0s autopkgtest [02:02:47]: starting date: 2024-03-18 1s autopkgtest [02:02:48]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 1s autopkgtest [02:02:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gw17lj0b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade macsyfinder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-24.secgroup --name adt-noble-arm64-macsyfinder-20240318-020247-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 99s autopkgtest [02:04:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 100s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 100s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 100s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 100s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 100s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 100s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 100s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 101s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 101s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 101s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 103s Fetched 9189 kB in 2s (5173 kB/s) 103s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 108s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 108s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 109s Reading package lists... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [02:04:39]: testbed dpkg architecture: arm64 113s autopkgtest [02:04:40]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 113s autopkgtest [02:04:40]: @@@@@@@@@@@@@@@@@@@@ apt-source macsyfinder 116s Get:1 http://ftpmaster.internal/ubuntu noble/universe macsyfinder 2.1.3-1 (dsc) [2460 B] 116s Get:2 http://ftpmaster.internal/ubuntu noble/universe macsyfinder 2.1.3-1 (tar) [37.8 MB] 116s Get:3 http://ftpmaster.internal/ubuntu noble/universe macsyfinder 2.1.3-1 (diff) [10.0 kB] 116s gpgv: Signature made Thu Feb 29 15:02:51 2024 UTC 116s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 116s gpgv: Can't check signature: No public key 116s dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.1.3-1.dsc: no acceptable signature found 117s autopkgtest [02:04:44]: testing package macsyfinder version 2.1.3-1 117s autopkgtest [02:04:44]: build not needed 123s autopkgtest [02:04:50]: test run-unit-test: preparing testbed 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 125s Starting 2 pkgProblemResolver with broken count: 0 125s Done 125s Done 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 126s The following additional packages will be installed: 126s fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libgfortran5 126s libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 126s libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libpython3.11-minimal 126s libpython3.11-stdlib macsyfinder ncbi-blast+ ncbi-data python3-colorama 126s python3-colorlog python3-dateutil python3-distutils python3-lib2to3 126s python3-networkx python3-numpy python3-packaging python3-pandas 126s python3-pandas-lib python3-setuptools python3.11 python3.11-minimal 126s sphinx-rtd-theme-common 126s Suggested packages: 126s hmmer-doc python-networkx-doc python3-gdal python3-matplotlib python3-pydot 126s python3-pygraphviz python3-scipy gcc gfortran python3-dev python3-pytest 126s python-pandas-doc python3-statsmodels python-setuptools-doc python3.11-venv 126s python3.11-doc binfmt-support 126s Recommended packages: 126s javascript-common python3-scipy python3-matplotlib python3-bottleneck 126s python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib 126s python3-lxml python3-tables 126s The following NEW packages will be installed: 126s fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libgfortran5 126s libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 126s libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libpython3.11-minimal 126s libpython3.11-stdlib macsyfinder ncbi-blast+ ncbi-data python3-colorama 126s python3-colorlog python3-dateutil python3-distutils python3-lib2to3 126s python3-networkx python3-numpy python3-packaging python3-pandas 126s python3-pandas-lib python3-setuptools python3.11 python3.11-minimal 126s sphinx-rtd-theme-common 127s 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. 127s 1 not fully installed or removed. 127s Need to get 62.3 MB of archives. 127s After this operation, 272 MB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 127s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-colorlog all 6.8.0-1 [21.0 kB] 127s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 127s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 127s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 127s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 127s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 127s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 127s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 127s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 127s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 127s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 127s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 127s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 128s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 128s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 128s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 128s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 128s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 128s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-lato all 2.015-1 [2781 kB] 128s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 128s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 128s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB] 128s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 128s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 128s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB] 128s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB] 128s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB] 128s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB] 128s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 macsyfinder arm64 2.1.3-1 [13.5 MB] 128s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 128s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 128s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] 129s Fetched 62.3 MB in 2s (29.5 MB/s) 129s Selecting previously unselected package python3-colorama. 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 129s Preparing to unpack .../00-python3-colorama_0.4.6-4_all.deb ... 129s Unpacking python3-colorama (0.4.6-4) ... 129s Selecting previously unselected package python3-colorlog. 129s Preparing to unpack .../01-python3-colorlog_6.8.0-1_all.deb ... 129s Unpacking python3-colorlog (6.8.0-1) ... 129s Selecting previously unselected package python3-networkx. 129s Preparing to unpack .../02-python3-networkx_2.8.8-1ubuntu1_all.deb ... 129s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 130s Selecting previously unselected package python3-packaging. 130s Preparing to unpack .../03-python3-packaging_23.2-1_all.deb ... 130s Unpacking python3-packaging (23.2-1) ... 130s Selecting previously unselected package python3-dateutil. 130s Preparing to unpack .../04-python3-dateutil_2.8.2-3_all.deb ... 130s Unpacking python3-dateutil (2.8.2-3) ... 130s Selecting previously unselected package libpython3.11-minimal:arm64. 130s Preparing to unpack .../05-libpython3.11-minimal_3.11.8-1_arm64.deb ... 130s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 130s Selecting previously unselected package python3.11-minimal. 130s Preparing to unpack .../06-python3.11-minimal_3.11.8-1_arm64.deb ... 130s Unpacking python3.11-minimal (3.11.8-1) ... 130s Selecting previously unselected package libpython3.11-stdlib:arm64. 130s Preparing to unpack .../07-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 130s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 130s Selecting previously unselected package python3.11. 130s Preparing to unpack .../08-python3.11_3.11.8-1_arm64.deb ... 130s Unpacking python3.11 (3.11.8-1) ... 130s Selecting previously unselected package libblas3:arm64. 130s Preparing to unpack .../09-libblas3_3.12.0-3_arm64.deb ... 130s Unpacking libblas3:arm64 (3.12.0-3) ... 130s Selecting previously unselected package libgfortran5:arm64. 130s Preparing to unpack .../10-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 130s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 130s Selecting previously unselected package liblapack3:arm64. 130s Preparing to unpack .../11-liblapack3_3.12.0-3_arm64.deb ... 130s Unpacking liblapack3:arm64 (3.12.0-3) ... 130s Selecting previously unselected package python3-numpy. 130s Preparing to unpack .../12-python3-numpy_1%3a1.24.2-2_arm64.deb ... 130s Unpacking python3-numpy (1:1.24.2-2) ... 130s Selecting previously unselected package python3-pandas-lib:arm64. 130s Preparing to unpack .../13-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 130s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 131s Selecting previously unselected package python3-pandas. 131s Preparing to unpack .../14-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 131s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 131s Selecting previously unselected package libjs-jquery. 131s Preparing to unpack .../15-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 131s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 131s Selecting previously unselected package libjs-underscore. 131s Preparing to unpack .../16-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 131s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 131s Selecting previously unselected package libjs-sphinxdoc. 131s Preparing to unpack .../17-libjs-sphinxdoc_7.2.6-4_all.deb ... 131s Unpacking libjs-sphinxdoc (7.2.6-4) ... 131s Selecting previously unselected package fonts-font-awesome. 131s Preparing to unpack .../18-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 131s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 131s Selecting previously unselected package fonts-lato. 131s Preparing to unpack .../19-fonts-lato_2.015-1_all.deb ... 131s Unpacking fonts-lato (2.015-1) ... 131s Selecting previously unselected package sphinx-rtd-theme-common. 131s Preparing to unpack .../20-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 131s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 131s Selecting previously unselected package libdivsufsort3:arm64. 131s Preparing to unpack .../21-libdivsufsort3_2.0.1-6_arm64.deb ... 131s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 131s Selecting previously unselected package hmmer. 131s Preparing to unpack .../22-hmmer_3.4+dfsg-2_arm64.deb ... 131s Unpacking hmmer (3.4+dfsg-2) ... 131s Selecting previously unselected package ncbi-data. 131s Preparing to unpack .../23-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 131s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 132s Selecting previously unselected package libgomp1:arm64. 132s Preparing to unpack .../24-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 132s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 132s Selecting previously unselected package libmbedcrypto7t64:arm64. 132s Preparing to unpack .../25-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ... 132s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 132s Selecting previously unselected package libmbedx509-1t64:arm64. 132s Preparing to unpack .../26-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ... 132s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 132s Selecting previously unselected package libmbedtls14t64:arm64. 132s Preparing to unpack .../27-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ... 132s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 132s Selecting previously unselected package ncbi-blast+. 132s Preparing to unpack .../28-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ... 132s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 132s Selecting previously unselected package macsyfinder. 132s Preparing to unpack .../29-macsyfinder_2.1.3-1_arm64.deb ... 132s Unpacking macsyfinder (2.1.3-1) ... 132s Selecting previously unselected package python3-lib2to3. 132s Preparing to unpack .../30-python3-lib2to3_3.11.5-1_all.deb ... 132s Unpacking python3-lib2to3 (3.11.5-1) ... 132s Selecting previously unselected package python3-distutils. 132s Preparing to unpack .../31-python3-distutils_3.11.5-1_all.deb ... 132s Unpacking python3-distutils (3.11.5-1) ... 132s Selecting previously unselected package python3-setuptools. 132s Preparing to unpack .../32-python3-setuptools_68.1.2-2_all.deb ... 132s Unpacking python3-setuptools (68.1.2-2) ... 132s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 132s Setting up fonts-lato (2.015-1) ... 132s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 132s Setting up python3-colorama (0.4.6-4) ... 133s Setting up python3-colorlog (6.8.0-1) ... 133s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 133s Setting up python3-networkx (2.8.8-1ubuntu1) ... 134s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 134s "graph [edge [ source u'u\4200' target u'u\4200' ] " 134s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 134s + "node [ id u'u\4200' label b ] ]" 134s Setting up libblas3:arm64 (3.12.0-3) ... 134s 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 134s Setting up python3-packaging (23.2-1) ... 134s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 134s Setting up python3-dateutil (2.8.2-3) ... 134s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 134s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 134s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 134s Setting up python3-lib2to3 (3.11.5-1) ... 135s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 135s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 135s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 135s Setting up python3-distutils (3.11.5-1) ... 135s python3.12: can't get files for byte-compilation 135s Setting up python3.11-minimal (3.11.8-1) ... 136s Setting up liblapack3:arm64 (3.12.0-3) ... 136s 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 136s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 136s Setting up python3-setuptools (68.1.2-2) ... 136s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 136s Setting up libjs-sphinxdoc (7.2.6-4) ... 136s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 137s Setting up hmmer (3.4+dfsg-2) ... 137s Setting up python3.11 (3.11.8-1) ... 137s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 137s Setting up python3-numpy (1:1.24.2-2) ... 139s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 139s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 143s Setting up macsyfinder (2.1.3-1) ... 143s /usr/lib/python3/dist-packages/macsypy/scripts/macsyconfig.py:282: SyntaxWarning: invalid escape sequence '\_' 143s """ 143s Setting up autopkgtest-satdep (0) ... 143s Processing triggers for systemd (255.2-3ubuntu2) ... 143s Processing triggers for man-db (2.12.0-3) ... 143s Processing triggers for libc-bin (2.39-0ubuntu2) ... 147s (Reading database ... 80391 files and directories currently installed.) 147s Removing autopkgtest-satdep (0) ... 149s autopkgtest [02:05:16]: test run-unit-test: [----------------------- 149s running test 149s WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. 149s /usr/lib/python3/dist-packages/setuptools/command/test.py:193: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 149s !! 149s 149s ******************************************************************************** 149s Requirements should be satisfied by a PEP 517 installer. 149s If you are using pip, you can try `pip install --use-pep517`. 149s ******************************************************************************** 149s 149s !! 149s ir_d = dist.fetch_build_eggs(dist.install_requires) 149s WARNING: The wheel package is not available. 149s /usr/lib/python3/dist-packages/setuptools/command/test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 149s !! 149s 149s ******************************************************************************** 149s Requirements should be satisfied by a PEP 517 installer. 149s If you are using pip, you can try `pip install --use-pep517`. 149s ******************************************************************************** 149s 149s !! 149s tr_d = dist.fetch_build_eggs(dist.tests_require or []) 149s WARNING: The wheel package is not available. 149s /usr/lib/python3/dist-packages/setuptools/command/test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 149s !! 149s 149s ******************************************************************************** 149s Requirements should be satisfied by a PEP 517 installer. 149s If you are using pip, you can try `pip install --use-pep517`. 149s ******************************************************************************** 149s 149s !! 149s er_d = dist.fetch_build_eggs( 149s WARNING: The wheel package is not available. 149s running egg_info 149s creating MacSyFinder.egg-info 149s writing MacSyFinder.egg-info/PKG-INFO 149s writing dependency_links to MacSyFinder.egg-info/dependency_links.txt 149s writing entry points to MacSyFinder.egg-info/entry_points.txt 149s writing requirements to MacSyFinder.egg-info/requires.txt 149s writing top-level names to MacSyFinder.egg-info/top_level.txt 149s writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' 149s reading manifest file 'MacSyFinder.egg-info/SOURCES.txt' 149s reading manifest template 'MANIFEST.in' 149s warning: no files found matching '*' under directory 'doc/build/html' 149s warning: no files found matching 'doc/build/latex/macsyfinder.pdf' 149s warning: no files found matching 'etc/macsyfinder.conf' 149s warning: no previously-included files matching '*' found under directory 'tests/__pycache__/' 149s warning: no previously-included files found matching 'tests/__init__.pyc' 149s warning: no previously-included files found matching '.coverage' 149s warning: no previously-included files found matching 'coverage_html/' 149s warning: no previously-included files found matching '.gitignore' 149s warning: no previously-included files found matching '.travis.yml' 149s warning: no previously-included files found matching '.github/' 149s warning: no files found matching 'CONTRIBUTORS' 149s warning: no files found matching 'NEWS' 149s adding license file 'COPYING' 149s writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' 149s running build_ext 149s /tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/__init__.py:128: SyntaxWarning: invalid escape sequence '\[' 149s red_pattern = "^\\x1b\[0?1;31m(.*)\\x1b\[0m$" 151s /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsyconfig.py:282: SyntaxWarning: invalid escape sequence '\_' 151s """ 151s test_Config (test_Config.TestConfig.test_Config) ... ok 151s test_Config_args (test_Config.TestConfig.test_Config_args) ... ok 151s test_Config_conf_file_virtualenv (test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok 151s test_Config_default_conf_file (test_Config.TestConfig.test_Config_default_conf_file) ... ok 151s test_Config_file_bad_values (test_Config.TestConfig.test_Config_file_bad_values) ... ok 151s test_Config_file_n_args (test_Config.TestConfig.test_Config_file_n_args) ... ok 151s test_bad_db_type (test_Config.TestConfig.test_bad_db_type) ... ok 151s test_bad_models_dir (test_Config.TestConfig.test_bad_models_dir) ... ok 151s test_bad_sequence_db (test_Config.TestConfig.test_bad_sequence_db) ... ok 151s test_bad_topology (test_Config.TestConfig.test_bad_topology) ... ok 151s test_bad_topology_file (test_Config.TestConfig.test_bad_topology_file) ... ok 151s test_bad_values (test_Config.TestConfig.test_bad_values) ... ok 151s test_cmd_config_file (test_Config.TestConfig.test_cmd_config_file) ... ok 151s test_config_file_2_dict (test_Config.TestConfig.test_config_file_2_dict) ... ok 151s test_cut_ga (test_Config.TestConfig.test_cut_ga) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/model_conf_parser.py:61: DeprecationWarning: Testing an element's truth value will raise an exception in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. 151s if filtering_node: 151s ok 151s test_e_value_search (test_Config.TestConfig.test_e_value_search) ... ok 151s test_hit_weights (test_Config.TestConfig.test_hit_weights) ... ok 151s test_hmmsearch (test_Config.TestConfig.test_hmmsearch) ... ok 151s test_hmmsearch_set_by_user (test_Config.TestConfig.test_hmmsearch_set_by_user) ... ok 151s test_model_conf (test_Config.TestConfig.test_model_conf) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/model_conf_parser.py:57: DeprecationWarning: Testing an element's truth value will raise an exception in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. 151s if weights_node: 151s ok 151s test_models_dir (test_Config.TestConfig.test_models_dir) ... ok 151s test_no_hmmsearch (test_Config.TestConfig.test_no_hmmsearch) ... 'hmmsearch' NOT found in your PATH, Please specify hmmsearch path with --hmmer opt or install 'hmmer' package. 151s ok 151s test_out_dir (test_Config.TestConfig.test_out_dir) ... ok 151s test_previous_n_sequence_db (test_Config.TestConfig.test_previous_n_sequence_db) ... ignore sequence_db '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/base/test_1.fasta' use sequence_db from previous_run '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/data_set/results_1'. 151s ok 151s test_previous_wo_cfg (test_Config.TestConfig.test_previous_wo_cfg) ... ok 151s test_project_config_file (test_Config.TestConfig.test_project_config_file) ... ok 151s test_save (test_Config.TestConfig.test_save) ... ok 151s test_set_log_level (test_Config.TestConfig.test_set_log_level) ... ok 151s test_set_option (test_Config.TestConfig.test_set_option) ... ok 151s test_str_2_tuple (test_Config.TestConfig.test_str_2_tuple) ... ok 151s test_working_dir (test_Config.TestConfig.test_working_dir) ... ok 151s test_NoneConfig (test_Config.TestNoneConfig.test_NoneConfig) ... ok 151s test_bad_exchangeable_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... Invalid model definition 'foo/bad_exchangeable_inter_gene_max_space': inter_gene_max_space must be an integer: 1.5 151s ok 151s test_bad_gene_inter_gene_max_space_2 (test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) ... Invalid model definition 'foo/bad_inter_gene_max_space_2': inter_gene_max_space must be an integer: 2.5 151s ok 151s test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... Invalid model definition (/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/definitions/bad_inter_gene_max_space.xml): inter_gene_max_space must be an integer: 12.5 151s ok 151s test_bad_max_nb_genes (test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... Invalid model definition (/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/definitions/bad_max_nb_genes.xml): max_nb_genes must be an integer: HOHOHO 151s ok 151s test_bad_min_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... model 'bad_min_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6 151s ok 151s test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... Invalid model definition (/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/definitions/bad_min_genes_required_2.xml): min_genes_required must be an integer: 16.5 151s ok 151s test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... Models Parsing 151s Models Parsing 151s Models Parsing 151s Models Parsing 151s Models Parsing 151s Models Parsing 151s model 'bad_min_mandatory_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6 151s ok 151s test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... Models Parsing 151s Models Parsing 151s ok 151s test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... Models Parsing 151s Invalid model definition (/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/definitions/bad_min_mandatory_genes_required_4.xml): min_mandatory_genes_required must be an integer: 12.5 151s ok 151s test_exchangeable_inheritance (test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... Models Parsing 151s ok 151s test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... Models Parsing 151s ok 151s test_gene_no_name (test_DefinitionParser.TestModelParser.test_gene_no_name) ... Models Parsing 151s Models Parsing 151s Invalid model definition 'foo/gene_no_name': gene without name 151s ok 151s test_gene_w_unkown_attr (test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... unable to parse model definition 'foo/gene_w_unknown_attribute' : The model definition gene_w_unknown_attribute.xml has an unknown attribute 'multi-system' for a gene. Please fix the definition. 151s ok 151s test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... Models Parsing 151s ok 151s test_invalid_homolog (test_DefinitionParser.TestModelParser.test_invalid_homolog) ... Models Parsing 151s ok 151s test_invalid_homolog_2 (test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... Models Parsing 151s Invalid model definition 'foo/invalid_homolog_2': gene without name 151s ok 151s test_invalid_presence (test_DefinitionParser.TestModelParser.test_invalid_presence) ... Models Parsing 151s Invalid model 'foo/fail_invalid_presence' definition: presence value must be either: 'mandatory', 'accessory', 'neutral', 'forbidden' not foo_bar 151s ok 151s test_loner (test_DefinitionParser.TestModelParser.test_loner) ... Models Parsing 151s Models Parsing 151s ok 151s test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... Models Parsing 151s Models Parsing 151s ok 151s test_min_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... Models Parsing 151s ok 151s test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... Models Parsing 151s ok 151s test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... Models Parsing 151s model 'bad_min_mandatory_genes_required_3' is not consistent: 'min_mandatory_genes_required': 6 must be lesser or equal than the number of 'mandatory' components in the model: 5 151s ok 151s test_model_w_unkown_attr (test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... Models Parsing 151s unable to parse model definition 'foo/model_w_unknown_attribute' : The model definition model_w_unknown_attribute.xml has an unknow attribute 'multi-loci'. Please fix the definition. 151s ok 151s test_multi_loci_cfg (test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... Models Parsing 151s ok 151s test_multi_model (test_DefinitionParser.TestModelParser.test_multi_model) ... ok 151s test_multi_system (test_DefinitionParser.TestModelParser.test_multi_system) ... Models Parsing 151s Models Parsing 151s ok 151s test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... Invalid model definition (/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/definitions/no_inter_gene_max_space.xml): inter_gene_max_space must be defined 151s ok 151s test_only_one_accessory (test_DefinitionParser.TestModelParser.test_only_one_accessory) ... Models Parsing 151s Models Parsing 151s model 'only_one_accessory' is not consistent: there is only one gene in your model. So its status should be 'mandatory'. 151s ok 151s test_parse_model_old_syntax (test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails' 151s test_parse_with_exchangeable (test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... Models Parsing 151s ok 151s test_wo_presence (test_DefinitionParser.TestModelParser.test_wo_presence) ... Models Parsing 151s Invalid model definition 'foo/fail_wo_presence': gene 'sctN_FLG' without presence 151s ok 151s test_add_exchangeable (test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok 151s test_alternate_of (test_Exchangeable.TestExchangeable.test_alternate_of) ... ok 151s test_is_exchangeable (test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok 151s test_loner (test_Exchangeable.TestExchangeable.test_loner) ... ok 151s test_model (test_Exchangeable.TestExchangeable.test_model) ... ok 151s test_multi_system (test_Exchangeable.TestExchangeable.test_multi_system) ... ok 151s test_add_get_gene (test_GeneBank.Test.test_add_get_gene) ... ok 151s test_contains (test_GeneBank.Test.test_contains) ... ok 151s test_genes_fqn (test_GeneBank.Test.test_genes_fqn) ... ok 151s test_get_uniq_object (test_GeneBank.Test.test_get_uniq_object) ... ok 151s test_iter (test_GeneBank.Test.test_iter) ... ok 151s test_fasta_iter (test_Indexes.TestFastaIter.test_fasta_iter) ... ok 151s test_fasta_iter_bad_fasta (test_Indexes.TestFastaIter.test_fasta_iter_bad_fasta) ... Error during sequence '/tmp/test_macsyfinder_fasta_iter/sequence.fa' parsing: Check the fasta format. 151s ok 151s test_build_force (test_Indexes.TestIndex.test_build_force) ... ok 151s test_build_idx_gzip_seq (test_Indexes.TestIndex.test_build_idx_gzip_seq) ... MacSyFinder does not support 'bz2' compression (only gzip). 151s MacSyFinder does not support 'zip' compression (only gzip). 151s ok 151s test_build_idx_older_than_fasta (test_Indexes.TestIndex.test_build_idx_older_than_fasta) ... ok 151s test_build_idx_point_wrong_fasta (test_Indexes.TestIndex.test_build_idx_point_wrong_fasta) ... The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file does not point to '/tmp/test_macsyfinder_indexes/test_1.fasta'. Force building 151s ok 151s test_build_my_indexes (test_Indexes.TestIndex.test_build_my_indexes) ... unable to index the sequence dataset: /tmp/test_macsyfinder_indexes/test_base_with_errors.fa : list index out of range 151s Traceback (most recent call last): 151s File "/tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/database.py", line 214, in _build_my_indexes 151s for seq_id, comment, length in f_iter: 151s File "/tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/database.py", line 53, in fasta_iter 151s _id = header[0] 151s ~~~~~~^^^ 151s IndexError: list index out of range 151s ok 151s test_build_no_idx (test_Indexes.TestIndex.test_build_no_idx) ... ok 151s test_build_not_writable (test_Indexes.TestIndex.test_build_not_writable) ... The '/tmp/test_macsyfinder_indexes' dir is not writable. 151s ok 151s test_build_with_idx (test_Indexes.TestIndex.test_build_with_idx) ... The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building. 151s The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building. 151s ok 151s test_empty_fasta (test_Indexes.TestIndex.test_empty_fasta) ... ok 151s test_find_my_indexes (test_Indexes.TestIndex.test_find_my_indexes) ... ok 151s test_index_dir (test_Indexes.TestIndex.test_index_dir) ... ok 151s test_iter (test_Indexes.TestIndex.test_iter) ... ok 151s test_allowed_hits (test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok 151s test_forbidden_hits (test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok 152s test_hits (test_LikelySystem.LikelySystemTest.test_hits) ... ok 152s test_init (test_LikelySystem.LikelySystemTest.test_init) ... ok 152s test_str (test_LikelySystem.LikelySystemTest.test_str) ... ok 152s test_hits (test_LikelySystem.UnlikelySystemTest.test_hits) ... ok 152s test_init (test_LikelySystem.UnlikelySystemTest.test_init) ... ok 152s test_reason (test_LikelySystem.UnlikelySystemTest.test_reason) ... ok 152s test_str (test_LikelySystem.UnlikelySystemTest.test_str) ... ok 152s test_MacsyDefaults_no_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok 152s test_MacsyDefaults_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok 152s test_ordered_match (test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok 152s test_sort_hits_by_status (test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... Gene 'fliE' not found in model 'foo/model_B' 152s ok 152s test_unordered_match (test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok 152s test_accessor_mutator (test_Model.TestModel.test_accessor_mutator) ... ok 152s test_eq (test_Model.TestModel.test_eq) ... ok 152s test_filter (test_Model.TestModel.test_filter) ... ok 152s test_fqn (test_Model.TestModel.test_fqn) ... ok 152s test_get_gene (test_Model.TestModel.test_get_gene) ... ok 152s test_gt (test_Model.TestModel.test_gt) ... ok 152s test_hash (test_Model.TestModel.test_hash) ... ok 152s test_inter_gene_max_space (test_Model.TestModel.test_inter_gene_max_space) ... ok 152s test_lt (test_Model.TestModel.test_lt) ... ok 152s test_max_nb_genes (test_Model.TestModel.test_max_nb_genes) ... ok 152s test_min_genes_required (test_Model.TestModel.test_min_genes_required) ... ok 152s test_min_mandatory_genes_required (test_Model.TestModel.test_min_mandatory_genes_required) ... ok 152s test_multi_loci (test_Model.TestModel.test_multi_loci) ... ok 152s test_str (test_Model.TestModel.test_str) ... ok 152s test_add_get_model (test_ModelBank.Test.test_add_get_model) ... ok 152s test_contains (test_ModelBank.Test.test_contains) ... ok 152s test_get_uniq_object (test_ModelBank.Test.test_get_uniq_object) ... ok 152s test_iter (test_ModelBank.Test.test_iter) ... ok 152s test_execute_hmm_protected_path (test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok 152s test_execute_hmm_w_GA_n_nocutga (test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok 152s test_execute_hmm_with_GA (test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping' 152s test_execute_hmm_wo_GA (test_Profile.TestProfile.test_execute_hmm_wo_GA) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) 152s ok 152s test_execute_hmmer_failed (test_Profile.TestProfile.test_execute_hmmer_failed) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) 152s an error occurred during Hmmer execution: command = "/tmp/hmmer_failed" --cpu 1 -o "/tmp/macsyfinder-20240318_02-05-19/hmmer_results/abc.search_hmm.out" -E 0.100000 "/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/profiles/abc.hmm" "/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240318_02-05-19/hmmer_results/abc.search_hmm.err 152s ok 152s test_execute_unknown_binary (test_Profile.TestProfile.test_execute_unknown_binary) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) 152s an error occurred during Hmmer execution: command = "Nimportnaoik" --cpu 1 -o "/tmp/macsyfinder-20240318_02-05-19/hmmer_results/abc.search_hmm.out" -E 0.100000 "/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/profiles/abc.hmm" "/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240318_02-05-19/hmmer_results/abc.search_hmm.err 152s ok 152s test_ga_threshold (test_Profile.TestProfile.test_ga_threshold) ... bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''. 152s GA score will not used for gene 'bad_GA'. 152s bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''. 152s GA score will not used for gene 'bad_GA'. 152s bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'. 152s GA score will not used for gene 'bad_GA_2'. 152s bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'. 152s GA score will not used for gene 'bad_GA_2'. 152s ok 152s test_len (test_Profile.TestProfile.test_len) ... MacSyFinder does not support 'bz2' compression (only gzip). 152s MacSyFinder does not support 'zip' compression (only gzip). 152s Cannot read profile /tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/models/foo/profiles/bad_ext.hmm.gz: Not a gzipped file (b'BZ') 152s ok 152s test_str (test_Profile.TestProfile.test_str) ... ok 152s test_get_profile (test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok 152s test_get_uniq_object (test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok 152s test_unknow_profile (test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok 152s test_hits (test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok 152s test_init (test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok 152s test_str (test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok 152s test_fill_gembase_min_max_default_topology (test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok 152s test_fill_gembase_min_max_with_topology (test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok 152s test_fill_ordered_replicon_min_max (test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok 152s test_fill_topology (test_RepliconDB.Test.test_fill_topology) ... ok 152s test_get (test_RepliconDB.Test.test_get) ... ok 152s test_getitem (test_RepliconDB.Test.test_getitem) ... ok 152s test_guess_if_really_gembase (test_RepliconDB.Test.test_guess_if_really_gembase) ... ok 152s test_in (test_RepliconDB.Test.test_in) ... ok 152s test_items (test_RepliconDB.Test.test_items) ... ok 152s test_iteritems (test_RepliconDB.Test.test_iteritems) ... ok 152s test_names (test_RepliconDB.Test.test_names) ... ok 152s test_replicon_infos (test_RepliconDB.Test.test_replicon_infos) ... ok 152s test_extract (test_Report.TestGembaseHMMReport.test_extract) ... ok 152s test_extract_concurent (test_Report.TestGembaseHMMReport.test_extract_concurent) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead 152s main_thread = threading.currentThread() 152s ok 152s test_extract (test_Report.TestGeneralHMMReport.test_extract) ... ok 152s test_extract_concurent (test_Report.TestGeneralHMMReport.test_extract_concurent) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/test_Report.py:541: DeprecationWarning: currentThread() is deprecated, use current_thread() instead 152s main_thread = threading.currentThread() 152s ok 152s test_HMMReport (test_Report.TestHMMReport.test_HMMReport) ... ok 152s test_best_hit (test_Report.TestHMMReport.test_best_hit) ... ok 152s test_build_my_db (test_Report.TestHMMReport.test_build_my_db) ... ok 152s test_fill_my_db (test_Report.TestHMMReport.test_fill_my_db) ... ok 152s test_hit_start (test_Report.TestHMMReport.test_hit_start) ... ok 152s test_parse_hmm_body (test_Report.TestHMMReport.test_parse_hmm_body) ... ok 152s test_parse_hmm_header (test_Report.TestHMMReport.test_parse_hmm_header) ... ok 152s test_save_extract (test_Report.TestHMMReport.test_save_extract) ... ok 152s test_str (test_Report.TestHMMReport.test_str) ... ok 152s test_extract (test_Report.TestOrderedHMMReport.test_extract) ... hit id 'NC_xxxxx_xx_056141' was not indexed, rebuild sequence 'test_base.fa' index 152s ok 152s test_extract_concurent (test_Report.TestOrderedHMMReport.test_extract_concurent) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/test_Report.py:461: DeprecationWarning: currentThread() is deprecated, use current_thread() instead 152s main_thread = threading.currentThread() 152s ok 152s test_HitSystemTracker (test_System.SystemTest.test_HitSystemTracker) ... ok 152s test_count (test_System.SystemTest.test_count) ... ok 152s test_fulfilled_function (test_System.SystemTest.test_fulfilled_function) ... ok 152s test_get_hits_encoding_multisystem (test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok 152s test_get_loners (test_System.SystemTest.test_get_loners) ... ok 152s test_get_multisystems (test_System.SystemTest.test_get_multisystems) ... ok 152s test_hits (test_System.SystemTest.test_hits) ... ok 152s test_init (test_System.SystemTest.test_init) ... ok 152s test_is_compatible (test_System.SystemTest.test_is_compatible) ... ok 152s test_loci_nb (test_System.SystemTest.test_loci_nb) ... ok 152s test_loci_num (test_System.SystemTest.test_loci_num) ... ok 152s test_multi_loci (test_System.SystemTest.test_multi_loci) ... ok 152s test_occurrence (test_System.SystemTest.test_occurrence) ... ok 152s test_position (test_System.SystemTest.test_position) ... ok 152s test_score (test_System.SystemTest.test_score) ... ok 152s test_wholeness (test_System.SystemTest.test_wholeness) ... ok 152s test_build_clusters (test_cluster.TestBuildCluster.test_build_clusters) ... ok 152s test_clusterize (test_cluster.TestBuildCluster.test_clusterize) ... ok 152s test_colocates (test_cluster.TestBuildCluster.test_colocates) ... ok 152s test_get_true_loners (test_cluster.TestBuildCluster.test_get_true_loners) ... ok 152s test_contains (test_cluster.TestCluster.test_contains) ... ok 152s test_fulfilled_function (test_cluster.TestCluster.test_fulfilled_function) ... ok 152s test_init (test_cluster.TestCluster.test_init) ... Cannot build a cluster from hits coming from different replicons 152s ok 152s test_len (test_cluster.TestCluster.test_len) ... ok 152s test_loner (test_cluster.TestCluster.test_loner) ... ok 152s test_merge (test_cluster.TestCluster.test_merge) ... ok 152s test_multi_system (test_cluster.TestCluster.test_multi_system) ... ok 152s test_replace (test_cluster.TestCluster.test_replace) ... ok 152s test_replicon_name (test_cluster.TestCluster.test_replicon_name) ... ok 152s test_score (test_cluster.TestCluster.test_score) ... ok 152s test_str (test_cluster.TestCluster.test_str) ... ok 152s test_2_systems_not_compatible (test_functional_test.Test.test_2_systems_not_compatible) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='UTF-8'> 152s self.tearDown() 152s ResourceWarning: Enable tracemalloc to get the object allocation traceback 152s ok 152s test_cfg_n_previous_run (test_functional_test.Test.test_cfg_n_previous_run) ... ok 152s test_degenerated_systems (test_functional_test.Test.test_degenerated_systems) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='UTF-8'> 152s self.tearDown() 152s ResourceWarning: Enable tracemalloc to get the object allocation traceback 152s ok 152s test_force (test_functional_test.Test.test_force) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_functional_test_ordered_circular/macsyfinder.log' mode='a' encoding='UTF-8'> 152s self.tearDown() 152s ResourceWarning: Enable tracemalloc to get the object allocation traceback 152s ok 152s test_gembase (test_functional_test.Test.test_gembase) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/model_conf_parser.py:61: DeprecationWarning: Testing an element's truth value will raise an exception in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. 152s if filtering_node: 156s /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_gzip (test_functional_test.Test.test_gzip) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gzip/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_index_dir (test_functional_test.Test.test_index_dir) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_model_unknown (test_functional_test.Test.test_model_unknown) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_no_db_type (test_functional_test.Test.test_no_db_type) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_no_models (test_functional_test.Test.test_no_models) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_no_seq_db (test_functional_test.Test.test_no_seq_db) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_no_sequence (test_functional_test.Test.test_no_sequence) ... The sequence-db file '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/base/empty.fasta' does not contains sequences. 156s /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_no_sequence/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_only_loners (test_functional_test.Test.test_only_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_1_cluster_3_loners (test_functional_test.Test.test_ordered_1_cluster_3_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_1_cluster_and_clusters_of_loners (test_functional_test.Test.test_ordered_1_cluster_and_clusters_of_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_and_clusters_of_loners/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_1_clusters_3_loners_w_exchangeable (test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_1_loner_exch_in_clust (test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_1_loner_in_clust (test_functional_test.Test.test_ordered_1_loner_in_clust) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_2_clusters_1_loner (test_functional_test.Test.test_ordered_2_clusters_1_loner) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_2_clusters_3_loners (test_functional_test.Test.test_ordered_2_clusters_3_loners) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_circular (test_functional_test.Test.test_ordered_circular) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_linear (test_functional_test.Test.test_ordered_linear) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_multi_loci (test_functional_test.Test.test_ordered_multi_loci) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_multi_model (test_functional_test.Test.test_ordered_multi_model) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_multi_system (test_functional_test.Test.test_ordered_multi_system) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_multi_system_out_system (test_functional_test.Test.test_ordered_multi_system_out_system) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_only_one_multi_model (test_functional_test.Test.test_ordered_only_one_multi_model) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 156s test_ordered_single_loci (test_functional_test.Test.test_ordered_single_loci) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='UTF-8'> 156s self.tearDown() 156s ResourceWarning: Enable tracemalloc to get the object allocation traceback 156s ok 160s test_timeout (test_functional_test.Test.test_timeout) ... Timeout is over. Aborting 160s The THHY002.0321.00001.C001 cannot be solved in time skip it! 160s The replicon THHY002.0321.00001.C001 cannot be solved before timeout. SKIP IT. 160s ok 160s test_uncomplete_degenerated_systems (test_functional_test.Test.test_uncomplete_degenerated_systems) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_unordered (test_functional_test.Test.test_unordered) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_unordered_no_hits (test_functional_test.Test.test_unordered_no_hits) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_unordered_only_forbidden (test_functional_test.Test.test_unordered_only_forbidden) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_working_dir_exists (test_functional_test.Test.test_working_dir_exists) ... ok 160s test_working_dir_exists_and_not_dir (test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok 160s test_core_gene (test_gene.TestCoreGene.test_core_gene) ... ok 160s test_str (test_gene.TestGeneStatus.test_str) ... ok 160s test_add_exchangeable (test_gene.TestModelGene.test_add_exchangeable) ... ok 160s test_alternate_of (test_gene.TestModelGene.test_alternate_of) ... ok 160s test_core_gene (test_gene.TestModelGene.test_core_gene) 160s test getter/setter for core_gene property ... ok 160s test_exhangeables (test_gene.TestModelGene.test_exhangeables) ... ok 160s test_hash (test_gene.TestModelGene.test_hash) ... ok 160s test_init (test_gene.TestModelGene.test_init) ... ok 160s test_inter_gene_max_space (test_gene.TestModelGene.test_inter_gene_max_space) 160s test getter for inter_gene_max_space property ... ok 160s test_is_Forbidden (test_gene.TestModelGene.test_is_Forbidden) 160s test if gene belong to model mandatory genes ... ok 160s test_is_accessory (test_gene.TestModelGene.test_is_accessory) 160s test if gene belong to model mandatory genes ... ok 160s test_is_exchangeable (test_gene.TestModelGene.test_is_exchangeable) ... ok 160s test_is_mandatory (test_gene.TestModelGene.test_is_mandatory) 160s test if gene belong to model mandatory genes ... ok 160s test_loner (test_gene.TestModelGene.test_loner) 160s test getter for loner property ... ok 160s test_model (test_gene.TestModelGene.test_model) 160s test getter/setter for model property ... ok 160s test_multi_model (test_gene.TestModelGene.test_multi_model) 160s test getter for multi_modelproperty ... ok 160s test_multi_system (test_gene.TestModelGene.test_multi_system) 160s test getter for multi_system property ... ok 160s test_str (test_gene.TestModelGene.test_str) ... ok 160s test_unknown_attribute (test_gene.TestModelGene.test_unknown_attribute) ... ok 160s test_cmp (test_hit.CoreHitTest.test_cmp) ... ok 160s test_eq (test_hit.CoreHitTest.test_eq) ... ok 160s test_get_position (test_hit.CoreHitTest.test_get_position) ... ok 160s test_hash (test_hit.CoreHitTest.test_hash) ... ok 160s test_str (test_hit.CoreHitTest.test_str) ... ok 160s test_compute_best_MSHit (test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok 160s test_get_best_hits (test_hit.GetBestHitTest.test_get_best_hits) ... ok 160s test_get_best_hits_4_func (test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok 160s test_sort_multisystem_hits (test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok 160s test_hit_weight_default (test_hit.HitWeightTest.test_hit_weight_default) ... ok 160s test_hit_weight_not_default (test_hit.HitWeightTest.test_hit_weight_not_default) ... ok 160s test_counterpart (test_hit.LonerMultiSystemTest.test_counterpart) ... Try to set counterpart for hit 'gspD' with non compatible hits: ['gspD', 'sctJ'] 160s ok 160s test_init (test_hit.LonerMultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system 160s ok 160s test_loner (test_hit.LonerMultiSystemTest.test_loner) ... ok 160s test_multi_system (test_hit.LonerMultiSystemTest.test_multi_system) ... ok 160s test_str (test_hit.LonerMultiSystemTest.test_str) ... ok 160s test_counterpart (test_hit.LonerTest.test_counterpart) ... ok 160s test_init (test_hit.LonerTest.test_init) ... hit_2 cannot be a loner gene_ref 'sctJ' not tag as loner 160s ok 160s test_len (test_hit.LonerTest.test_len) ... ok 160s test_loner (test_hit.LonerTest.test_loner) ... ok 160s test_multi_system (test_hit.LonerTest.test_multi_system) ... ok 160s test_str (test_hit.LonerTest.test_str) ... ok 160s test_delegation (test_hit.ModelHitTest.test_delegation) ... ok 160s test_eq (test_hit.ModelHitTest.test_eq) ... ok 160s test_hash (test_hit.ModelHitTest.test_hash) ... ok 160s test_init (test_hit.ModelHitTest.test_init) ... ok 160s test_loner (test_hit.ModelHitTest.test_loner) ... ok 160s test_multi_model (test_hit.ModelHitTest.test_multi_model) ... ok 160s test_multi_system (test_hit.ModelHitTest.test_multi_system) ... ok 160s test_counterpart (test_hit.MultiSystemTest.test_counterpart) ... ok 160s test_init (test_hit.MultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system 160s ok 160s test_len (test_hit.MultiSystemTest.test_len) ... ok 160s test_loner (test_hit.MultiSystemTest.test_loner) ... ok 160s test_multi_system (test_hit.MultiSystemTest.test_multi_system) ... ok 160s test_str (test_hit.MultiSystemTest.test_str) ... ok 160s test_functional_split (test_macsy_gembase_split.TestSplit.test_functional_split) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpoqkit0ez/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_functional_split_out_error (test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... /tmp/tmppf01emp_/macsyfinder_test_split/base is not a directory 160s ok 160s test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... /tmp/tmp0boonswc/macsyfinder_test_split/base is not writable 160s Cannot create /tmp/tmp0boonswc/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmp0boonswc/macsyfinder_test_split/base' 160s ok 160s test_functional_merge (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv' 160s Merging 'best_solution.tsv' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_best_solution.tsv' 160s Merging 'all_systems.tsv' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_all_systems.tsv' 160s Merging 'best_solution_multisystems.tsv' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv' 160s Merging 'best_solution_loners.tsv' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv' 160s Merging 'rejected_candidates.tsv' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv' 160s Merging 'all_systems.txt' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_all_systems.txt' 160s Merging 'rejected_candidates.txt' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt' 160s Merging 'best_solution_summary' in to '/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv' 160s /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpo4jp88bz/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_functional_merge_one_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpxygfxtuq/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'> 160s self.tearDown() 160s ResourceWarning: Enable tracemalloc to get the object allocation traceback 160s ok 160s test_functional_merge_out_error (test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... /tmp/tmpa15i7spg/macsyfinder_test_merge/merged_results is not a directory 160s ok 160s test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... /tmp/tmptt5ig0jd/macsyfinder_test_merge/merged_results is not writable 160s Cannot create /tmp/tmptt5ig0jd/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmptt5ig0jd/macsyfinder_test_merge/merged_results' 160s ok 161s test_functional_merge_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpm4pomysr/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'> 161s self.tearDown() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s ok 161s test_get_warning (test_macsy_merge_results.TestMerge.test_get_warning) ... ok 161s test_merge_and_reindex_invalid_solid (test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... Cannot reindex int(GCF_000006845) + 1: invalid literal for int() with base 10: 'GCF_000006845' 161s ok 161s test_add_comment (test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok 161s test_write (test_macsyconfig.TestConfigParserWithComment.test_write) ... ok 161s test_ask (test_macsyconfig.TestMacsyconfig.test_ask) ... ok 161s test_ask_bad_value (test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok 161s test_ask_default_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok 161s test_ask_use_default (test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok 161s test_ask_value_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok 161s test_check_bool (test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok 161s test_check_choice (test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok 161s test_check_dir (test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok 161s test_check_exe (test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok 161s test_check_file (test_macsyconfig.TestMacsyconfig.test_check_file) ... ok 161s test_check_float (test_macsyconfig.TestMacsyconfig.test_check_float) ... ok 161s test_check_positive_int (test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok 161s test_check_str (test_macsyconfig.TestMacsyconfig.test_check_str) ... ok 161s test_functional_dark_theme (test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok 161s test_functional_file_already_exists (test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok 161s test_parse_args (test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok 161s test_set_base_options (test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok 161s test_set_general_options (test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok 161s test_set_hmmer_options (test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok 161s test_set_path_options (test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok 161s test_set_path_options_with_system_models_dir (test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok 161s test_set_score_options (test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok 161s test_set_section (test_macsyconfig.TestMacsyconfig.test_set_section) ... ok 161s test_set_section_use_defaults (test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok 161s test_available (test_macsydata.TestMacsydata.test_available) ... ok 161s test_build_argparser (test_macsydata.TestMacsydata.test_build_argparser) ... ok 161s test_check (test_macsydata.TestMacsydata.test_check) ... If everyone were like you, I'd be out of business 161s To push the models in organization: 161s cd /tmp/tmpeias8085/fake_1 161s Transform the models into a git repository 161s git init . 161s git add . 161s git commit -m 'initial commit' 161s add a remote repository to host the models 161s for instance if you want to add the models to 'macsy-models' 161s git remote add origin https://github.com/macsy-models/ 161s git tag 0.0b2 161s git push origin 0.0b2 161s ok 161s test_check_with_errors (test_macsydata.TestMacsydata.test_check_with_errors) ... The package 'fake_1' have no 'definitions' directory. 161s The package 'fake_1' have no 'profiles' directory. 161s Please fix issues above, before publishing these models. 161s ok 161s test_check_with_warnings (test_macsydata.TestMacsydata.test_check_with_warnings) ... The package 'fake_1' have not any LICENSE file. May be you have not right to use it. 161s The package 'fake_1' have not any README file. 161s 161s macsydata says: You're only giving me a partial QA payment? 161s I'll take it this time, but I'm not happy. 161s I'll be really happy, if you fix warnings above, before to publish these models. 161s ok 161s test_cite (test_macsydata.TestMacsydata.test_cite) ... Models 'nimportnaoik' not found locally. 161s ok 161s test_cmd_name (test_macsydata.TestMacsydata.test_cmd_name) ... ok 161s test_definition_all_def (test_macsydata.TestMacsydata.test_definition_all_def) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpqa0fgn8v/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='UTF-8'> 161s return open(path, 'r').read() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpqa0fgn8v/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'> 161s return open(path, 'r').read() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s ok 161s test_definition_bad_def (test_macsydata.TestMacsydata.test_definition_bad_def) ... Model 'fake_1/niportnaoik' not found. 161s ok 161s test_definition_bad_pack (test_macsydata.TestMacsydata.test_definition_bad_pack) ... Package 'nimportnaoik' not found. 161s ok 161s test_definition_bad_subfamily (test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... 'niportnaoik' not found in package 'fake_1'. 161s ok 161s test_definition_models_dir (test_macsydata.TestMacsydata.test_definition_models_dir) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpsmftrj2e/model_dir/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='UTF-8'> 161s return open(path, 'r').read() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpsmftrj2e/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'> 161s return open(path, 'r').read() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s ok 161s test_definition_one_def (test_macsydata.TestMacsydata.test_definition_one_def) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmps7d2prv6/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='UTF-8'> 161s return open(path, 'r').read() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmps7d2prv6/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'> 161s return open(path, 'r').read() 161s ResourceWarning: Enable tracemalloc to get the object allocation traceback 161s ok 161s test_download (test_macsydata.TestMacsydata.test_download) ... Downloading fake_1 1.0 161s Successfully downloaded packaging fake_1 in /tmp/tmp1ia31_26/fake_1-1.0.tar.gz 161s No version that satisfy requirements '>2.0' for 'fake_1'. 161s Available versions: 1.0 161s Downloading fake_1 1.0 161s github limit error 161s ok 161s test_freeze (test_macsydata.TestMacsydata.test_freeze) ... ok 161s test_help (test_macsydata.TestMacsydata.test_help) ... Models 'nimportnaoik' not found locally. 161s ok 161s test_info (test_macsydata.TestMacsydata.test_info) ... Models 'nimportnaoik' not found locally. 161s ok 161s test_init_package_complete (test_macsydata.TestMacsydata.test_init_package_complete) ... The skeleton of complete_pack is ready. 161s The package is located at /tmp/tmp4l3uo73p/models/complete_pack 161s 161s - Edit metadata.yml and fill how to cite your package and where to find documentation about it. 161s - Add hmm profiles in /tmp/tmp4l3uo73p/models/complete_pack/profiles directory 161s - A skeleton of model definitions has been added in /tmp/tmp4l3uo73p/models/complete_pack/definitions. 161s For complete documentation about model grammar read https://macsyfinder.readthedocs.io/en/latest/modeler_guide/modeling.html 161s - A configuration file has been added (model_conf.xml) with default value tweak this file if needed. 161s (https://macsyfinder.readthedocs.io/en/latest/modeler_guide/package.html#model-configuration) 161s 161s Before to publish your package you can use `macsydata check` to verify it's integrity. 161s 161s Read macsyfinder modeler guide for further details: https://macsyfinder.readthedocs.io/en/latest/modeler_guide/index.html 161s ok 161s test_init_package_minimal (test_macsydata.TestMacsydata.test_init_package_minimal) ... Consider to add copyright to protect your rights. 161s Consider licensing minimal_pack to give the end-user the right to use your package,and protect your rights. https://data.europa.eu/elearning/en/module4/#/id/co-01 161s The skeleton of minimal_pack is ready. 161s The package is located at /tmp/tmp377368kw/models/minimal_pack 161s 161s - Edit metadata.yml and fill how to cite your package and where to find documentation about it. 161s - Add hmm profiles in /tmp/tmp377368kw/models/minimal_pack/profiles directory 161s - A skeleton of model definitions has been added in /tmp/tmp377368kw/models/minimal_pack/definitions. 161s For complete documentation about model grammar read https://macsyfinder.readthedocs.io/en/latest/modeler_guide/modeling.html 161s - A configuration file has been added (model_conf.xml) with default value tweak this file if needed. 161s (https://macsyfinder.readthedocs.io/en/latest/modeler_guide/package.html#model-configuration) 161s 161s Before to publish your package you can use `macsydata check` to verify it's integrity. 161s 161s Read macsyfinder modeler guide for further details: https://macsyfinder.readthedocs.io/en/latest/modeler_guide/index.html 161s ok 161s test_install_bad_target (test_macsydata.TestMacsydata.test_install_bad_target) ... ok 161s test_install_installed_package_corrupted (test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... Extracting fake_pack (0.0b2). 161s /usr/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. 161s warnings.warn( 161s Installing fake_pack (0.0b2) in /tmp/tmpxj_l1ml1/models 161s Cleaning. 161s The models fake_pack (0.0b2) have been installed successfully. 161s fake_pack locally installed is corrupted. 161s You can fix it by removing '/tmp/tmpxj_l1ml1/models/fake_pack'. 161s ok 161s test_install_local (test_macsydata.TestMacsydata.test_install_local) ... Extracting fake_pack (3.0). 161s Installing fake_pack (3.0) in /tmp/tmponq9_w6v/models 161s Cleaning. 161s The models fake_pack (3.0) have been installed successfully. 161s ok 161s test_install_local_already_installed (test_macsydata.TestMacsydata.test_install_local_already_installed) ... Extracting fake_pack (0.0b2). 161s Installing fake_pack (0.0b2) in /tmp/tmpdo58n16c/models 161s Cleaning. 161s The models fake_pack (0.0b2) have been installed successfully. 161s Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmpdo58n16c/models/fake_pack. 161s To force installation use option -f --force-reinstall. 161s ok 161s test_install_local_already_installed_force (test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... Extracting fake_pack (0.0b2). 161s Installing fake_pack (0.0b2) in /tmp/tmp3x1ax3oo/models 161s Cleaning. 161s The models fake_pack (0.0b2) have been installed successfully. 161s Extracting fake_pack (0.0b2). 161s Installing fake_pack (0.0b2) in /tmp/tmp3x1ax3oo/models 161s Cleaning. 161s The models fake_pack (0.0b2) have been installed successfully. 161s ok 161s test_install_remote (test_macsydata.TestMacsydata.test_install_remote) ... Downloading fake_pack (0.0b2). 161s Extracting fake_pack (0.0b2). 161s Installing fake_pack (0.0b2) in /tmp/tmp7gzex4tt/models 161s Cleaning. 161s The models fake_pack (0.0b2) have been installed successfully. 161s ok 161s test_install_remote_already_in_local (test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmpst3tr5oi/models/fake_pack. 161s To force installation use option -f --force-reinstall. 161s ok 161s test_install_remote_already_in_local_force (test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... Downloading fake_pack (0.0b2). 161s Extracting fake_pack (0.0b2). 161s Installing fake_pack (0.0b2) in /tmp/tmp5g2cxle9/models 161s Cleaning. 161s The models fake_pack (0.0b2) have been installed successfully. 161s ok 161s test_install_remote_lower_in_local (test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... fake_pack (0.0b2) is already installed but 1.0 version is available. 161s To install it please run 'macsydata install --upgrade fake_pack' 161s ok 161s test_install_remote_permision_error (test_macsydata.TestMacsydata.test_install_remote_permision_error) ... /tmp/tmpqhkneq13/models is not readable: [Errno 13] Permission denied: '/tmp/tmpqhkneq13/models' : skip it. 161s Downloading fake_pack (0.0b2). 161s Extracting fake_pack (0.0b2). 161s Installing fake_pack (0.0b2) in /tmp/tmpqhkneq13/models 161s /tmp/tmpqhkneq13/models is not writable: [Errno 13] Permission denied: '/tmp/tmpqhkneq13/models/fake_pack' 161s Maybe you can use --user option to install in your HOME. 161s ok 161s test_install_remote_spec_not_found (test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... Could not find version that satisfied 'fake_pack>0.0b2' 161s ok 161s test_install_remote_upper_in_local (test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... fake_pack (0.0b2) is already installed. 161s To downgrade to 0.0b1 use option -f --force-reinstall. 161s ok 161s test_install_target (test_macsydata.TestMacsydata.test_install_target) ... Extracting fake_pack (3.0). 161s Installing fake_pack (3.0) in /tmp/tmpp6exr8zp/target 161s Cleaning. 161s The models fake_pack (3.0) have been installed successfully. 161s ok 161s test_list (test_macsydata.TestMacsydata.test_list) ... ok 161s test_list_long (test_macsydata.TestMacsydata.test_list_long) ... ok 161s test_list_outdated (test_macsydata.TestMacsydata.test_list_outdated) ... ok 161s test_list_uptodate (test_macsydata.TestMacsydata.test_list_uptodate) ... ok 161s test_list_verbose (test_macsydata.TestMacsydata.test_list_verbose) ... [Errno 2] No such file or directory: '/tmp/tmpcvu9t9n0/models/fake_1/metadata.yml' 161s ok 161s test_no_subcommand (test_macsydata.TestMacsydata.test_no_subcommand) ... ok 161s test_search_in_pack_desc (test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok 161s test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok 161s test_search_in_pack_name (test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok 161s test_search_in_pack_name_match_case (test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok 161s test_search_reach_limit (test_macsydata.TestMacsydata.test_search_reach_limit) ... bla 161s ok 161s test_uninstall (test_macsydata.TestMacsydata.test_uninstall) ... models 'fake_1' in /tmp/tmpmrppu5cr/models/fake_1 uninstalled. 161s Models 'foo' not found locally. 161s ok 161s test_verbosity_to_log_level (test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok 161s test_db_type_set_to_gembase (test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... GA bit thresholds unavailable on profile T4P_pilA. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilC. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilX. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilQ. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilM. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilE. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile ComM_comC. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilU. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilV. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_fimT. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilW. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T2SS_gspO. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilB. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilO. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilD. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilT. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilN. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilP. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile MSH_mshM. Switch to e-value threshold (-E 0.100000) 161s GA bit thresholds unavailable on profile T4P_pilY. Switch to e-value threshold (-E 0.100000) 161s Most of replicons contains only ONE sequence are you sure that '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/base/ordered_replicon_base.fasta' is a 'gembase'. 161s ok 161s test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok 161s test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok 161s test_list_models (test_macsyfinder.TestMacsyfinder.test_list_models) ... ok 161s test_loners_to_tsv (test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok 161s test_multisystem_to_tsv (test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok 161s test_parse_args (test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok 161s test_rejected_candidates_to_tsv (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok 161s test_rejected_candidates_to_txt (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok 165s test_search_systems (test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok 168s test_search_systems_unordered (test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok 168s test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok 168s test_summary_best_solution (test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok 168s test_summary_best_solution_empty (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok 168s test_summary_best_solution_lack_models (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok 168s test_summary_best_solution_lack_models_replicons (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok 168s test_summary_best_solution_lack_replicon (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok 168s test_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok 168s test_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok 168s test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok 168s test_LightHit (test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok 168s test_build_my_db (test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok 168s test_fill_my_db (test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok 168s test_functional (test_macsyprofile.TestMacsyprofile.test_functional) ... ok 168s test_functional_best_score (test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok 168s test_functional_coverage (test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok 168s test_functional_evalue (test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok 168s test_functional_no_hits (test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok 168s test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... nimportnaoik: No such directory. 168s ok 168s test_functional_out_exists (test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... The file /tmp/tmpq0orrd67 already exists. Remove it or specify a new output name --out or use --force option 168s ok 168s test_functional_pattern (test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok 168s test_getProfile_len (test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok 168s test_get_gene_name (test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok 168s test_header (test_macsyprofile.TestMacsyprofile.test_header) ... ok 168s test_hit_start (test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok 168s test_parse (test_macsyprofile.TestMacsyprofile.test_parse) ... ok 168s test_parse_hmm_body (test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok 168s test_parse_hmm_header (test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok 168s test_pasre_args (test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok 168s test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok 168s test_init_logger_default (test_macsypy.Test.test_init_logger_default) ... ok 168s test_init_logger_logfile (test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpuhohv1uu' mode='a' encoding='UTF-8'> 168s self.tearDown() 168s ResourceWarning: Enable tracemalloc to get the object allocation traceback 168s ok 168s test_init_logger_no_out (test_macsypy.Test.test_init_logger_no_out) ... ok 168s test_logger_set_level_bad_level (test_macsypy.Test.test_logger_set_level_bad_level) ... ok 168s test_logger_set_level_default (test_macsypy.Test.test_logger_set_level_default) ... ok 168s test_logger_set_level_error (test_macsypy.Test.test_logger_set_level_error) ... ok 168s test_logger_set_level_handlers (test_macsypy.Test.test_logger_set_level_handlers) ... ok 168s test_parse (test_model_conf_parser.TestModelConfParser.test_parse) ... /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/model_conf_parser.py:57: DeprecationWarning: Testing an element's truth value will raise an exception in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. 168s if weights_node: 168s /tmp/autopkgtest.ZbI7k7/build.IXy/src/macsypy/model_conf_parser.py:61: DeprecationWarning: Testing an element's truth value will raise an exception in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. 168s if filtering_node: 168s ok 168s test_parse_bad_file (test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... unable to parse model configuration '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/conf_files/project.conf' : syntax error: line 2, column 0 168s ok 168s test_parse_filtering (test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... cannot parse 'cut_ga' element in '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/conf_files/model_conf.xml' expect True, 1, False, 0 got : 'FOO' 168s ok 168s test_parse_w_bad_value (test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... The model configuration file '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/conf_files/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO' 168s ok 168s test_parse_w_unkown_tag (test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... unknown element 'nimportnaoik' in '/tmp/autopkgtest.ZbI7k7/build.IXy/src/tests/data/conf_files/model_conf.xml' ignore it. 168s ok 168s test_parse_weights (test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok 168s test_parse_wo_filtering (test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok 168s test_parse_wo_weights (test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok 168s test_init (test_package.TestLocalModelIndex.test_init) ... ok 168s test_init (test_package.TestModelIndex.test_init) ... ok 168s test_check (test_package.TestPackage.test_check) ... ok 168s test_check_metadata (test_package.TestPackage.test_check_metadata) ... ok 168s test_check_model_conf (test_package.TestPackage.test_check_model_conf) ... ok 168s test_check_model_conf_bad_conf (test_package.TestPackage.test_check_model_conf_bad_conf) ... The model configuration file '/tmp/macsy_test_package/fake_model/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO' 168s ok 168s test_check_model_conf_no_conf (test_package.TestPackage.test_check_model_conf_no_conf) ... ok 168s test_check_model_consistency (test_package.TestPackage.test_check_model_consistency) ... ok 168s test_check_model_consistency_bad_definitions (test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok 168s test_check_model_consistency_extra_profile (test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok 168s test_check_model_consistency_lack_one_profile (test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok 168s test_check_no_readme_n_no_license (test_package.TestPackage.test_check_no_readme_n_no_license) ... ok 168s test_check_structure (test_package.TestPackage.test_check_structure) ... ok 168s test_check_structure_bad_path (test_package.TestPackage.test_check_structure_bad_path) ... ok 168s test_check_structure_no_def (test_package.TestPackage.test_check_structure_no_def) ... ok 168s test_check_structure_no_license (test_package.TestPackage.test_check_structure_no_license) ... ok 168s test_check_structure_no_metadata (test_package.TestPackage.test_check_structure_no_metadata) ... ok 168s test_check_structure_no_profiles (test_package.TestPackage.test_check_structure_no_profiles) ... ok 168s test_check_structure_no_readme (test_package.TestPackage.test_check_structure_no_readme) ... ok 168s test_find_readme (test_package.TestPackage.test_find_readme) ... ok 168s test_help (test_package.TestPackage.test_help) ... ok 168s test_info (test_package.TestPackage.test_info) ... ok 168s test_init (test_package.TestPackage.test_init) ... ok 168s test_metadata (test_package.TestPackage.test_metadata) ... ok 168s test_parse_arch_path (test_package.TestPackageFunc.test_parse_arch_path) ... ok 168s test_download (test_package.TestRemoteModelIndex.test_download) ... ok 168s test_get_metadata (test_package.TestRemoteModelIndex.test_get_metadata) ... ok 168s test_init (test_package.TestRemoteModelIndex.test_init) ... ok 168s test_list_package_vers (test_package.TestRemoteModelIndex.test_list_package_vers) ... ok 168s test_list_packages (test_package.TestRemoteModelIndex.test_list_packages) ... ok 169s test_remote_exists (test_package.TestRemoteModelIndex.test_remote_exists) ... ok 169s test_unarchive (test_package.TestRemoteModelIndex.test_unarchive) ... /usr/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. 169s warnings.warn( 169s ok 169s test_url_json (test_package.TestRemoteModelIndex.test_url_json) ... ok 169s test_url_json_reach_limit (test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok 169s test_DefinitionLocationn (test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok 169s test_add_submodel (test_registries.DefinitionLocationTest.test_add_submodel) ... ok 169s test_all (test_registries.DefinitionLocationTest.test_all) ... ok 169s test_eq (test_registries.DefinitionLocationTest.test_eq) ... ok 169s test_family_name (test_registries.DefinitionLocationTest.test_family_name) ... ok 169s test_greater (test_registries.DefinitionLocationTest.test_greater) ... ok 169s test_hash (test_registries.DefinitionLocationTest.test_hash) ... ok 169s test_lesser (test_registries.DefinitionLocationTest.test_lesser) ... ok 169s test_root_name (test_registries.DefinitionLocationTest.test_root_name) ... ok 169s test_separator (test_registries.DefinitionLocationTest.test_separator) ... ok 169s test_split_fqn (test_registries.DefinitionLocationTest.test_split_fqn) ... ok 169s test_str (test_registries.DefinitionLocationTest.test_str) ... ok 169s test_ModelLocation (test_registries.ModelLocationTest.test_ModelLocation) ... ok 169s test_get_all_definitions (test_registries.ModelLocationTest.test_get_all_definitions) ... ok 169s test_get_definition (test_registries.ModelLocationTest.test_get_definition) ... ok 169s test_get_definitions (test_registries.ModelLocationTest.test_get_definitions) ... ok 169s test_get_profile (test_registries.ModelLocationTest.test_get_profile) ... ok 169s test_get_profiles_names (test_registries.ModelLocationTest.test_get_profiles_names) ... ok 169s test_str (test_registries.ModelLocationTest.test_str) ... ok 169s test_version (test_registries.ModelLocationTest.test_version) ... ok 169s test_version_no_metadata (test_registries.ModelLocationTest.test_version_no_metadata) ... The models package 'simple' is not versioned contact the package manager to fix it. 169s ok 169s test_add_get (test_registries.ModelRegistryTest.test_add_get) ... ok 169s test_models (test_registries.ModelRegistryTest.test_models) ... ok 169s test_scan_models_dir (test_registries.ModelRegistryTest.test_scan_models_dir) ... ok 169s test_str (test_registries.ModelRegistryTest.test_str) ... ok 169s test_join_def_path (test_registries.RegitriesUtilsTest.test_join_def_path) ... ok 169s test_split_def_name (test_registries.RegitriesUtilsTest.test_split_def_name) ... ok 169s test_search (test_search_genes.TestSearchGenes.test_search) ... ok 169s test_search_fail (test_search_genes.TestSearchGenes.test_search_fail) ... ok 169s test_search_recover (test_search_genes.TestSearchGenes.test_search_recover) ... ok 169s test_worker_cpu (test_search_genes.TestSearchGenes.test_worker_cpu) ... ok 169s test_LikelySystemSerializer_txt (test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok 169s test_RejectedClusters_tsv (test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok 169s test_SolutionSerializer_tsv (test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok 169s test_SpecialHitSerializer_tsv (test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok 169s test_SystemSerializer_str (test_serialization.SerializationTest.test_SystemSerializer_str) ... ok 169s test_SystemSerializer_tsv (test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok 169s test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok 169s test_combine_clusters (test_solution.SolutionExplorerTest.test_combine_clusters) ... ok 169s test_combine_multisystems (test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok 169s test_find_best_solution (test_solution.SolutionExplorerTest.test_find_best_solution) ... ok 169s test_average_wholeness (test_solution.SolutionTest.test_average_wholeness) ... ok 169s test_gt (test_solution.SolutionTest.test_gt) ... ok 169s test_hits_number (test_solution.SolutionTest.test_hits_number) ... ok 169s test_hits_positions (test_solution.SolutionTest.test_hits_positions) ... ok 169s test_iteration (test_solution.SolutionTest.test_iteration) ... ok 169s test_lt (test_solution.SolutionTest.test_lt) ... ok 169s test_score (test_solution.SolutionTest.test_score) ... ok 169s test_sorting (test_solution.SolutionTest.test_sorting) ... ok 169s test_systems (test_solution.SolutionTest.test_systems) ... ok 169s test_get_def_to_detect (test_utils.TestUtils.test_get_def_to_detect) ... ok 169s test_get_replicon_names_bad_type (test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok 169s test_get_replicon_names_gembase (test_utils.TestUtils.test_get_replicon_names_gembase) ... ok 169s test_get_replicon_names_ordered (test_utils.TestUtils.test_get_replicon_names_ordered) ... ok 169s test_get_replicon_names_unordered (test_utils.TestUtils.test_get_replicon_names_unordered) ... ok 169s test_parse_time (test_utils.TestUtils.test_parse_time) ... ok 169s test_threads_available (test_utils.TestUtils.test_threads_available) ... ok 169s 169s ---------------------------------------------------------------------- 169s Ran 509 tests in 18.008s 169s 169s OK (skipped=2) 170s autopkgtest [02:05:37]: test run-unit-test: -----------------------] 170s autopkgtest [02:05:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 170s run-unit-test PASS 171s autopkgtest [02:05:38]: @@@@@@@@@@@@@@@@@@@@ summary 171s run-unit-test PASS 175s Creating nova instance adt-noble-arm64-macsyfinder-20240318-020247-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...