-1) ... 54s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 54s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 54s Setting up libfribidi0:s390x (1.0.16-3) ... 54s Setting up libatomic1:s390x (15.2.0-7ubuntu1) ... 54s Setting up publicsuffix (20251016.1743-0.1) ... 54s Setting up libstdc++6:s390x (15.2.0-7ubuntu1) ... 54s Processing triggers for libc-bin (2.42-0ubuntu3) ... 54s autopkgtest [10:37:16]: upgrading testbed (apt dist-upgrade and autopurge) 54s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Solving dependencies... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s autopkgtest [10:37:20]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 58s autopkgtest [10:37:20]: @@@@@@@@@@@@@@@@@@@@ apt-source presto 60s Get:1 http://ftpmaster.internal/ubuntu resolute/universe presto 0.7.2-2 (dsc) [2258 B] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/universe presto 0.7.2-2 (tar) [362 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute/universe presto 0.7.2-2 (diff) [21.8 kB] 60s gpgv: Signature made Mon Dec 9 21:07:49 2024 UTC 60s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 60s gpgv: issuer "tille@debian.org" 60s gpgv: Can't check signature: No public key 60s dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-2.dsc: no acceptable signature found 60s autopkgtest [10:37:22]: testing package presto version 0.7.2-2 61s autopkgtest [10:37:23]: build not needed 61s autopkgtest [10:37:23]: test pybuild-autopkgtest: preparing testbed 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Solving dependencies... 62s The following NEW packages will be installed: 62s autoconf automake autopoint autotools-dev build-essential cd-hit cpp cpp-15 62s cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit dh-autoreconf 62s dh-python dh-strip-nondeterminism dwz fontconfig-config fonts-urw-base35 g++ 62s g++-15 g++-15-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-15 62s gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu gettext intltool-debian 62s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl 62s libdeflate0 libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 62s libfreetype6 libgcc-15-dev libgfortran5 libgomp1 libgraphite2-3 62s libharfbuzz0b libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 62s libjpeg8 liblapack3 liblcms2-2 libmbedcrypto16 libmbedtls21 libmbedx509-7 62s libmpc3 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 libsharpyuv0 62s libstdc++-15-dev libtiff6 libtool libubsan1 libwebp7 libwebpdemux2 62s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 m4 ncbi-blast+ ncbi-data 62s po-debconf presto pybuild-plugin-autopkgtest python3-all python3-biopython 62s python3-cairo python3-charset-normalizer python3-dateutil python3-decorator 62s python3-freetype python3-numpy python3-numpy-dev python3-packaging 62s python3-pandas python3-pandas-lib python3-pil python3-presto python3-pytz 62s python3-reportlab python3-rlpycairo python3-scipy sgml-base w3c-sgml-lib 62s x11-common xfonts-encodings xfonts-utils xml-core 62s 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 135 MB of archives. 62s After this operation, 525 MB of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 62s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 63s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-7ubuntu1 [629 kB] 63s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 64s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 65s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x m4 s390x 1.4.20-2 [223 kB] 65s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x autoconf all 2.72-3.1ubuntu1 [384 kB] 65s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x autotools-dev all 20240727.1 [43.4 kB] 65s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x automake all 1:1.17-4ubuntu1 [572 kB] 65s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x autopoint all 0.23.1-2build2 [619 kB] 65s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1 [704 kB] 65s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-1build3 [57.6 kB] 65s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-7ubuntu1 [10.2 MB] 66s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-7ubuntu1 [1022 B] 66s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 66s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 66s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-7ubuntu1 [50.0 kB] 66s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-7ubuntu1 [154 kB] 66s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-7ubuntu1 [30.9 kB] 66s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-7ubuntu1 [2968 kB] 66s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-7ubuntu1 [1211 kB] 66s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-7ubuntu1 [1045 kB] 66s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-7ubuntu1 [19.9 MB] 67s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-7ubuntu1 [513 kB] 67s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 67s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 67s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++-15-dev s390x 15.2.0-7ubuntu1 [2659 kB] 67s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15-s390x-linux-gnu s390x 15.2.0-7ubuntu1 [11.7 MB] 67s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15 s390x 15.2.0-7ubuntu1 [23.7 kB] 67s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x g++-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [956 B] 67s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x g++ s390x 4:15.2.0-4ubuntu1 [1078 B] 67s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x build-essential s390x 12.12ubuntu1 [5090 B] 67s Get:33 http://ftpmaster.internal/ubuntu resolute/universe s390x cd-hit s390x 4.8.1-4 [521 kB] 67s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libdebhelper-perl all 13.24.2ubuntu1 [95.7 kB] 67s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libtool all 2.5.4-4build1 [169 kB] 67s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x dh-autoreconf all 21 [12.5 kB] 67s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 67s Get:38 http://ftpmaster.internal/ubuntu resolute/main s390x libfile-stripnondeterminism-perl all 1.15.0-1 [20.5 kB] 67s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x dh-strip-nondeterminism all 1.15.0-1 [5090 B] 67s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x debugedit s390x 1:5.2-3 [52.8 kB] 67s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x dwz s390x 0.16-2 [121 kB] 67s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x gettext s390x 0.23.1-2build2 [1062 kB] 68s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] 68s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x po-debconf all 1.0.21+nmu1 [233 kB] 68s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x debhelper all 13.24.2ubuntu1 [896 kB] 68s Get:46 http://ftpmaster.internal/ubuntu resolute/universe s390x dh-python all 6.20250414 [119 kB] 68s Get:47 http://ftpmaster.internal/ubuntu resolute/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 68s Get:48 http://ftpmaster.internal/ubuntu resolute/main s390x libfreetype6 s390x 2.13.3+dfsg-1build1 [430 kB] 68s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x x11-common all 1:7.7+24ubuntu1 [22.4 kB] 68s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 68s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 68s Get:52 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 68s Get:53 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig-config s390x 2.15.0-2.3ubuntu1 [38.1 kB] 68s Get:54 http://ftpmaster.internal/ubuntu resolute/main s390x libfontconfig1 s390x 2.15.0-2.3ubuntu1 [149 kB] 68s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x libpixman-1-0 s390x 0.46.4-1 [217 kB] 68s Get:56 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-render0 s390x 1.17.0-2build1 [16.9 kB] 68s Get:57 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-shm0 s390x 1.17.0-2build1 [5916 B] 68s Get:58 http://ftpmaster.internal/ubuntu resolute/main s390x libxrender1 s390x 1:0.9.12-1 [20.9 kB] 68s Get:59 http://ftpmaster.internal/ubuntu resolute/main s390x libcairo2 s390x 1.18.4-1build1 [580 kB] 68s Get:60 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 68s Get:61 http://ftpmaster.internal/ubuntu resolute/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 68s Get:62 http://ftpmaster.internal/ubuntu resolute/main s390x libharfbuzz0b s390x 12.1.0-1 [576 kB] 68s Get:63 http://ftpmaster.internal/ubuntu resolute/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 68s Get:64 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 68s Get:65 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 68s Get:66 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 68s Get:67 http://ftpmaster.internal/ubuntu resolute/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB] 68s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB] 68s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB] 68s Get:70 http://ftpmaster.internal/ubuntu resolute/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 68s Get:71 http://ftpmaster.internal/ubuntu resolute/main s390x libraqm0 s390x 0.10.3-1 [15.6 kB] 68s Get:72 http://ftpmaster.internal/ubuntu resolute/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 68s Get:73 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 68s Get:74 http://ftpmaster.internal/ubuntu resolute/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 68s Get:75 http://ftpmaster.internal/ubuntu resolute/main s390x libtiff6 s390x 4.7.0-3ubuntu3 [222 kB] 68s Get:76 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 68s Get:77 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 68s Get:78 http://ftpmaster.internal/ubuntu resolute/universe s390x ncbi-data all 6.1.20170106+dfsg2-6 [3969 kB] 68s Get:79 http://ftpmaster.internal/ubuntu resolute/universe s390x ncbi-blast+ s390x 2.16.0+ds-7 [15.2 MB] 69s Get:80 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-charset-normalizer s390x 3.4.2-1 [129 kB] 69s Get:81 http://ftpmaster.internal/ubuntu resolute/main s390x libopenjp2-7 s390x 2.5.3-2.1 [207 kB] 69s Get:82 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pil s390x 11.3.0-1ubuntu2 [542 kB] 69s Get:83 http://ftpmaster.internal/ubuntu resolute/main s390x python3-cairo s390x 1.27.0-2build1 [140 kB] 69s Get:84 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-freetype all 2.5.1-2 [92.2 kB] 69s Get:85 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rlpycairo all 0.3.0-4 [9332 B] 69s Get:86 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-reportlab all 4.4.4-2 [1147 kB] 69s Get:87 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 69s Get:88 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19 [20.3 kB] 69s Get:89 http://ftpmaster.internal/ubuntu resolute/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 69s Get:90 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-biopython s390x 1.85+dfsg-4 [1745 kB] 69s Get:91 http://ftpmaster.internal/ubuntu resolute/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 69s Get:92 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pytz all 2025.2-4 [32.3 kB] 69s Get:93 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-1ubuntu1 [8668 kB] 69s Get:94 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 69s Get:95 http://ftpmaster.internal/ubuntu resolute/main s390x python3-decorator all 5.2.1-2 [28.1 kB] 69s Get:96 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-scipy s390x 1.16.3-1 [19.6 MB] 69s Get:97 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 69s Get:98 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-presto s390x 0.7.2-2 [80.8 kB] 69s Get:99 http://ftpmaster.internal/ubuntu resolute/universe s390x presto all 0.7.2-2 [240 kB] 69s Get:100 http://ftpmaster.internal/ubuntu resolute/universe s390x pybuild-plugin-autopkgtest all 6.20250414 [1746 B] 70s Get:101 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.7-1 [886 B] 70s Fetched 135 MB in 8s (17.7 MB/s) 70s Selecting previously unselected package python3-numpy-dev:s390x. 70s (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 ... 56953 files and directories currently installed.) 70s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 70s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 70s Selecting previously unselected package libblas3:s390x. 70s Preparing to unpack .../001-libblas3_3.12.1-6build1_s390x.deb ... 70s Unpacking libblas3:s390x (3.12.1-6build1) ... 70s Selecting previously unselected package libgfortran5:s390x. 70s Preparing to unpack .../002-libgfortran5_15.2.0-7ubuntu1_s390x.deb ... 70s Unpacking libgfortran5:s390x (15.2.0-7ubuntu1) ... 70s Selecting previously unselected package liblapack3:s390x. 70s Preparing to unpack .../003-liblapack3_3.12.1-6build1_s390x.deb ... 70s Unpacking liblapack3:s390x (3.12.1-6build1) ... 70s Selecting previously unselected package python3-numpy. 70s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 70s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 70s Selecting previously unselected package m4. 70s Preparing to unpack .../005-m4_1.4.20-2_s390x.deb ... 70s Unpacking m4 (1.4.20-2) ... 70s Selecting previously unselected package autoconf. 70s Preparing to unpack .../006-autoconf_2.72-3.1ubuntu1_all.deb ... 70s Unpacking autoconf (2.72-3.1ubuntu1) ... 70s Selecting previously unselected package autotools-dev. 70s Preparing to unpack .../007-autotools-dev_20240727.1_all.deb ... 70s Unpacking autotools-dev (20240727.1) ... 70s Selecting previously unselected package automake. 70s Preparing to unpack .../008-automake_1%3a1.17-4ubuntu1_all.deb ... 70s Unpacking automake (1:1.17-4ubuntu1) ... 70s Selecting previously unselected package autopoint. 70s Preparing to unpack .../009-autopoint_0.23.1-2build2_all.deb ... 70s Unpacking autopoint (0.23.1-2build2) ... 70s Selecting previously unselected package libisl23:s390x. 70s Preparing to unpack .../010-libisl23_0.27-1_s390x.deb ... 70s Unpacking libisl23:s390x (0.27-1) ... 70s Selecting previously unselected package libmpc3:s390x. 70s Preparing to unpack .../011-libmpc3_1.3.1-1build3_s390x.deb ... 70s Unpacking libmpc3:s390x (1.3.1-1build3) ... 70s Selecting previously unselected package cpp-15-s390x-linux-gnu. 70s Preparing to unpack .../012-cpp-15-s390x-linux-gnu_15.2.0-7ubuntu1_s390x.deb ... 70s Unpacking cpp-15-s390x-linux-gnu (15.2.0-7ubuntu1) ... 70s Selecting previously unselected package cpp-15. 70s Preparing to unpack .../013-cpp-15_15.2.0-7ubuntu1_s390x.deb ... 70s Unpacking cpp-15 (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package cpp-s390x-linux-gnu. 71s Preparing to unpack .../014-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 71s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 71s Selecting previously unselected package cpp. 71s Preparing to unpack .../015-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 71s Unpacking cpp (4:15.2.0-4ubuntu1) ... 71s Selecting previously unselected package libcc1-0:s390x. 71s Preparing to unpack .../016-libcc1-0_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libcc1-0:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package libgomp1:s390x. 71s Preparing to unpack .../017-libgomp1_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libgomp1:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package libitm1:s390x. 71s Preparing to unpack .../018-libitm1_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libitm1:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package libasan8:s390x. 71s Preparing to unpack .../019-libasan8_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libasan8:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package libubsan1:s390x. 71s Preparing to unpack .../020-libubsan1_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libubsan1:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package libgcc-15-dev:s390x. 71s Preparing to unpack .../021-libgcc-15-dev_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libgcc-15-dev:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package gcc-15-s390x-linux-gnu. 71s Preparing to unpack .../022-gcc-15-s390x-linux-gnu_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking gcc-15-s390x-linux-gnu (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package gcc-15. 71s Preparing to unpack .../023-gcc-15_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking gcc-15 (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package gcc-s390x-linux-gnu. 71s Preparing to unpack .../024-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 71s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 71s Selecting previously unselected package gcc. 71s Preparing to unpack .../025-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 71s Unpacking gcc (4:15.2.0-4ubuntu1) ... 71s Selecting previously unselected package libstdc++-15-dev:s390x. 71s Preparing to unpack .../026-libstdc++-15-dev_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking libstdc++-15-dev:s390x (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package g++-15-s390x-linux-gnu. 71s Preparing to unpack .../027-g++-15-s390x-linux-gnu_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking g++-15-s390x-linux-gnu (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package g++-15. 71s Preparing to unpack .../028-g++-15_15.2.0-7ubuntu1_s390x.deb ... 71s Unpacking g++-15 (15.2.0-7ubuntu1) ... 71s Selecting previously unselected package g++-s390x-linux-gnu. 71s Preparing to unpack .../029-g++-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 71s Unpacking g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 71s Selecting previously unselected package g++. 71s Preparing to unpack .../030-g++_4%3a15.2.0-4ubuntu1_s390x.deb ... 71s Unpacking g++ (4:15.2.0-4ubuntu1) ... 71s Selecting previously unselected package build-essential. 71s Preparing to unpack .../031-build-essential_12.12ubuntu1_s390x.deb ... 71s Unpacking build-essential (12.12ubuntu1) ... 71s Selecting previously unselected package cd-hit. 71s Preparing to unpack .../032-cd-hit_4.8.1-4_s390x.deb ... 71s Unpacking cd-hit (4.8.1-4) ... 71s Selecting previously unselected package libdebhelper-perl. 71s Preparing to unpack .../033-libdebhelper-perl_13.24.2ubuntu1_all.deb ... 71s Unpacking libdebhelper-perl (13.24.2ubuntu1) ... 71s Selecting previously unselected package libtool. 71s Preparing to unpack .../034-libtool_2.5.4-4build1_all.deb ... 71s Unpacking libtool (2.5.4-4build1) ... 71s Selecting previously unselected package dh-autoreconf. 71s Preparing to unpack .../035-dh-autoreconf_21_all.deb ... 71s Unpacking dh-autoreconf (21) ... 71s Selecting previously unselected package libarchive-zip-perl. 71s Preparing to unpack .../036-libarchive-zip-perl_1.68-1_all.deb ... 71s Unpacking libarchive-zip-perl (1.68-1) ... 71s Selecting previously unselected package libfile-stripnondeterminism-perl. 71s Preparing to unpack .../037-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... 71s Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... 71s Selecting previously unselected package dh-strip-nondeterminism. 71s Preparing to unpack .../038-dh-strip-nondeterminism_1.15.0-1_all.deb ... 71s Unpacking dh-strip-nondeterminism (1.15.0-1) ... 71s Selecting previously unselected package debugedit. 71s Preparing to unpack .../039-debugedit_1%3a5.2-3_s390x.deb ... 71s Unpacking debugedit (1:5.2-3) ... 71s Selecting previously unselected package dwz. 71s Preparing to unpack .../040-dwz_0.16-2_s390x.deb 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fonts-urw-base35 (20200910-8) ... 72s Selecting previously unselected package fontconfig-config. 72s Preparing to unpack .../052-fontconfig-config_2.15.0-2.3ubuntu1_s390x.deb ... 72s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 72s Selecting previously unselected package libfontconfig1:s390x. 72s Preparing to unpack .../053-libfontconfig1_2.15.0-2.3ubuntu1_s390x.deb ... 72s Unpacking libfontconfig1:s390x (2.15.0-2.3ubuntu1) ... 72s Selecting previously unselected package libpixman-1-0:s390x. 72s Preparing to unpack .../054-libpixman-1-0_0.46.4-1_s390x.deb ... 72s Unpacking libpixman-1-0:s390x (0.46.4-1) ... 72s Selecting previously unselected package libxcb-render0:s390x. 72s Preparing to unpack .../055-libxcb-render0_1.17.0-2build1_s390x.deb ... 72s Unpacking libxcb-render0:s390x (1.17.0-2build1) ... 72s Selecting previously unselected package libxcb-shm0:s390x. 72s Preparing to unpack .../056-libxcb-shm0_1.17.0-2build1_s390x.deb ... 72s Unpacking libxcb-shm0:s390x (1.17.0-2build1) ... 72s Selecting previously unselected package libxrender1:s390x. 72s Preparing to unpack .../057-libxrender1_1%3a0.9.12-1_s390x.deb ... 72s Unpacking libxrender1:s390x (1:0.9.12-1) ... 72s Selecting previously unselected package libcairo2:s390x. 72s Preparing to unpack .../058-libcairo2_1.18.4-1build1_s390x.deb ... 72s Unpacking libcairo2:s390x (1.18.4-1build1) ... 72s Selecting previously unselected package libdeflate0:s390x. 72s Preparing to unpack .../059-libdeflate0_1.23-2_s390x.deb ... 72s Unpacking libdeflate0:s390x (1.23-2) ... 72s Selecting previously unselected package libgraphite2-3:s390x. 72s Preparing to unpack .../060-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 72s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 72s Selecting previously unselected package libharfbuzz0b:s390x. 72s Preparing to unpack .../061-libharfbuzz0b_12.1.0-1_s390x.deb ... 72s Unpacking libharfbuzz0b:s390x (12.1.0-1) ... 72s Selecting previously unselected package libimagequant0:s390x. 72s Preparing to unpack .../062-libimagequant0_2.18.0-1build1_s390x.deb ... 72s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 72s Selecting previously unselected package libjpeg-turbo8:s390x. 72s Preparing to unpack .../063-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 72s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 72s Selecting previously unselected package libjpeg8:s390x. 72s Preparing to unpack .../064-libjpeg8_8c-2ubuntu11_s390x.deb ... 72s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 72s Selecting previously unselected package liblcms2-2:s390x. 72s Preparing to unpack .../065-liblcms2-2_2.16-2_s390x.deb ... 72s Unpacking liblcms2-2:s390x (2.16-2) ... 72s Selecting previously unselected package libmbedcrypto16:s390x. 72s Preparing to unpack .../066-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ... 72s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 72s Selecting previously unselected package libmbedx509-7:s390x. 72s Preparing to unpack .../067-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ... 72s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 72s Selecting previously unselected package libmbedtls21:s390x. 72s Preparing to unpack .../068-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ... 72s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ... 72s Selecting previously unselected package libqhull-r8.0:s390x. 72s Preparing to unpack .../069-libqhull-r8.0_2020.2-6build1_s390x.deb ... 72s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 72s Selecting previously unselected package libraqm0:s390x. 72s Preparing to unpack .../070-libraqm0_0.10.3-1_s390x.deb ... 72s Unpacking libraqm0:s390x (0.10.3-1) ... 72s Selecting previously unselected package libsharpyuv0:s390x. 72s Preparing to unpack .../071-libsharpyuv0_1.5.0-0.1_s390x.deb ... 72s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 72s Selecting previously unselected package libjbig0:s390x. 72s Preparing to unpack .../072-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 72s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 72s Selecting previously unselected package libwebp7:s390x. 72s Preparing to unpack .../073-libwebp7_1.5.0-0.1_s390x.deb ... 72s Unpacking libwebp7:s390x (1.5.0-0.1) ... 72s Selecting previously unselected package libtiff6:s390x. 72s Preparing to unpack .../074-libtiff6_4.7.0-3ubuntu3_s390x.deb ... 72s Unpacking libtiff6:s390x (4.7.0-3ubuntu3) ... 72s Selecting previously unselected package libwebpdemux2:s390x. 72s Preparing to unpack .../075-libwebpdemux2_1.5.0-0.1_s390x.deb ... 72s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 72s Selecting previously unselected package libwebpmux3:s390x. 72s Preparing to unpack .../076-libwebpmux3_1.5.0-0.1_s390x.deb ... 72s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 72s Selecting previously unselected package ncbi-data. 72s Preparing to unpack .../077-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... 72s Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... 72s Selecting previously unselected package ncbi-blast+. 72s 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... 73s Unpacking python3-freetype (2.5.1-2) ... 73s Selecting previously unselected package python3-rlpycairo. 73s Preparing to unpack .../084-python3-rlpycairo_0.3.0-4_all.deb ... 73s Unpacking python3-rlpycairo (0.3.0-4) ... 73s Selecting previously unselected package python3-reportlab. 73s Preparing to unpack .../085-python3-reportlab_4.4.4-2_all.deb ... 73s Unpacking python3-reportlab (4.4.4-2) ... 73s Selecting previously unselected package sgml-base. 73s Preparing to unpack .../086-sgml-base_1.31+nmu1_all.deb ... 73s Unpacking sgml-base (1.31+nmu1) ... 73s Selecting previously unselected package xml-core. 73s Preparing to unpack .../087-xml-core_0.19_all.deb ... 73s Unpacking xml-core (0.19) ... 73s Selecting previously unselected package w3c-sgml-lib. 73s Preparing to unpack .../088-w3c-sgml-lib_1.3-3_all.deb ... 73s Unpacking w3c-sgml-lib (1.3-3) ... 73s Selecting previously unselected package python3-biopython. 73s Preparing to unpack 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Unpacking python3-decorator (5.2.1-2) ... 73s Selecting previously unselected package python3-scipy. 73s Preparing to unpack .../095-python3-scipy_1.16.3-1_s390x.deb ... 73s Unpacking python3-scipy (1.16.3-1) ... 73s Selecting previously unselected package python3-packaging. 73s Preparing to unpack .../096-python3-packaging_25.0-1_all.deb ... 73s Unpacking python3-packaging (25.0-1) ... 73s Selecting previously unselected package python3-presto. 73s Preparing to unpack .../097-python3-presto_0.7.2-2_s390x.deb ... 73s Unpacking python3-presto (0.7.2-2) ... 73s Selecting previously unselected package presto. 73s Preparing to unpack .../098-presto_0.7.2-2_all.deb ... 73s Unpacking presto (0.7.2-2) ... 73s Selecting previously unselected package pybuild-plugin-autopkgtest. 73s Preparing to unpack .../099-pybuild-plugin-autopkgtest_6.20250414_all.deb ... 73s Unpacking pybuild-plugin-autopkgtest (6.20250414) ... 73s Selecting previously unselected package python3-all. 73s Preparing to unpack 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74s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 74s Setting up gettext (0.23.1-2build2) ... 74s Setting up libgcc-15-dev:s390x (15.2.0-7ubuntu1) ... 74s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 74s Setting up python3-freetype (2.5.1-2) ... 74s Setting up xfonts-utils (1:7.7+7) ... 74s Setting up intltool-debian (0.35.0+20060710.6) ... 74s Setting up libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 74s Setting up libstdc++-15-dev:s390x (15.2.0-7ubuntu1) ... 74s Setting up libraqm0:s390x (0.10.3-1) ... 74s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 76s Setting up libmbedtls21:s390x (3.6.2-3ubuntu1) ... 76s Setting up dh-strip-nondeterminism (1.15.0-1) ... 76s Setting up libtiff6:s390x (4.7.0-3ubuntu3) ... 76s Setting up xml-core (0.19) ... 76s Setting up cpp-15-s390x-linux-gnu (15.2.0-7ubuntu1) ... 76s Setting up gcc-15-s390x-linux-gnu (15.2.0-7ubuntu1) ... 76s Setting up g++-15-s390x-linux-gnu (15.2.0-7ubuntu1) ... 76s Setting up python3-scipy (1.16.3-1) ... 79s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 79s Setting up po-debconf (1.0.21+nmu1) ... 79s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 79s Setting up fonts-urw-base35 (20200910-8) ... 79s Setting up ncbi-blast+ (2.16.0+ds-7) ... 79s Setting up python3-pil:s390x (11.3.0-1ubuntu2) ... 79s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 83s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 83s Setting up cpp-15 (15.2.0-7ubuntu1) ... 83s Setting up cpp (4:15.2.0-4ubuntu1) ... 83s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 84s Setting up g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 84s Setting up gcc-15 (15.2.0-7ubuntu1) ... 84s Setting up libfontconfig1:s390x (2.15.0-2.3ubuntu1) ... 84s Setting up g++-15 (15.2.0-7ubuntu1) ... 84s Setting up libtool (2.5.4-4build1) ... 84s Setting up libcairo2:s390x (1.18.4-1build1) ... 84s Setting up gcc (4:15.2.0-4ubuntu1) ... 84s Setting up dh-autoreconf (21) ... 84s Setting up g++ (4:15.2.0-4ubuntu1) ... 84s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 84s Setting up build-essential (12.12ubuntu1) ... 84s Setting up python3-cairo (1.27.0-2build1) ... 84s Setting up debhelper (13.24.2ubuntu1) ... 84s Setting up python3-rlpycairo (0.3.0-4) ... 84s Setting up python3-reportlab (4.4.4-2) ... 84s Setting up pybuild-plugin-autopkgtest (6.20250414) ... 84s Processing triggers for libc-bin (2.42-0ubuntu3) ... 84s Processing triggers for man-db (2.13.1-1) ... 85s Processing triggers for install-info (7.1.1-1ubuntu1) ... 86s Processing triggers for sgml-base (1.31+nmu1) ... 86s Setting up w3c-sgml-lib (1.3-3) ... 107s Setting up python3-biopython (1.85+dfsg-4) ... 107s Setting up python3-presto (0.7.2-2) ... 107s Setting up presto (0.7.2-2) ... 108s autopkgtest [10:38:10]: test pybuild-autopkgtest: pybuild-autopkgtest 108s autopkgtest [10:38:10]: test pybuild-autopkgtest: [----------------------- 109s pybuild-autopkgtest 109s I: pybuild pybuild:308: cp -r /tmp/autopkgtest.IduuLJ/build.lnW/src/bin /tmp/autopkgtest.IduuLJ/autopkgtest_tmp/build; rm /tmp/autopkgtest.IduuLJ/build.lnW/src/tests/test_ClusterSets.py || echo "Test file already removed or moved"; 109s I: pybuild base:311: cd /tmp/autopkgtest.IduuLJ/autopkgtest_tmp/build; python3.13 -m unittest discover -v 110s test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok 110s test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok 110s test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok 110s test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok 110s test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' 110s test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' 110s test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' 110s test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' 110s test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' 110s test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' 110s test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok 110s test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok 110s test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok 110s test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok 110s test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok 110s test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok 110s test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok 110s test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok 110s test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok 110s test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok 110s test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok 110s test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok 110s test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. 110s warnings.warn( 110s ok 110s test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok 110s -> test_collapseAnnotation() 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) 110s <- test_collapseAnnotation() 0.000 110s -> test_getCoordKey() 110s ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] 110s ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] 110s ['000034_0199_0169', 'GXGJ56Z01AE06X'] 110s <- test_getCoordKey() 0.000 110s -> test_mergeAnnotation() 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) 110s <- test_mergeAnnotation() 0.000 110s -> test_renameAnnotation() 110s OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) 110s OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) 110s <- test_renameAnnotation() 0.000 110s -> test_calculateSetError() 110s Frequency consensus error> 110s REF> CGGCGTAA 110s SEQ1> CGGCGTAA 110s SEQ2> CCNNGTAA 110s SEQ3> CGGC--TA 110s SEQ4> CGNN--TA 110s SEQ5> CGGC--AA 110s ERROR> 0.250000 110s Quality consensus error> 110s REF> CGGCNNAA 110s SEQ1> CGGCGTAA 110s SEQ2> CCNNGTAA 110s SEQ3> CGGC--TA 110s SEQ4> CGNN--TA 110s SEQ5> CGGC--AA 110s ERROR> 0.233333 110s <- test_calculateSetError() 0.000 110s -> test_deleteSeqPositions() 110s MAX_GAP=0.4> CGGCAA 110s MAX_GAP=0.8> CGGCGTAA 110s <- test_deleteSeqPositions() 0.000 110s -> test_findGapPositions() 110s MAX_GAP=0.4> [4, 5] 110s MAX_GAP=0.8> [] 110s <- test_findGapPositions() 0.000 110s -> test_frequencyConsensus() 110s MIN_FREQ=0.2> CGGCGTAA 110s MIN_FREQ=0.8> CGGCGTNA 110s <- test_frequencyConsensus() 0.000 110s -> test_qualityConsensus() 110s MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] 110s MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] 110s MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] 110s <- test_qualityConsensus() 0.000 110s -> test_checkSeqEqual() 110s DNA Equality> 110s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 110s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 110s EQUAL> True 110s 110s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 110s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 110s EQUAL> False 110s 110s SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA 110s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 110s EQUAL> True 110s 110s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 110s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 110s EQUAL> False 110s 110s SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA 110s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 110s EQUAL> True 110s 110s SEQ3|COUNT=3> CCACGTTTTACTAATTAATA 110s SEQ4|COUNT=4> CCACGTTTTANTAATTAATA 110s EQUAL> True 110s 110s <- test_checkSeqEqual() 0.000 110s -> test_convert454Header() 110s OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) 110s OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) 110s <- test_convert454Header() 0.000 110s -> test_convertGenbankHeader() 110s OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 110s OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) 110s <- test_convertGenbankHeader() 0.000 110s -> test_convertGenericHeader() 110s OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 110s OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) 110s OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) 110s 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'_"}) 110s 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_'}) 110s OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) 110s <- test_convertGenericHeader() 0.000 110s -> test_convertIMGTHeader() 110s OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) 110s OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) 110s OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) 110s OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) 110s OrderedDict({'ID': 'IGHV1-18*01'}) 110s OrderedDict({'ID': 'IGHV1-69*07'}) 110s OrderedDict({'ID': 'IGHV(III)-22-2*01'}) 110s OrderedDict({'ID': 'TRAV11*01'}) 110s <- test_convertIMGTHeader() 0.000 110s -> test_convertIlluminaHeader() 110s OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) 110s OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) 110s OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) 110s <- test_convertIlluminaHeader() 0.000 110s -> test_convertSRAHeader() 110s OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) 110s OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) 110s OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) 110s OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) 110s OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) 110s <- test_convertSRAHeader() 0.000 110s -> test_calculateDistances() 110s <- test_calculateDistances() 0.001 110s -> test_countMismatches() 110s <- test_countMismatches() 0.001 110s -> test_initializeMismatchDictionary() 110s <- test_initializeMismatchDictionary() 0.000 110s -> test_getFileType() 110s <- test_getFileType() 0.000 110s -> test_extractAlignment() 110s SEQ1> 110s SEQ> CCACGTTTTAGTAATTAATA 110s ALN-SEQ> CCACGTTTTAGT 110s ALN-PR> ----GTTTTAGT 110s PRIMER> GTTTTAGT 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ2> 110s SEQ> CCNCGTTTTAGTAATTAATA 110s ALN-SEQ> CCNCGTTTTAGT 110s ALN-PR> ----GTTTTAGT 110s PRIMER> GTTTTAGT 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ3> 110s SEQ> GGGCGTTTTAGTAATTAATA 110s ALN-SEQ> GGGCGTTTTAGT 110s ALN-PR> ----GTTTTAGT 110s PRIMER> GTTTTAGT 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ4> 110s SEQ> GGNNGTTTTACTAATTAATA 110s ALN-SEQ> GGNNGTTTTACT 110s ALN-PR> ----GTTTTACT 110s PRIMER> GTTTTACT 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ5> 110s SEQ> NNGCNNNNNACTAATTAATA 110s ALN-SEQ> NNGCNNNNNACT 110s ALN-PR> ----NNNNNACT 110s PRIMER> NNNNNACT 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ6> 110s SEQ> GGGATANNNACTAATTAATA 110s ALN-SEQ> GGGATANNNACT 110s ALN-PR> ----TANNNACT 110s PRIMER> TANNNACT 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ7> 110s SEQ> NNNNNNNNNNNNNNNNNNNN 110s ALN-SEQ> NNNNNNNNNNNN 110s ALN-PR> ----NNNNNNNN 110s PRIMER> NNNNNNNN 110s START> 4 110s END> 12 110s GAPS> 0 110s ERROR> 0.000000 110s 110s <- test_extractAlignment() 0.000 110s -> test_localAlignment() 110s TEST Ns> 110s SEQ1> 110s SEQ> CCACGTTTTAGTAATTAATA 110s ALN-SEQ> CCACGTTTTAGTAATTAATA 110s ALN-PR> -CACGTTTT----------- 110s PRIMER> PR1 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ2> 110s SEQ> CCNCGTTTTAGTAATTAATA 110s ALN-SEQ> CCNCGTTTTAGTAATTAATA 110s ALN-PR> -CACGTTTT----------- 110s PRIMER> PR1 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.125000 110s 110s SEQ3> 110s SEQ> GGGCGTTTTAGTAATTAATA 110s ALN-SEQ> GGGCGTTTTAGTAATTAATA 110s ALN-PR> -GGCGTTTT----------- 110s PRIMER> PR2 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ4> 110s SEQ> GGNNGTTTTACTAATTAATA 110s ALN-SEQ> GGNNGTTTTACTAATTAATA 110s ALN-PR> GGC-GTTTT----------- 110s PRIMER> PR2 110s START> 0 110s END> 9 110s GAPS> 1 110s ERROR> 0.250000 110s 110s SEQ5> 110s SEQ> NNGCNNNNNACTAATTAATA 110s ALN-SEQ> NNGCNNNNNACTAATTAATA 110s ALN-PR> ------------ANATAA-- 110s PRIMER> PR3 110s START> 12 110s END> 18 110s GAPS> 0 110s ERROR> 0.375000 110s 110s SEQ6> 110s SEQ> GGGATANNNACTAATTAATA 110s ALN-SEQ> GGGATANNNACTAATTAATA 110s ALN-PR> -GGANA-------------- 110s PRIMER> PR3 110s START> 1 110s END> 6 110s GAPS> 0 110s ERROR> 0.375000 110s 110s SEQ7> 110s SEQ> NNNNNNNNNNNNNNNNNNNN 110s ALN-SEQ> None 110s ALN-PR> None 110s PRIMER> None 110s START> None 110s END> None 110s GAPS> 0 110s ERROR> 1.000000 110s 110s TEST INDELS> 110s SEQ1> 110s SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG 110s ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG 110s ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ 110s PRIMER> PR1 110s START> 15 110s END> 38 110s GAPS> 0 110s ERROR> 0.083333 110s 110s SEQ2> 110s SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG 110s ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG 110s ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ 110s PRIMER> PR1 110s START> 14 110s END> 38 110s GAPS> 2 110s ERROR> 0.208333 110s 110s SEQ3> 110s SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG 110s ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG 110s ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ 110s PRIMER> PR1 110s START> 15 110s END> 38 110s GAPS> 1 110s ERROR> 0.125000 110s 110s SEQ4> 110s SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT 110s ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT 110s ALN-PR> ------CATCT-TCCTCTA------------------------------------------- 110s PRIMER> PR2 110s START> 6 110s END> 19 110s GAPS> 1 110s ERROR> 0.250000 110s 110s SEQ5> 110s SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG 110s ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG 110s ALN-PR> ------CATCTTCCTCTA-------------------------------------------- 110s PRIMER> PR2 110s START> 6 110s END> 18 110s GAPS> 0 110s ERROR> 0.166667 110s 110s SEQ6> 110s SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA 110s ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA 110s ALN-PR> TCT-TCCTCTA--------------------------------------------------- 110s PRIMER> PR2 110s START> 0 110s END> 11 110s GAPS> 1 110s ERROR> 0.250000 110s 110s SEQ7> 110s SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 110s ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 110s ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- 110s PRIMER> PR3 110s START> 2 110s END> 15 110s GAPS> 1 110s ERROR> 0.083333 110s 110s SEQ8> 110s SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 110s ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 110s ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- 110s PRIMER> PR3 110s START> 3 110s END> 15 110s GAPS> 1 110s ERROR> 0.166667 110s 110s SEQ9> 110s SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 110s ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC 110s ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- 110s PRIMER> PR3 110s START> 3 110s END> 15 110s GAPS> 1 110s ERROR> 0.333333 110s 110s SEQ10> 110s SEQ> -------------------------------------------------------------- 110s ALN-SEQ> None 110s ALN-PR> None 110s PRIMER> None 110s START> None 110s END> None 110s GAPS> 0 110s ERROR> 1.000000 110s 110s <- test_localAlignment() 0.019 110s -> test_maskSeq() 110s TEST CUT> 110s ID> SEQ|PRIMER=A|BARCODE=CCA 110s SEQ> AGTAATTAATA 110s 110s TEST MASK> 110s ID> SEQ|PRIMER=A|BARCODE=CCA 110s SEQ> NNNNNNAGTAATTAATA 110s 110s TEST TRIM> 110s ID> SEQ|PRIMER=A|BARCODE=CCA 110s SEQ> CGTTTTAGTAATTAATA 110s 110s TEST TAG> 110s ID> SEQ|PRIMER=A|BARCODE=CCA 110s SEQ> CCACGTTTTAGTAATTAATA 110s 110s <- test_maskSeq() 0.001 110s -> test_scoreAlignment() 110s SEQ1> 110s SEQ> CCACGTTTTAGTAATTAATA 110s ALN-SEQ> CCACGTTTT 110s ALN-PR> -CACGTTTT 110s PRIMER> PR1 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ2> 110s SEQ> CCNCGTTTTAGTAATTAATA 110s ALN-SEQ> CCNCGTTTT 110s ALN-PR> -CACGTTTT 110s PRIMER> PR1 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.125000 110s 110s SEQ3> 110s SEQ> GGGCGTTTTAGTAATTAATA 110s ALN-SEQ> GGGCGTTTT 110s ALN-PR> -GGCGTTTT 110s PRIMER> PR2 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.000000 110s 110s SEQ4> 110s SEQ> GGNNGTTTTACTAATTAATA 110s ALN-SEQ> GGNNGTTTT 110s ALN-PR> -GGCGTTTT 110s PRIMER> PR2 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.250000 110s 110s SEQ5> 110s SEQ> NNGCNNNNNACTAATTAATA 110s ALN-SEQ> NNGCNNNNN 110s ALN-PR> -GGCGTTTT 110s PRIMER> PR2 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.750000 110s 110s SEQ6> 110s SEQ> GGGATANNNACTAATTAATA 110s ALN-SEQ> GGGATANNN 110s ALN-PR> -GGANATAA 110s PRIMER> PR3 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 0.375000 110s 110s SEQ7> 110s SEQ> NNNNNNNNNNNNNNNNNNNN 110s ALN-SEQ> NNNNNNNNN 110s ALN-PR> -CACGTTTT 110s PRIMER> None 110s START> 1 110s END> 9 110s GAPS> 0 110s ERROR> 1.000000 110s 110s <- test_scoreAlignment() 0.006 110s -> test_calculateSetError() 110s REF> CGGCGTAA 0.4347826086956522 110s REF> NNNNNNNN 1.0 110s <- test_calculateSetError() 0.000 110s -> test_filterQuality() 110s RESULT> True 25 110s RESULT> False 5 110s RESULT> False 0 110s <- test_filterQuality() 0.000 110s -> test_meanQuality() 110s RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] 110s RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] 110s RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] 110s <- test_meanQuality() 0.000 110s -> test_scoreDNA() 110s Default DNA Scores> 110s A==A> 1 110s A==T> 0 110s A==R> 1 110s U==T> 1 110s A==N> 1 110s N==A> 1 110s A==-> 0 110s -==A> 0 110s Symmetric DNA Scores> 110s A==A> 1 110s A==T> 0 110s A==R> 1 110s U==T> 1 110s A==N> 1 110s N==A> 1 110s A==-> 1 110s -==A> 1 110s Asymmetric DNA Scores> 110s A==A> 1 110s A==T> 0 110s A==R> 1 110s U==T> 1 110s A==N> 1 110s N==A> 0 110s A==-> 1 110s -==A> 0 110s <- test_scoreDNA() 0.000 110s -> test_scoreSeqPair() 110s Default DNA Scores> 110s SEQ1> CGGCGTAA 110s SEQ2> CGNNGTAG 110s SCORE> 7 110s WEIGHT> 8 110s ERROR> 0.125000 110s 110s SEQ1> CGGCGTAA 110s SEQ3> CGGC--AA 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ1> CGGCGTAA 110s SEQ4> CGNN--AG 110s SCORE> 5 110s WEIGHT> 8 110s ERROR> 0.375000 110s 110s SEQ1> CGGCGTAA 110s SEQ5> NNNNNNNN 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ6> NNNNNNAA 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ2> CGNNGTAG 110s SEQ3> CGGC--AA 110s SCORE> 5 110s WEIGHT> 8 110s ERROR> 0.375000 110s 110s SEQ2> CGNNGTAG 110s SEQ4> CGNN--AG 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ2> CGNNGTAG 110s SEQ5> NNNNNNNN 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ2> CGNNGTAG 110s SEQ6> NNNNNNAA 110s SCORE> 7 110s WEIGHT> 8 110s ERROR> 0.125000 110s 110s SEQ2> CGNNGTAG 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ2> CGNNGTAG 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ3> CGGC--AA 110s SEQ4> CGNN--AG 110s SCORE> 7 110s WEIGHT> 8 110s ERROR> 0.125000 110s 110s SEQ3> CGGC--AA 110s SEQ5> NNNNNNNN 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ3> CGGC--AA 110s SEQ6> NNNNNNAA 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ3> CGGC--AA 110s SEQ7> -------- 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ3> CGGC--AA 110s SEQ8> CG------ 110s SCORE> 4 110s WEIGHT> 8 110s ERROR> 0.500000 110s 110s SEQ4> CGNN--AG 110s SEQ5> NNNNNNNN 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ4> CGNN--AG 110s SEQ6> NNNNNNAA 110s SCORE> 5 110s WEIGHT> 8 110s ERROR> 0.375000 110s 110s SEQ4> CGNN--AG 110s SEQ7> -------- 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ4> CGNN--AG 110s SEQ8> CG------ 110s SCORE> 4 110s WEIGHT> 8 110s ERROR> 0.500000 110s 110s SEQ5> NNNNNNNN 110s SEQ6> NNNNNNAA 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ5> NNNNNNNN 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ5> NNNNNNNN 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ6> NNNNNNAA 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ6> NNNNNNAA 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ7> -------- 110s SEQ8> CG------ 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s Asymmetric DNA Scores> 110s SEQ1> CGGCGTAA 110s SEQ2> CGNNGTAG 110s SCORE> 7 110s WEIGHT> 8 110s ERROR> 0.125000 110s 110s SEQ1> CGGCGTAA 110s SEQ3> CGGC--AA 110s SCORE> 8test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok 110s test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok 110s test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok 110s test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... ok 110s test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok 110s test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok 110s test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok 110s test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok 110s test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok 110s test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok 110s test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... ok 110s test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok 110s test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok 110s test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok 110s 110s ---------------------------------------------------------------------- 110s Ran 38 tests in 0.036s 110s 110s OK (skipped=6) 110s 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ4> CGNN--AG 110s SCORE> 7 110s WEIGHT> 8 110s ERROR> 0.125000 110s 110s SEQ1> CGGCGTAA 110s SEQ5> NNNNNNNN 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ6> NNNNNNAA 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ7> -------- 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ8> CG------ 110s SCORE> 8 110s WEIGHT> 8 110s ERROR> 0.000000 110s 110s SEQ2> CGNNGTAG 110s SEQ3> CGGC--AA 110s SCORE> 5 110s WEIGHT> 8 110s ERROR> 0.375000 110s 110s SEQ2> CGNNGTAG 110s SEQ4> CGNN--AG 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ2> CGNNGTAG 110s SEQ5> NNNNNNNN 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ2> CGNNGTAG 110s SEQ6> NNNNNNAA 110s SCORE> 5 110s WEIGHT> 8 110s ERROR> 0.375000 110s 110s SEQ2> CGNNGTAG 110s SEQ7> -------- 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ2> CGNNGTAG 110s SEQ8> CG------ 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ3> CGGC--AA 110s SEQ4> CGNN--AG 110s SCORE> 5 110s WEIGHT> 8 110s ERROR> 0.375000 110s 110s SEQ3> CGGC--AA 110s SEQ5> NNNNNNNN 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ3> CGGC--AA 110s SEQ6> NNNNNNAA 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ3> CGGC--AA 110s SEQ7> -------- 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ3> CGGC--AA 110s SEQ8> CG------ 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ4> CGNN--AG 110s SEQ5> NNNNNNNN 110s SCORE> 4 110s WEIGHT> 8 110s ERROR> 0.500000 110s 110s SEQ4> CGNN--AG 110s SEQ6> NNNNNNAA 110s SCORE> 3 110s WEIGHT> 8 110s ERROR> 0.625000 110s 110s SEQ4> CGNN--AG 110s SEQ7> -------- 110s SCORE> 4 110s WEIGHT> 8 110s ERROR> 0.500000 110s 110s SEQ4> CGNN--AG 110s SEQ8> CG------ 110s SCORE> 4 110s WEIGHT> 8 110s ERROR> 0.500000 110s 110s SEQ5> NNNNNNNN 110s SEQ6> NNNNNNAA 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ5> NNNNNNNN 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ5> NNNNNNNN 110s SEQ8> CG------ 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ6> NNNNNNAA 110s SEQ7> -------- 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ6> NNNNNNAA 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ7> -------- 110s SEQ8> CG------ 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s Masked DNA Scores> 110s SEQ1> CGGCGTAA 110s SEQ2> CGNNGTAG 110s SCORE> 5 110s WEIGHT> 6 110s ERROR> 0.166667 110s 110s SEQ1> CGGCGTAA 110s SEQ3> CGGC--AA 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s SEQ1> CGGCGTAA 110s SEQ4> CGNN--AG 110s SCORE> 3 110s WEIGHT> 6 110s ERROR> 0.500000 110s 110s SEQ1> CGGCGTAA 110s SEQ5> NNNNNNNN 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ6> NNNNNNAA 110s SCORE> 2 110s WEIGHT> 2 110s ERROR> 0.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 8 110s ERROR> 1.000000 110s 110s SEQ1> CGGCGTAA 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ2> CGNNGTAG 110s SEQ3> CGGC--AA 110s SCORE> 3 110s WEIGHT> 6 110s ERROR> 0.500000 110s 110s SEQ2> CGNNGTAG 110s SEQ4> CGNN--AG 110s SCORE> 4 110s WEIGHT> 6 110s ERROR> 0.333333 110s 110s SEQ2> CGNNGTAG 110s SEQ5> NNNNNNNN 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ2> CGNNGTAG 110s SEQ6> NNNNNNAA 110s SCORE> 1 110s WEIGHT> 2 110s ERROR> 0.500000 110s 110s SEQ2> CGNNGTAG 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 6 110s ERROR> 1.000000 110s 110s SEQ2> CGNNGTAG 110s SEQ8> CG------ 110s SCORE> 2 110s WEIGHT> 6 110s ERROR> 0.666667 110s 110s SEQ3> CGGC--AA 110s SEQ4> CGNN--AG 110s SCORE> 5 110s WEIGHT> 6 110s ERROR> 0.166667 110s 110s SEQ3> CGGC--AA 110s SEQ5> NNNNNNNN 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ3> CGGC--AA 110s SEQ6> NNNNNNAA 110s SCORE> 2 110s WEIGHT> 2 110s ERROR> 0.000000 110s 110s SEQ3> CGGC--AA 110s SEQ7> -------- 110s SCORE> 2 110s WEIGHT> 8 110s ERROR> 0.750000 110s 110s SEQ3> CGGC--AA 110s SEQ8> CG------ 110s SCORE> 4 110s WEIGHT> 8 110s ERROR> 0.500000 110s 110s SEQ4> CGNN--AG 110s SEQ5> NNNNNNNN 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ4> CGNN--AG 110s SEQ6> NNNNNNAA 110s SCORE> 1 110s WEIGHT> 2 110s ERROR> 0.500000 110s 110s SEQ4> CGNN--AG 110s SEQ7> -------- 110s SCORE> 2 110s WEIGHT> 6 110s ERROR> 0.666667 110s 110s SEQ4> CGNN--AG 110s SEQ8> CG------ 110s SCORE> 4 110s WEIGHT> 6 110s ERROR> 0.333333 110s 110s SEQ5> NNNNNNNN 110s SEQ6> NNNNNNAA 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ5> NNNNNNNN 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ5> NNNNNNNN 110s SEQ8> CG------ 110s SCORE> 0 110s WEIGHT> 0 110s ERROR> 1.000000 110s 110s SEQ6> NNNNNNAA 110s SEQ7> -------- 110s SCORE> 0 110s WEIGHT> 2 110s ERROR> 1.000000 110s 110s SEQ6> NNNNNNAA 110s SEQ8> CG------ 110s SCORE> 0 110s WEIGHT> 2 110s ERROR> 1.000000 110s 110s SEQ7> -------- 110s SEQ8> CG------ 110s SCORE> 6 110s WEIGHT> 8 110s ERROR> 0.250000 110s 110s <- test_scoreSeqPair() 0.004 110s -> test_weightDNA() 110s DNA Weight> 110s SEQ1> 8 110s SEQ2> 6 110s SEQ3> 8 110s SEQ4> 6 110s SEQ5> 0 110s SEQ6> 2 110s SEQ7> 8 110s SEQ8> 8 110s AA Weight> 110s SEQ1> 8 110s SEQ2> 6 110s SEQ3> 8 110s SEQ4> 6 110s <- test_weightDNA() 0.000 110s -> test_consensusUnify() 110s ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 110s ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 110s ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 110s ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 110s ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 110s ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 110s ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 110s ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 110s <- test_consensusUnify() 0.000 110s -> test_deletionUnify() 110s ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False 110s ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False 110s ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False 110s ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False 110s ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False 110s ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False 110s ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True 110s ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True 110s <- test_deletionUnify() 0.000 110s autopkgtest [10:38:12]: test pybuild-autopkgtest: -----------------------] 111s autopkgtest [10:38:13]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 111s pybuild-autopkgtest PASS 111s autopkgtest [10:38:13]: @@@@@@@@@@@@@@@@@@@@ summary 111s pybuild-autopkgtest PASS