0s autopkgtest [13:54:49]: starting date and time: 2025-11-17 13:54:49+0000
  0s autopkgtest [13:54:49]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [13:54:49]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mmpycoqo/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade busco --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-8.secgroup --name adt-resolute-arm64-busco-20251117-133229-juju-7f2275-prod-proposed-migration-environment-15-60093ae3-4beb-4ae2-83da-6a8f9c488fba --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  3s Creating nova instance adt-resolute-arm64-busco-20251117-133229-juju-7f2275-prod-proposed-migration-environment-15-60093ae3-4beb-4ae2-83da-6a8f9c488fba from image adt/ubuntu-resolute-arm64-server-20251117.img (UUID 1cd33fbb-18df-4c5a-b8f0-2dcb25269485)...
 66s autopkgtest [13:55:55]: testbed dpkg architecture: arm64
 66s autopkgtest [13:55:55]: testbed apt version: 3.1.11
 67s autopkgtest [13:55:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 67s autopkgtest [13:55:56]: testbed release detected to be: None
 68s autopkgtest [13:55:57]: updating testbed package index (apt update)
 68s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB]
 68s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 68s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 68s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 68s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB]
 69s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B]
 69s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB]
 69s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB]
 69s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [149 kB]
 69s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3084 B]
 69s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [107 kB]
 69s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B]
 69s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [577 kB]
 69s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [17.8 kB]
 69s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [12.5 kB]
 69s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [576 B]
 70s Fetched 1938 kB in 1s (1676 kB/s)
 71s Reading package lists...
 71s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 71s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 71s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 72s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 72s Reading package lists...
 72s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 73s Calculating upgrade...
 73s The following packages will be upgraded:
 73s   libpython3-stdlib python3 python3-minimal usbutils
 73s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s Need to get 144 kB of archives.
 73s After this operation, 0 B of additional disk space will be used.
 73s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB]
 74s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB]
 74s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB]
 74s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 usbutils arm64 1:019-1 [81.7 kB]
 74s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 74s Fetched 144 kB in 0s (390 kB/s)
 74s (Reading database ... 
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(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 ... 88137 files and directories currently installed.)
 74s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ...
 74s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ...
 75s Setting up python3-minimal (3.13.7-2) ...
 75s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 88137 files and directories currently installed.)
 75s Preparing to unpack .../python3_3.13.7-2_arm64.deb ...
 75s running python pre-rtupdate hooks for python3.13...
 75s Unpacking python3 (3.13.7-2) over (3.13.7-1) ...
 75s Preparing to unpack .../libpython3-stdlib_3.13.7-2_arm64.deb ...
 75s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ...
 75s Preparing to unpack .../usbutils_1%3a019-1_arm64.deb ...
 75s Unpacking usbutils (1:019-1) over (1:018-2) ...
 75s Setting up usbutils (1:019-1) ...
 75s Setting up libpython3-stdlib:arm64 (3.13.7-2) ...
 75s Setting up python3 (3.13.7-2) ...
 75s running python rtupdate hooks for python3.13...
 75s running python post-rtupdate hooks for python3.13...
 75s Processing triggers for man-db (2.13.1-1) ...
 78s autopkgtest [13:56:06]: upgrading testbed (apt dist-upgrade and autopurge)
 78s Reading package lists...
 78s Building dependency tree...
 78s Reading state information...
 78s Calculating upgrade...
 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 78s Reading package lists...
 78s Building dependency tree...
 78s Reading state information...
 78s Solving dependencies...
 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 81s autopkgtest [13:56:10]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025
 82s autopkgtest [13:56:11]: @@@@@@@@@@@@@@@@@@@@ apt-source busco
 83s Get:1 http://ftpmaster.internal/ubuntu resolute/universe busco 5.5.0-3 (dsc) [2079 B]
 83s Get:2 http://ftpmaster.internal/ubuntu resolute/universe busco 5.5.0-3 (tar) [392 kB]
 83s Get:3 http://ftpmaster.internal/ubuntu resolute/universe busco 5.5.0-3 (diff) [8608 B]
 84s gpgv: Signature made Thu Dec  5 18:33:36 2024 UTC
 84s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 84s gpgv:                issuer "tille@debian.org"
 84s gpgv: Can't check signature: No public key
 84s dpkg-source: warning: cannot verify inline signature for ./busco_5.5.0-3.dsc: no acceptable signature found
 84s autopkgtest [13:56:13]: testing package busco version 5.5.0-3
 84s autopkgtest [13:56:13]: build not needed
 85s autopkgtest [13:56:14]: test run-unit-test: preparing testbed
 86s Reading package lists...
 86s Building dependency tree...
 86s Reading state information...
 87s Solving dependencies...
 88s The following NEW packages will be installed:
 88s   bbmap busco ca-certificates-java default-jre-headless diffstat
 88s   fontconfig-config fonts-urw-base35 gettext hmmer java-common
 88s   libapache-pom-java libblas3 libcairo2 libcommons-cli-java
 88s   libcommons-codec-java libcommons-io-java libcommons-parent-java libdeflate0
 88s   libdivsufsort3 libfontconfig1 libfontenc1 libgfortran5 libgomp1
 88s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
 88s   liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java libmpj-java libopenjp2-7
 88s   libpcsclite1 libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib
 88s   libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3
 88s   libxcb-render0 libxcb-shm0 libxrender1 openjdk-21-jre-headless prodigal
 88s   python3-all python3-biopython python3-cairo python3-charset-normalizer
 88s   python3-freetype python3-numpy python3-numpy-dev python3-pandas
 88s   python3-pandas-lib python3-pil python3-pytz python3-reportlab
 88s   python3-rlpycairo python3.14 python3.14-minimal quilt sgml-base w3c-sgml-lib
 88s   x11-common xfonts-encodings xfonts-utils xml-core
 88s 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded.
 88s Need to get 104 MB of archives.
 88s After this operation, 415 MB of additional disk space will be used.
 88s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB]
 88s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB]
 88s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-7ubuntu1 [450 kB]
 88s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB]
 89s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB]
 89s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.0-4 [903 kB]
 89s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.0-4 [2543 kB]
 89s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB]
 89s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapache-pom-java all 33-2 [5874 B]
 89s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-parent-java all 56-1 [10.7 kB]
 89s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-codec-java all 1.18.0-1 [303 kB]
 89s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-io-java all 2.19.0-1 [491 kB]
 89s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB]
 89s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB]
 89s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 ca-certificates-java all 20240118 [11.6 kB]
 89s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 java-common all 0.76 [6852 B]
 89s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB]
 89s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB]
 89s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
 89s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcsclite1 arm64 2.4.0-2 [24.4 kB]
 89s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 openjdk-21-jre-headless arm64 21.0.9+10-1 [45.9 MB]
 91s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B]
 91s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 bbmap all 39.20+dfsg-3 [10.6 MB]
 92s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-4 [32.3 kB]
 92s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-1ubuntu1 [6979 kB]
 92s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB]
 92s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.3-1 [165 kB]
 92s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-7ubuntu1 [147 kB]
 92s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
 92s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB]
 92s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
 92s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB]
 92s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB]
 92s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB]
 92s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
 92s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
 92s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
 92s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
 92s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB]
 92s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB]
 92s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB]
 92s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu2 [492 kB]
 92s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB]
 92s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
 92s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
 92s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB]
 92s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
 93s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB]
 93s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB]
 93s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB]
 93s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB]
 93s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B]
 93s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB]
 93s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB]
 93s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB]
 93s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB]
 93s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B]
 93s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.4-2 [1147 kB]
 93s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB]
 93s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB]
 93s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
 93s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.85+dfsg-4 [1710 kB]
 93s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 libdivsufsort3 arm64 2.0.1-7 [42.7 kB]
 93s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB]
 93s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB]
 93s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 busco arm64 5.5.0-3 [295 kB]
 93s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 diffstat arm64 1.68-1 [29.1 kB]
 93s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 gettext arm64 0.23.2-1 [998 kB]
 93s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.0-4 [2349 kB]
 93s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.0-4 [805 kB]
 93s Get:71 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.13.7-2 [890 B]
 93s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 quilt all 0.68-1 [439 kB]
 94s Fetched 104 MB in 6s (18.7 MB/s)
 94s Selecting previously unselected package python3-numpy-dev:arm64.
 94s (Reading database ... 
(Reading database ... 5%
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(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 ... 88137 files and directories currently installed.)
 94s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ...
 94s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ...
 94s Selecting previously unselected package libblas3:arm64.
 94s Preparing to unpack .../01-libblas3_3.12.1-7_arm64.deb ...
 94s Unpacking libblas3:arm64 (3.12.1-7) ...
 94s Selecting previously unselected package libgfortran5:arm64.
 94s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_arm64.deb ...
 94s Unpacking libgfortran5:arm64 (15.2.0-7ubuntu1) ...
 94s Selecting previously unselected package liblapack3:arm64.
 94s Preparing to unpack .../03-liblapack3_3.12.1-7_arm64.deb ...
 94s Unpacking liblapack3:arm64 (3.12.1-7) ...
 94s Selecting previously unselected package python3-numpy.
 94s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ...
 94s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ...
 94s Selecting previously unselected package libpython3.14-minimal:arm64.
 94s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_arm64.deb ...
 94s Unpacking libpython3.14-minimal:arm64 (3.14.0-4) ...
 94s Selecting previously unselected package python3.14-minimal.
 94s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_arm64.deb ...
 94s Unpacking python3.14-minimal (3.14.0-4) ...
 94s Selecting previously unselected package libcommons-cli-java.
 94s Preparing to unpack .../07-libcommons-cli-java_1.6.0-1_all.deb ...
 94s Unpacking libcommons-cli-java (1.6.0-1) ...
 94s Selecting previously unselected package libapache-pom-java.
 94s Preparing to unpack .../08-libapache-pom-java_33-2_all.deb ...
 94s Unpacking libapache-pom-java (33-2) ...
 94s Selecting previously unselected package libcommons-parent-java.
 95s Preparing to unpack .../09-libcommons-parent-java_56-1_all.deb ...
 95s Unpacking libcommons-parent-java (56-1) ...
 95s Selecting previously unselected package libcommons-codec-java.
 95s Preparing to unpack .../10-libcommons-codec-java_1.18.0-1_all.deb ...
 95s Unpacking libcommons-codec-java (1.18.0-1) ...
 95s Selecting previously unselected package libcommons-io-java.
 95s Preparing to unpack .../11-libcommons-io-java_2.19.0-1_all.deb ...
 95s Unpacking libcommons-io-java (2.19.0-1) ...
 95s Selecting previously unselected package liblog4j1.2-java.
 95s Preparing to unpack .../12-liblog4j1.2-java_1.2.17-11_all.deb ...
 95s Unpacking liblog4j1.2-java (1.2.17-11) ...
 95s Selecting previously unselected package libmpj-java.
 95s Preparing to unpack .../13-libmpj-java_0.44+dfsg-4_all.deb ...
 95s Unpacking libmpj-java (0.44+dfsg-4) ...
 95s Selecting previously unselected package ca-certificates-java.
 95s Preparing to unpack .../14-ca-certificates-java_20240118_all.deb ...
 95s Unpacking ca-certificates-java (20240118) ...
 95s Selecting previously unselected package java-common.
 95s Preparing to unpack .../15-java-common_0.76_all.deb ...
 95s Unpacking java-common (0.76) ...
 95s Selecting previously unselected package liblcms2-2:arm64.
 95s Preparing to unpack .../16-liblcms2-2_2.17-1_arm64.deb ...
 95s Unpacking liblcms2-2:arm64 (2.17-1) ...
 95s Selecting previously unselected package libjpeg-turbo8:arm64.
 95s Preparing to unpack .../17-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ...
 95s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ...
 95s Selecting previously unselected package libjpeg8:arm64.
 95s Preparing to unpack .../18-libjpeg8_8c-2ubuntu11_arm64.deb ...
 95s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
 95s Selecting previously unselected package libpcsclite1:arm64.
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100s Setting up x11-common (1:7.7+24ubuntu1) ...
100s Setting up libdeflate0:arm64 (1.23-2) ...
100s Setting up liblog4j1.2-java (1.2.17-11) ...
100s Setting up python3-pytz (2025.2-4) ...
101s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ...
101s Setting up libgomp1:arm64 (15.2.0-7ubuntu1) ...
101s Setting up python3-freetype (2.5.1-2) ...
101s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
101s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ...
101s Setting up libblas3:arm64 (3.12.1-7) ...
101s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
101s Setting up libapache-pom-java (33-2) ...
101s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
101s Setting up diffstat (1.68-1) ...
101s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
101s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ...
101s Setting up libpcsclite1:arm64 (2.4.0-2) ...
101s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ...
101s Setting up libgfortran5:arm64 (15.2.0-7ubuntu1) ...
101s Setting up libwebp7:arm64 (1.5.0-0.1) ...
101s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ...
101s Setting up libharfbuzz0b:arm64 (12.1.0-1) ...
101s Setting up sgml-base (1.31+nmu1) ...
101s Setting up ca-certificates-java (20240118) ...
101s No JRE found. Skipping Java certificates setup.
101s Setting up libdivsufsort3:arm64 (2.0.1-7) ...
101s Setting up libwebpmux3:arm64 (1.5.0-0.1) ...
101s Setting up python3.14-minimal (3.14.0-4) ...
102s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
102s Setting up liblapack3:arm64 (3.12.1-7) ...
102s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
102s Setting up gettext (0.23.2-1) ...
102s Setting up openjdk-21-jre-headless:arm64 (21.0.9+10-1) ...
102s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
102s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
102s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
102s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
102s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
102s Setting up libpython3.14-stdlib:arm64 (3.14.0-4) ...
102s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ...
102s Setting up libcommons-parent-java (56-1) ...
102s Setting up quilt (0.68-1) ...
102s Setting up xfonts-utils (1:7.7+7) ...
102s Setting up libraqm0:arm64 (0.10.3-1) ...
102s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ...
106s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ...
106s Setting up xml-core (0.19) ...
106s Setting up hmmer (3.4+dfsg-2) ...
106s Setting up python3.14 (3.14.0-4) ...
107s Setting up libcommons-codec-java (1.18.0-1) ...
107s Setting up libcommons-io-java (2.19.0-1) ...
107s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ...
107s Setting up python3-all (3.13.7-2) ...
107s Setting up fonts-urw-base35 (20200910-8) ...
107s Setting up libmpj-java (0.44+dfsg-4) ...
107s Setting up python3-pil:arm64 (11.3.0-1ubuntu2) ...
108s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ...
118s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ...
118s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ...
118s Setting up libcairo2:arm64 (1.18.4-1build1) ...
118s Setting up python3-cairo (1.27.0-2build1) ...
119s Setting up python3-rlpycairo (0.3.0-4) ...
119s Setting up python3-reportlab (4.4.4-2) ...
120s Processing triggers for libc-bin (2.42-2ubuntu2) ...
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121s Processing triggers for ca-certificates-java (20240118) ...
122s Adding debian:ACCVRAIZ1.pem
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122s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
122s Adding debian:ANF_Secure_Server_Root_CA.pem
122s Adding debian:Actalis_Authentication_Root_CA.pem
122s Adding debian:AffirmTrust_Commercial.pem
122s Adding debian:AffirmTrust_Networking.pem
122s Adding debian:AffirmTrust_Premium.pem
122s Adding debian:AffirmTrust_Premium_ECC.pem
122s Adding debian:Amazon_Root_CA_1.pem
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122s Adding debian:Amazon_Root_CA_4.pem
122s Adding debian:Atos_TrustedRoot_2011.pem
122s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
122s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
122s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
122s Adding debian:BJCA_Global_Root_CA1.pem
122s Adding debian:BJCA_Global_Root_CA2.pem
122s Adding debian:Baltimore_CyberTrust_Root.pem
122s Adding debian:Buypass_Class_2_Root_CA.pem
122s Adding debian:Buypass_Class_3_Root_CA.pem
122s Adding debian:CA_Disig_Root_R2.pem
122s Adding debian:CFCA_EV_ROOT.pem
122s Adding debian:COMODO_Certification_Authority.pem
122s Adding debian:COMODO_ECC_Certification_Authority.pem
122s Adding debian:COMODO_RSA_Certification_Authority.pem
122s Adding debian:Certainly_Root_E1.pem
122s Adding debian:Certainly_Root_R1.pem
122s Adding debian:Certigna.pem
122s Adding debian:Certigna_Root_CA.pem
122s Adding debian:Certum_EC-384_CA.pem
122s Adding debian:Certum_Trusted_Network_CA.pem
122s Adding debian:Certum_Trusted_Network_CA_2.pem
122s Adding debian:Certum_Trusted_Root_CA.pem
122s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
122s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
122s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
122s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
122s Adding debian:Comodo_AAA_Services_root.pem
122s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
122s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem
122s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
122s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem
122s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
122s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
122s Adding debian:DigiCert_Assured_ID_Root_CA.pem
122s Adding debian:DigiCert_Assured_ID_Root_G2.pem
122s Adding debian:DigiCert_Assured_ID_Root_G3.pem
122s Adding debian:DigiCert_Global_Root_CA.pem
122s Adding debian:DigiCert_Global_Root_G2.pem
122s Adding debian:DigiCert_Global_Root_G3.pem
122s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
122s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
122s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
122s Adding debian:DigiCert_Trusted_Root_G4.pem
122s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
122s Adding debian:Entrust_Root_Certification_Authority.pem
122s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
122s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
122s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
122s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
122s Adding debian:GLOBALTRUST_2020.pem
122s Adding debian:GTS_Root_R1.pem
122s Adding debian:GTS_Root_R2.pem
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122s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
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122s Adding debian:GlobalSign_Root_CA_-_R3.pem
122s Adding debian:GlobalSign_Root_CA_-_R6.pem
122s Adding debian:GlobalSign_Root_E46.pem
122s Adding debian:GlobalSign_Root_R46.pem
122s Adding debian:Go_Daddy_Class_2_CA.pem
122s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
122s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
122s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
122s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
122s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
122s Adding debian:HiPKI_Root_CA_-_G1.pem
122s Adding debian:Hongkong_Post_Root_CA_3.pem
122s Adding debian:ISRG_Root_X1.pem
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122s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
122s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
122s Adding debian:Izenpe.com.pem
122s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
122s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
122s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
122s Adding debian:NAVER_Global_Root_Certification_Authority.pem
122s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
122s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
122s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
122s Adding debian:QuoVadis_Root_CA_1_G3.pem
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122s Adding debian:QuoVadis_Root_CA_3.pem
122s Adding debian:QuoVadis_Root_CA_3_G3.pem
122s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
122s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
122s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
122s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
122s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
122s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
122s Adding debian:SZAFIR_ROOT_CA2.pem
122s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
122s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
122s Adding debian:SecureSign_Root_CA12.pem
122s Adding debian:SecureSign_Root_CA14.pem
122s Adding debian:SecureSign_Root_CA15.pem
122s Adding debian:SecureTrust_CA.pem
122s Adding debian:Secure_Global_CA.pem
122s Adding debian:Security_Communication_ECC_RootCA1.pem
122s Adding debian:Security_Communication_RootCA2.pem
122s Adding debian:Starfield_Class_2_CA.pem
122s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
122s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
122s Adding debian:SwissSign_Gold_CA_-_G2.pem
122s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
122s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
122s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
122s Adding debian:TWCA_CYBER_Root_CA.pem
122s Adding debian:TWCA_Global_Root_CA.pem
122s Adding debian:TWCA_Root_Certification_Authority.pem
122s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
122s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
122s Adding debian:TeliaSonera_Root_CA_v1.pem
122s Adding debian:Telia_Root_CA_v2.pem
122s Adding debian:TrustAsia_Global_Root_CA_G3.pem
122s Adding debian:TrustAsia_Global_Root_CA_G4.pem
122s Adding debian:Trustwave_Global_Certification_Authority.pem
122s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
122s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
122s Adding debian:TunTrust_Root_CA.pem
122s Adding debian:UCA_Extended_Validation_Root.pem
122s Adding debian:UCA_Global_G2_Root.pem
122s Adding debian:USERTrust_ECC_Certification_Authority.pem
122s Adding debian:USERTrust_RSA_Certification_Authority.pem
122s Adding debian:XRamp_Global_CA_Root.pem
122s Adding debian:certSIGN_ROOT_CA.pem
122s Adding debian:certSIGN_Root_CA_G2.pem
122s Adding debian:e-Szigno_Root_CA_2017.pem
122s Adding debian:ePKI_Root_Certification_Authority.pem
122s Adding debian:emSign_ECC_Root_CA_-_C3.pem
122s Adding debian:emSign_ECC_Root_CA_-_G3.pem
122s Adding debian:emSign_Root_CA_-_C1.pem
122s Adding debian:emSign_Root_CA_-_G1.pem
122s Adding debian:vTrus_ECC_Root_CA.pem
122s Adding debian:vTrus_Root_CA.pem
122s done.
122s Setting up default-jre-headless (2:1.21-76) ...
122s Setting up bbmap (39.20+dfsg-3) ...
122s Processing triggers for sgml-base (1.31+nmu1) ...
122s Setting up w3c-sgml-lib (1.3-3) ...
149s Setting up python3-biopython (1.85+dfsg-4) ...
151s Setting up busco (5.5.0-3) ...
151s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\['
151s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
151s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: "\[" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\["? A raw string is also an option.
151s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
151s /usr/lib/python3/dist-packages/busco/busco_tools/hmmer.py:225: SyntaxWarning: 'return' in a 'finally' block
151s   return hmmer_version
152s autopkgtest [13:57:21]: test run-unit-test: [-----------------------
153s File series fully applied, ends at patch debian/patches/python3.12-syntax.patch
153s Testing with python3.14 in /tmp/autopkgtest.oGhpgC/autopkgtest_tmp:
153s unittest_runner (unittest.loader._FailedTest.unittest_runner) ... ERROR
153s 
153s ======================================================================
153s ERROR: unittest_runner (unittest.loader._FailedTest.unittest_runner)
153s ----------------------------------------------------------------------
153s ImportError: Failed to import test module: unittest_runner
153s Traceback (most recent call last):
153s   File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName
153s     module = __import__(module_name)
153s   File "/tmp/autopkgtest.oGhpgC/autopkgtest_tmp/tests/unittest_runner.py", line 2, in <module>
153s     from tests.unittests import run_BUSCO_unittests
153s   File "/tmp/autopkgtest.oGhpgC/autopkgtest_tmp/tests/unittests/run_BUSCO_unittests.py", line 2, in <module>
153s     from busco import run_BUSCO
153s   File "/usr/lib/python3/dist-packages/busco/run_BUSCO.py", line 25, in <module>
153s     from busco.BuscoRunner import AnalysisRunner, BatchRunner, SingleRunner
153s   File "/usr/lib/python3/dist-packages/busco/BuscoRunner.py", line 2, in <module>
153s     from busco.analysis.BuscoAnalysis import BuscoAnalysis
153s   File "/usr/lib/python3/dist-packages/busco/analysis/BuscoAnalysis.py", line 14, in <module>
153s     from busco.BuscoConfig import BaseConfig, BuscoConfigAuto
153s   File "/usr/lib/python3/dist-packages/busco/BuscoConfig.py", line 9, in <module>
153s     from busco.BuscoDownloadManager import BuscoDownloadManager
153s   File "/usr/lib/python3/dist-packages/busco/BuscoDownloadManager.py", line 22, in <module>
153s     import pandas as pd
153s   File "/usr/lib/python3/dist-packages/pandas/__init__.py", line 19, in <module>
153s     raise ImportError(
153s         "Unable to import required dependencies:\n" + "\n".join(_missing_dependencies)
153s     )
153s ImportError: Unable to import required dependencies:
153s numpy: Error importing numpy: you should not try to import numpy from
153s         its source directory; please exit the numpy source tree, and relaunch
153s         your python interpreter from there.
153s 
153s 
153s ----------------------------------------------------------------------
153s Ran 1 test in 0.000s
153s 
153s FAILED (errors=1)
153s autopkgtest [13:57:22]: test run-unit-test: -----------------------]
154s run-unit-test        FAIL non-zero exit status 1
154s autopkgtest [13:57:23]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
154s autopkgtest [13:57:23]: test run-busco-analysis: preparing testbed
174s Creating nova instance adt-resolute-arm64-busco-20251117-133229-juju-7f2275-prod-proposed-migration-environment-15-60093ae3-4beb-4ae2-83da-6a8f9c488fba from image adt/ubuntu-resolute-arm64-server-20251117.img (UUID 1cd33fbb-18df-4c5a-b8f0-2dcb25269485)...
227s autopkgtest [13:58:36]: testbed dpkg architecture: arm64
227s autopkgtest [13:58:36]: testbed apt version: 3.1.11
227s autopkgtest [13:58:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup
228s autopkgtest [13:58:37]: testbed release detected to be: resolute
228s autopkgtest [13:58:37]: updating testbed package index (apt update)
229s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB]
229s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
229s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
229s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
229s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB]
229s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB]
229s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB]
229s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B]
229s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [149 kB]
230s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3084 B]
230s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [107 kB]
230s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B]
230s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [577 kB]
230s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [17.8 kB]
230s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [12.5 kB]
230s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [576 B]
231s Fetched 1938 kB in 1s (1776 kB/s)
231s Reading package lists...
232s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
232s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
232s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
233s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
233s Reading package lists...
233s Reading package lists...
234s Building dependency tree...
234s Reading state information...
234s Calculating upgrade...
234s The following packages will be upgraded:
234s   libpython3-stdlib python3 python3-minimal usbutils
235s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
235s Need to get 144 kB of archives.
235s After this operation, 0 B of additional disk space will be used.
235s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB]
235s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB]
235s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB]
235s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 usbutils arm64 1:019-1 [81.7 kB]
235s dpkg-preconfigure: unable to re-open stdin: No such file or directory
235s Fetched 144 kB in 0s (331 kB/s)
236s (Reading database ... 
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(Reading database ... 88137 files and directories currently installed.)
236s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ...
236s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ...
236s Setting up python3-minimal (3.13.7-2) ...
236s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 88137 files and directories currently installed.)
236s Preparing to unpack .../python3_3.13.7-2_arm64.deb ...
236s running python pre-rtupdate hooks for python3.13...
236s Unpacking python3 (3.13.7-2) over (3.13.7-1) ...
236s Preparing to unpack .../libpython3-stdlib_3.13.7-2_arm64.deb ...
236s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ...
236s Preparing to unpack .../usbutils_1%3a019-1_arm64.deb ...
236s Unpacking usbutils (1:019-1) over (1:018-2) ...
236s Setting up usbutils (1:019-1) ...
236s Setting up libpython3-stdlib:arm64 (3.13.7-2) ...
236s Setting up python3 (3.13.7-2) ...
236s running python rtupdate hooks for python3.13...
236s running python post-rtupdate hooks for python3.13...
237s Processing triggers for man-db (2.13.1-1) ...
238s autopkgtest [13:58:47]: upgrading testbed (apt dist-upgrade and autopurge)
238s Reading package lists...
239s Building dependency tree...
239s Reading state information...
239s Calculating upgrade...
239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
239s Reading package lists...
240s Building dependency tree...
240s Reading state information...
240s Solving dependencies...
240s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
243s Reading package lists...
244s Building dependency tree...
244s Reading state information...
244s Solving dependencies...
244s The following NEW packages will be installed:
244s   bbmap busco ca-certificates-java default-jre-headless fontconfig-config
244s   fonts-urw-base35 hmmer java-common libapache-pom-java libblas3 libcairo2
244s   libcommons-cli-java libcommons-codec-java libcommons-io-java
244s   libcommons-parent-java libdeflate0 libdivsufsort3 libfontconfig1 libfontenc1
244s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0
244s   libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java
244s   libmpj-java libopenjp2-7 libpcsclite1 libpixman-1-0 libpython3.14-minimal
244s   libpython3.14-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
244s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 openjdk-21-jre-headless
244s   prodigal python3-all python3-biopython python3-cairo
244s   python3-charset-normalizer python3-freetype python3-numpy python3-numpy-dev
244s   python3-pandas python3-pandas-lib python3-pil python3-pytz python3-reportlab
244s   python3-rlpycairo python3.14 python3.14-minimal sgml-base w3c-sgml-lib
244s   x11-common xfonts-encodings xfonts-utils xml-core
244s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded.
244s Need to get 103 MB of archives.
244s After this operation, 410 MB of additional disk space will be used.
244s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB]
245s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB]
245s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-7ubuntu1 [450 kB]
245s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB]
245s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB]
245s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.0-4 [903 kB]
245s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.0-4 [2543 kB]
245s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB]
245s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapache-pom-java all 33-2 [5874 B]
245s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-parent-java all 56-1 [10.7 kB]
245s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-codec-java all 1.18.0-1 [303 kB]
245s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-io-java all 2.19.0-1 [491 kB]
245s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB]
245s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB]
245s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 ca-certificates-java all 20240118 [11.6 kB]
245s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 java-common all 0.76 [6852 B]
245s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB]
245s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB]
245s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
245s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcsclite1 arm64 2.4.0-2 [24.4 kB]
245s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 openjdk-21-jre-headless arm64 21.0.9+10-1 [45.9 MB]
247s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B]
247s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 bbmap all 39.20+dfsg-3 [10.6 MB]
247s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-4 [32.3 kB]
247s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-1ubuntu1 [6979 kB]
247s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB]
247s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.3-1 [165 kB]
247s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-7ubuntu1 [147 kB]
247s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
247s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB]
247s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
247s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB]
247s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB]
247s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB]
247s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
247s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
247s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
247s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
247s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB]
247s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB]
247s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB]
247s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu2 [492 kB]
247s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB]
247s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
247s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
247s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB]
247s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
247s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB]
247s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB]
247s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB]
247s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB]
247s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B]
247s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB]
247s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB]
247s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB]
247s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB]
248s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B]
248s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.4-2 [1147 kB]
248s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB]
248s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB]
248s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
248s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.85+dfsg-4 [1710 kB]
248s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 libdivsufsort3 arm64 2.0.1-7 [42.7 kB]
248s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB]
248s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB]
248s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 busco arm64 5.5.0-3 [295 kB]
248s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.0-4 [2349 kB]
248s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.0-4 [805 kB]
248s Get:69 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.13.7-2 [890 B]
248s Fetched 103 MB in 4s (28.1 MB/s)
248s Selecting previously unselected package python3-numpy-dev:arm64.
248s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
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248s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ...
248s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ...
248s Selecting previously unselected package libblas3:arm64.
248s Preparing to unpack .../01-libblas3_3.12.1-7_arm64.deb ...
248s Unpacking libblas3:arm64 (3.12.1-7) ...
248s Selecting previously unselected package libgfortran5:arm64.
248s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_arm64.deb ...
248s Unpacking libgfortran5:arm64 (15.2.0-7ubuntu1) ...
248s Selecting previously unselected package liblapack3:arm64.
248s Preparing to unpack .../03-liblapack3_3.12.1-7_arm64.deb ...
248s Unpacking liblapack3:arm64 (3.12.1-7) ...
248s Selecting previously unselected package python3-numpy.
248s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ...
248s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ...
249s Selecting previously unselected package libpython3.14-minimal:arm64.
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249s Selecting previously unselected package python3.14-minimal.
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249s Selecting previously unselected package libcommons-cli-java.
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249s Selecting previously unselected package libapache-pom-java.
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249s Selecting previously unselected package libcommons-parent-java.
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249s Selecting previously unselected package libcommons-io-java.
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249s Selecting previously unselected package liblog4j1.2-java.
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249s Selecting previously unselected package libmpj-java.
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249s Selecting previously unselected package ca-certificates-java.
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249s Selecting previously unselected package liblcms2-2:arm64.
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249s Selecting previously unselected package libjpeg-turbo8:arm64.
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250s Selecting previously unselected package default-jre-headless.
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251s Selecting previously unselected package python3-pandas-lib:arm64.
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251s Selecting previously unselected package python3-pandas.
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251s Selecting previously unselected package libgomp1:arm64.
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251s Selecting previously unselected package libimagequant0:arm64.
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251s Selecting previously unselected package libopenjp2-7:arm64.
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251s Selecting previously unselected package libgraphite2-3:arm64.
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251s Selecting previously unselected package libharfbuzz0b:arm64.
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251s Selecting previously unselected package libraqm0:arm64.
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251s Selecting previously unselected package libdeflate0:arm64.
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251s Selecting previously unselected package libjbig0:arm64.
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251s Selecting previously unselected package liblerc4:arm64.
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251s Selecting previously unselected package libsharpyuv0:arm64.
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251s Selecting previously unselected package libwebp7:arm64.
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252s Selecting previously unselected package libtiff6:arm64.
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252s Selecting previously unselected package libwebpdemux2:arm64.
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252s Selecting previously unselected package libwebpmux3:arm64.
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252s Selecting previously unselected package python3-pil:arm64.
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252s Unpacking python3-pil:arm64 (11.3.0-1ubuntu2) ...
252s Selecting previously unselected package libfontenc1:arm64.
252s Preparing to unpack .../42-libfontenc1_1%3a1.1.8-1build1_arm64.deb ...
252s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ...
252s Selecting previously unselected package x11-common.
252s Preparing to unpack .../43-x11-common_1%3a7.7+24ubuntu1_all.deb ...
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252s Selecting previously unselected package xfonts-encodings.
252s Preparing to unpack .../44-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
252s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
252s Selecting previously unselected package xfonts-utils.
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252s Unpacking xfonts-utils (1:7.7+7) ...
252s Selecting previously unselected package fonts-urw-base35.
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252s Unpacking fonts-urw-base35 (20200910-8) ...
252s Selecting previously unselected package fontconfig-config.
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252s Selecting previously unselected package libfontconfig1:arm64.
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252s Selecting previously unselected package libpixman-1-0:arm64.
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252s Selecting previously unselected package libxcb-render0:arm64.
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253s Selecting previously unselected package libxrender1:arm64.
253s Preparing to unpack .../52-libxrender1_1%3a0.9.12-1_arm64.deb ...
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253s Selecting previously unselected package libcairo2:arm64.
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253s Selecting previously unselected package python3-cairo.
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253s Selecting previously unselected package python3-rlpycairo.
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253s Selecting previously unselected package python3-reportlab.
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253s Selecting previously unselected package sgml-base.
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253s Selecting previously unselected package xml-core.
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253s Selecting previously unselected package w3c-sgml-lib.
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253s Selecting previously unselected package python3-biopython.
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253s Selecting previously unselected package libdivsufsort3:arm64.
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253s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
253s Setting up liblcms2-2:arm64 (2.17-1) ...
253s Setting up libpixman-1-0:arm64 (0.46.4-1) ...
253s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
254s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
254s Setting up java-common (0.76) ...
254s Setting up libxrender1:arm64 (1:0.9.12-1) ...
254s Setting up libcommons-cli-java (1.6.0-1) ...
254s Setting up libxcb-render0:arm64 (1.17.0-2build1) ...
254s Setting up prodigal (1:2.6.3-6) ...
254s Setting up python3-charset-normalizer (3.4.3-1) ...
254s Setting up libpython3.14-minimal:arm64 (3.14.0-4) ...
254s Setting up x11-common (1:7.7+24ubuntu1) ...
254s Setting up libdeflate0:arm64 (1.23-2) ...
254s Setting up liblog4j1.2-java (1.2.17-11) ...
254s Setting up python3-pytz (2025.2-4) ...
255s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ...
255s Setting up libgomp1:arm64 (15.2.0-7ubuntu1) ...
255s Setting up python3-freetype (2.5.1-2) ...
255s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
255s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ...
255s Setting up libblas3:arm64 (3.12.1-7) ...
255s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
255s Setting up libapache-pom-java (33-2) ...
255s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
255s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
255s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ...
255s Setting up libpcsclite1:arm64 (2.4.0-2) ...
255s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ...
255s Setting up libgfortran5:arm64 (15.2.0-7ubuntu1) ...
255s Setting up libwebp7:arm64 (1.5.0-0.1) ...
255s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ...
255s Setting up libharfbuzz0b:arm64 (12.1.0-1) ...
255s Setting up sgml-base (1.31+nmu1) ...
255s Setting up ca-certificates-java (20240118) ...
255s No JRE found. Skipping Java certificates setup.
255s Setting up libdivsufsort3:arm64 (2.0.1-7) ...
255s Setting up libwebpmux3:arm64 (1.5.0-0.1) ...
255s Setting up python3.14-minimal (3.14.0-4) ...
256s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
256s Setting up liblapack3:arm64 (3.12.1-7) ...
256s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
256s Setting up openjdk-21-jre-headless:arm64 (21.0.9+10-1) ...
256s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
256s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
256s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
256s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
256s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
256s Setting up libpython3.14-stdlib:arm64 (3.14.0-4) ...
256s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ...
256s Setting up libcommons-parent-java (56-1) ...
256s Setting up xfonts-utils (1:7.7+7) ...
256s Setting up libraqm0:arm64 (0.10.3-1) ...
256s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ...
260s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ...
260s Setting up xml-core (0.19) ...
260s Setting up hmmer (3.4+dfsg-2) ...
260s Setting up python3.14 (3.14.0-4) ...
261s Setting up libcommons-codec-java (1.18.0-1) ...
261s Setting up libcommons-io-java (2.19.0-1) ...
261s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ...
261s Setting up python3-all (3.13.7-2) ...
261s Setting up fonts-urw-base35 (20200910-8) ...
261s Setting up libmpj-java (0.44+dfsg-4) ...
261s Setting up python3-pil:arm64 (11.3.0-1ubuntu2) ...
262s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ...
272s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ...
272s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ...
272s Setting up libcairo2:arm64 (1.18.4-1build1) ...
272s Setting up python3-cairo (1.27.0-2build1) ...
272s Setting up python3-rlpycairo (0.3.0-4) ...
272s Setting up python3-reportlab (4.4.4-2) ...
274s Processing triggers for libc-bin (2.42-2ubuntu2) ...
274s Processing triggers for systemd (257.9-0ubuntu2) ...
274s Processing triggers for man-db (2.13.1-1) ...
275s Processing triggers for ca-certificates-java (20240118) ...
275s Adding debian:ACCVRAIZ1.pem
275s Adding debian:AC_RAIZ_FNMT-RCM.pem
275s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
275s Adding debian:ANF_Secure_Server_Root_CA.pem
275s Adding debian:Actalis_Authentication_Root_CA.pem
275s Adding debian:AffirmTrust_Commercial.pem
275s Adding debian:AffirmTrust_Networking.pem
275s Adding debian:AffirmTrust_Premium.pem
275s Adding debian:AffirmTrust_Premium_ECC.pem
275s Adding debian:Amazon_Root_CA_1.pem
275s Adding debian:Amazon_Root_CA_2.pem
275s Adding debian:Amazon_Root_CA_3.pem
275s Adding debian:Amazon_Root_CA_4.pem
275s Adding debian:Atos_TrustedRoot_2011.pem
275s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
275s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
275s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
275s Adding debian:BJCA_Global_Root_CA1.pem
275s Adding debian:BJCA_Global_Root_CA2.pem
275s Adding debian:Baltimore_CyberTrust_Root.pem
275s Adding debian:Buypass_Class_2_Root_CA.pem
275s Adding debian:Buypass_Class_3_Root_CA.pem
275s Adding debian:CA_Disig_Root_R2.pem
275s Adding debian:CFCA_EV_ROOT.pem
275s Adding debian:COMODO_Certification_Authority.pem
275s Adding debian:COMODO_ECC_Certification_Authority.pem
275s Adding debian:COMODO_RSA_Certification_Authority.pem
275s Adding debian:Certainly_Root_E1.pem
275s Adding debian:Certainly_Root_R1.pem
275s Adding debian:Certigna.pem
275s Adding debian:Certigna_Root_CA.pem
275s Adding debian:Certum_EC-384_CA.pem
275s Adding debian:Certum_Trusted_Network_CA.pem
275s Adding debian:Certum_Trusted_Network_CA_2.pem
275s Adding debian:Certum_Trusted_Root_CA.pem
275s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
275s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
275s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
275s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
275s Adding debian:Comodo_AAA_Services_root.pem
275s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
275s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem
275s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
275s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem
275s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
275s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
275s Adding debian:DigiCert_Assured_ID_Root_CA.pem
275s Adding debian:DigiCert_Assured_ID_Root_G2.pem
275s Adding debian:DigiCert_Assured_ID_Root_G3.pem
275s Adding debian:DigiCert_Global_Root_CA.pem
275s Adding debian:DigiCert_Global_Root_G2.pem
275s Adding debian:DigiCert_Global_Root_G3.pem
275s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
275s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
276s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
276s Adding debian:DigiCert_Trusted_Root_G4.pem
276s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
276s Adding debian:Entrust_Root_Certification_Authority.pem
276s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
276s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
276s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
276s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
276s Adding debian:GLOBALTRUST_2020.pem
276s Adding debian:GTS_Root_R1.pem
276s Adding debian:GTS_Root_R2.pem
276s Adding debian:GTS_Root_R3.pem
276s Adding debian:GTS_Root_R4.pem
276s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
276s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
276s Adding debian:GlobalSign_Root_CA.pem
276s Adding debian:GlobalSign_Root_CA_-_R3.pem
276s Adding debian:GlobalSign_Root_CA_-_R6.pem
276s Adding debian:GlobalSign_Root_E46.pem
276s Adding debian:GlobalSign_Root_R46.pem
276s Adding debian:Go_Daddy_Class_2_CA.pem
276s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
276s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
276s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
276s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
276s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
276s Adding debian:HiPKI_Root_CA_-_G1.pem
276s Adding debian:Hongkong_Post_Root_CA_3.pem
276s Adding debian:ISRG_Root_X1.pem
276s Adding debian:ISRG_Root_X2.pem
276s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
276s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
276s Adding debian:Izenpe.com.pem
276s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
276s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
276s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
276s Adding debian:NAVER_Global_Root_Certification_Authority.pem
276s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
276s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
276s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
276s Adding debian:QuoVadis_Root_CA_1_G3.pem
276s Adding debian:QuoVadis_Root_CA_2.pem
276s Adding debian:QuoVadis_Root_CA_2_G3.pem
276s Adding debian:QuoVadis_Root_CA_3.pem
276s Adding debian:QuoVadis_Root_CA_3_G3.pem
276s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
276s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
276s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
276s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
276s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
276s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
276s Adding debian:SZAFIR_ROOT_CA2.pem
276s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
276s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
276s Adding debian:SecureSign_Root_CA12.pem
276s Adding debian:SecureSign_Root_CA14.pem
276s Adding debian:SecureSign_Root_CA15.pem
276s Adding debian:SecureTrust_CA.pem
276s Adding debian:Secure_Global_CA.pem
276s Adding debian:Security_Communication_ECC_RootCA1.pem
276s Adding debian:Security_Communication_RootCA2.pem
276s Adding debian:Starfield_Class_2_CA.pem
276s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
276s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
276s Adding debian:SwissSign_Gold_CA_-_G2.pem
276s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
276s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
276s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
276s Adding debian:TWCA_CYBER_Root_CA.pem
276s Adding debian:TWCA_Global_Root_CA.pem
276s Adding debian:TWCA_Root_Certification_Authority.pem
276s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
276s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
276s Adding debian:TeliaSonera_Root_CA_v1.pem
276s Adding debian:Telia_Root_CA_v2.pem
276s Adding debian:TrustAsia_Global_Root_CA_G3.pem
276s Adding debian:TrustAsia_Global_Root_CA_G4.pem
276s Adding debian:Trustwave_Global_Certification_Authority.pem
276s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
276s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
276s Adding debian:TunTrust_Root_CA.pem
276s Adding debian:UCA_Extended_Validation_Root.pem
276s Adding debian:UCA_Global_G2_Root.pem
276s Adding debian:USERTrust_ECC_Certification_Authority.pem
276s Adding debian:USERTrust_RSA_Certification_Authority.pem
276s Adding debian:XRamp_Global_CA_Root.pem
276s Adding debian:certSIGN_ROOT_CA.pem
276s Adding debian:certSIGN_Root_CA_G2.pem
276s Adding debian:e-Szigno_Root_CA_2017.pem
276s Adding debian:ePKI_Root_Certification_Authority.pem
276s Adding debian:emSign_ECC_Root_CA_-_C3.pem
276s Adding debian:emSign_ECC_Root_CA_-_G3.pem
276s Adding debian:emSign_Root_CA_-_C1.pem
276s Adding debian:emSign_Root_CA_-_G1.pem
276s Adding debian:vTrus_ECC_Root_CA.pem
276s Adding debian:vTrus_Root_CA.pem
276s done.
276s Setting up default-jre-headless (2:1.21-76) ...
276s Setting up bbmap (39.20+dfsg-3) ...
276s Processing triggers for sgml-base (1.31+nmu1) ...
276s Setting up w3c-sgml-lib (1.3-3) ...
302s Setting up python3-biopython (1.85+dfsg-4) ...
305s Setting up busco (5.5.0-3) ...
305s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\['
305s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
305s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: "\[" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\["? A raw string is also an option.
305s   "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]"
305s /usr/lib/python3/dist-packages/busco/busco_tools/hmmer.py:225: SyntaxWarning: 'return' in a 'finally' block
305s   return hmmer_version
311s autopkgtest [14:00:00]: test run-busco-analysis: [-----------------------
311s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
311s   "cannot import name '(?P<module_name>[\w]+)", err.msg
312s 2025-11-17 14:00:00 INFO:	***** Start a BUSCO v5.5.0 analysis, current time: 11/17/2025 14:00:00 *****
312s 2025-11-17 14:00:00 INFO:	Configuring BUSCO with local environment
312s 2025-11-17 14:00:00 INFO:	Mode is genome
312s 2025-11-17 14:00:00 INFO:	Downloading information on latest versions of BUSCO data...
314s 2025-11-17 14:00:03 INFO:	Input file is /tmp/autopkgtest.oGhpgC/autopkgtest_tmp/genome.fna
314s 2025-11-17 14:00:03 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz'
316s 2025-11-17 14:00:05 INFO:	Decompressing file '/tmp/autopkgtest.oGhpgC/autopkgtest_tmp/busco_downloads/lineages/bacteria_odb10.tar.gz'
316s 2025-11-17 14:00:05 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2024-01-08)
316s 2025-11-17 14:00:05 INFO:	Running 1 job(s) on bbmap, starting at 11/17/2025 14:00:05
316s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
316s   "cannot import name '(?P<module_name>[\w]+)", err.msg
317s 2025-11-17 14:00:06 INFO:	[bbmap]	1 of 1 task(s) completed
317s 2025-11-17 14:00:06 INFO:	***** Run Prodigal on input to predict and extract genes *****
317s 2025-11-17 14:00:06 INFO:	Running Prodigal with genetic code 11 in single mode
317s 2025-11-17 14:00:06 INFO:	Running 1 job(s) on prodigal, starting at 11/17/2025 14:00:06
317s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
317s   "cannot import name '(?P<module_name>[\w]+)", err.msg
318s 2025-11-17 14:00:07 INFO:	[prodigal]	1 of 1 task(s) completed
318s 2025-11-17 14:00:07 INFO:	Genetic code 11 selected as optimal
318s 2025-11-17 14:00:07 INFO:	***** Run HMMER on gene sequences *****
318s 2025-11-17 14:00:07 INFO:	Running 124 job(s) on hmmsearch, starting at 11/17/2025 14:00:07
318s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
318s   "cannot import name '(?P<module_name>[\w]+)", err.msg
319s 2025-11-17 14:00:08 INFO:	[hmmsearch]	13 of 124 task(s) completed
319s 2025-11-17 14:00:08 INFO:	[hmmsearch]	25 of 124 task(s) completed
319s 2025-11-17 14:00:08 INFO:	[hmmsearch]	38 of 124 task(s) completed
319s 2025-11-17 14:00:08 INFO:	[hmmsearch]	50 of 124 task(s) completed
320s 2025-11-17 14:00:08 INFO:	[hmmsearch]	63 of 124 task(s) completed
320s 2025-11-17 14:00:09 INFO:	[hmmsearch]	75 of 124 task(s) completed
320s 2025-11-17 14:00:09 INFO:	[hmmsearch]	87 of 124 task(s) completed
320s 2025-11-17 14:00:09 INFO:	[hmmsearch]	100 of 124 task(s) completed
320s 2025-11-17 14:00:09 INFO:	[hmmsearch]	112 of 124 task(s) completed
320s 2025-11-17 14:00:09 INFO:	[hmmsearch]	124 of 124 task(s) completed
321s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w'
321s   "cannot import name '(?P<module_name>[\w]+)", err.msg
321s 2025-11-17 14:00:10 INFO:	Results:	C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124	   
321s 
321s 2025-11-17 14:00:10 INFO:	
321s 
321s 	---------------------------------------------------
321s 	|Results from dataset bacteria_odb10               |
321s 	---------------------------------------------------
321s 	|C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124      |
321s 	|26	Complete BUSCOs (C)                        |
321s 	|26	Complete and single-copy BUSCOs (S)        |
321s 	|0	Complete and duplicated BUSCOs (D)         |
321s 	|1	Fragmented BUSCOs (F)                      |
321s 	|97	Missing BUSCOs (M)                         |
321s 	|124	Total BUSCO groups searched                |
321s 	---------------------------------------------------
321s 2025-11-17 14:00:10 INFO:	BUSCO analysis done. Total running time: 7 seconds
321s 2025-11-17 14:00:10 INFO:	Results written in /tmp/autopkgtest.oGhpgC/autopkgtest_tmp/test_bacteria
321s 2025-11-17 14:00:10 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
321s 
321s 2025-11-17 14:00:10 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
321s Output Directory Generated
321s PASS
322s autopkgtest [14:00:11]: test run-busco-analysis: -----------------------]
322s autopkgtest [14:00:11]: test run-busco-analysis:  - - - - - - - - - - results - - - - - - - - - -
322s run-busco-analysis   PASS
322s autopkgtest [14:00:11]: @@@@@@@@@@@@@@@@@@@@ summary
322s run-unit-test        FAIL non-zero exit status 1
322s run-busco-analysis   PASS