0s autopkgtest [15:26:46]: starting date and time: 2024-03-23 15:26:46+0000 0s autopkgtest [15:26:46]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:26:46]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fwj6r8nf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade macsyfinder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-12.secgroup --name adt-noble-arm64-macsyfinder-20240323-152646-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 198s autopkgtest [15:30:04]: testbed dpkg architecture: arm64 198s autopkgtest [15:30:04]: testbed apt version: 2.7.12 198s autopkgtest [15:30:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 199s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 200s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 200s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 200s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 200s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 200s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [667 kB] 200s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 200s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 200s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 200s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4345 kB] 200s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 200s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 200s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 206s Fetched 9770 kB in 3s (3514 kB/s) 206s Reading package lists... 210s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s Calculating upgrade... 213s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 215s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 216s sh: Attempting to set up Debian/Ubuntu apt sources automatically 216s sh: Distribution appears to be Ubuntu 217s Reading package lists... 218s Building dependency tree... 218s Reading state information... 219s eatmydata is already the newest version (131-1). 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s Reading package lists... 220s Building dependency tree... 220s Reading state information... 221s dbus is already the newest version (1.14.10-4ubuntu1). 221s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 223s rng-tools-debian is already the newest version (2.4). 223s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s The following packages will be REMOVED: 224s cloud-init* python3-configobj* python3-debconf* 225s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 225s After this operation, 3256 kB disk space will be freed. 225s (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 ... 75911 files and directories currently installed.) 225s Removing cloud-init (24.1.2-0ubuntu1) ... 226s Removing python3-configobj (5.0.8-3) ... 226s Removing python3-debconf (1.5.86) ... 227s Processing triggers for man-db (2.12.0-3) ... 227s (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 ... 75522 files and directories currently installed.) 227s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 229s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 229s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 229s invoke-rc.d: policy-rc.d denied execution of try-restart. 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 231s linux-generic is already the newest version (6.8.0-11.11+1). 231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 231s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 231s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 231s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 236s Reading package lists... 236s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s Calculating upgrade... 239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 240s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 241s autopkgtest [15:30:47]: rebooting testbed after setup commands that affected boot 399s autopkgtest [15:33:25]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 402s autopkgtest [15:33:28]: @@@@@@@@@@@@@@@@@@@@ apt-source macsyfinder 405s Get:1 http://ftpmaster.internal/ubuntu noble/universe macsyfinder 2.1.3-1 (dsc) [2460 B] 405s Get:2 http://ftpmaster.internal/ubuntu noble/universe macsyfinder 2.1.3-1 (tar) [37.8 MB] 405s Get:3 http://ftpmaster.internal/ubuntu noble/universe macsyfinder 2.1.3-1 (diff) [10.0 kB] 406s gpgv: Signature made Thu Feb 29 15:02:51 2024 UTC 406s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 406s gpgv: Can't check signature: No public key 406s dpkg-source: warning: cannot verify inline signature for ./macsyfinder_2.1.3-1.dsc: no acceptable signature found 409s autopkgtest [15:33:35]: testing package macsyfinder version 2.1.3-1 409s autopkgtest [15:33:35]: build not needed 461s autopkgtest [15:34:27]: test run-unit-test: preparing testbed 463s Reading package lists... 464s Building dependency tree... 464s Reading state information... 465s Starting pkgProblemResolver with broken count: 0 465s Starting 2 pkgProblemResolver with broken count: 0 465s Done 466s The following additional packages will be installed: 466s fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libgfortran5 466s libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 466s libmbedcrypto7 libmbedtls14 libmbedx509-1 macsyfinder ncbi-blast+ ncbi-data 466s python3-colorama python3-colorlog python3-dateutil python3-networkx 466s python3-numpy python3-packaging python3-pandas python3-pandas-lib 466s sphinx-rtd-theme-common 466s Suggested packages: 466s hmmer-doc python-networkx-doc python3-gdal python3-matplotlib python3-pydot 466s python3-pygraphviz python3-scipy gcc gfortran python3-dev python3-pytest 466s python-pandas-doc python3-statsmodels 466s Recommended packages: 466s javascript-common python3-scipy python3-matplotlib python3-bottleneck 466s python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib 466s python3-lxml python3-tables 466s The following NEW packages will be installed: 466s autopkgtest-satdep fonts-font-awesome fonts-lato hmmer libblas3 466s libdivsufsort3 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc 466s libjs-underscore liblapack3 libmbedcrypto7 libmbedtls14 libmbedx509-1 466s macsyfinder ncbi-blast+ ncbi-data python3-colorama python3-colorlog 466s python3-dateutil python3-networkx python3-numpy python3-packaging 466s python3-pandas python3-pandas-lib sphinx-rtd-theme-common 466s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 466s Need to get 56.2 MB/56.2 MB of archives. 466s After this operation, 245 MB of additional disk space will be used. 466s Get:1 /tmp/autopkgtest.H3FgLD/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 467s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-lato all 2.015-1 [2781 kB] 467s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 467s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 468s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 468s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 468s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 468s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 468s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 468s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 468s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 468s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 468s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 468s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 468s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 469s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-colorlog all 6.8.0-1 [21.0 kB] 469s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 469s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 469s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 469s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 469s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 469s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 470s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 470s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB] 470s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 470s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 470s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 macsyfinder arm64 2.1.3-1 [13.5 MB] 472s Fetched 56.2 MB in 5s (12.0 MB/s) 472s Selecting previously unselected package fonts-lato. 472s (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 ... 75467 files and directories currently installed.) 472s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 472s Unpacking fonts-lato (2.015-1) ... 473s Selecting previously unselected package fonts-font-awesome. 473s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 473s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 473s Selecting previously unselected package libblas3:arm64. 473s Preparing to unpack .../02-libblas3_3.12.0-3_arm64.deb ... 473s Unpacking libblas3:arm64 (3.12.0-3) ... 473s Selecting previously unselected package libdivsufsort3:arm64. 473s Preparing to unpack .../03-libdivsufsort3_2.0.1-6_arm64.deb ... 473s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 473s Selecting previously unselected package libgfortran5:arm64. 473s Preparing to unpack .../04-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 473s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 473s Selecting previously unselected package libgomp1:arm64. 473s Preparing to unpack .../05-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 473s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 473s Selecting previously unselected package libjs-jquery. 473s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 473s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 473s Selecting previously unselected package libjs-underscore. 473s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 473s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 473s Selecting previously unselected package libjs-sphinxdoc. 473s Preparing to unpack .../08-libjs-sphinxdoc_7.2.6-4_all.deb ... 473s Unpacking libjs-sphinxdoc (7.2.6-4) ... 473s Selecting previously unselected package liblapack3:arm64. 473s Preparing to unpack .../09-liblapack3_3.12.0-3_arm64.deb ... 473s Unpacking liblapack3:arm64 (3.12.0-3) ... 473s Selecting previously unselected package libmbedcrypto7:arm64. 473s Preparing to unpack .../10-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 473s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 473s Selecting previously unselected package libmbedx509-1:arm64. 473s Preparing to unpack .../11-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 473s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 473s Selecting previously unselected package libmbedtls14:arm64. 473s Preparing to unpack .../12-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 473s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 473s Selecting previously unselected package python3-colorama. 473s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 473s Unpacking python3-colorama (0.4.6-4) ... 473s Selecting previously unselected package python3-colorlog. 473s Preparing to unpack .../14-python3-colorlog_6.8.0-1_all.deb ... 473s Unpacking python3-colorlog (6.8.0-1) ... 474s Selecting previously unselected package python3-networkx. 474s Preparing to unpack .../15-python3-networkx_2.8.8-1ubuntu1_all.deb ... 474s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 474s Selecting previously unselected package python3-packaging. 474s Preparing to unpack .../16-python3-packaging_23.2-1_all.deb ... 474s Unpacking python3-packaging (23.2-1) ... 474s Selecting previously unselected package python3-dateutil. 474s Preparing to unpack .../17-python3-dateutil_2.8.2-3_all.deb ... 474s Unpacking python3-dateutil (2.8.2-3) ... 474s Selecting previously unselected package python3-numpy. 474s Preparing to unpack .../18-python3-numpy_1%3a1.24.2-2_arm64.deb ... 474s Unpacking python3-numpy (1:1.24.2-2) ... 475s Selecting previously unselected package python3-pandas-lib:arm64. 475s Preparing to unpack .../19-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 475s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 475s Selecting previously unselected package python3-pandas. 475s Preparing to unpack .../20-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 475s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 476s Selecting previously unselected package sphinx-rtd-theme-common. 476s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 476s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 476s Selecting previously unselected package hmmer. 476s Preparing to unpack .../22-hmmer_3.4+dfsg-2_arm64.deb ... 476s Unpacking hmmer (3.4+dfsg-2) ... 476s Selecting previously unselected package ncbi-data. 476s Preparing to unpack .../23-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 476s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 477s Selecting previously unselected package ncbi-blast+. 477s Preparing to unpack .../24-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 477s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 478s Selecting previously unselected package macsyfinder. 478s Preparing to unpack .../25-macsyfinder_2.1.3-1_arm64.deb ... 478s Unpacking macsyfinder (2.1.3-1) ... 478s Selecting previously unselected package autopkgtest-satdep. 478s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 478s Unpacking autopkgtest-satdep (0) ... 478s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 478s Setting up fonts-lato (2.015-1) ... 478s Setting up python3-colorama (0.4.6-4) ... 479s Setting up python3-colorlog (6.8.0-1) ... 479s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 479s Setting up python3-networkx (2.8.8-1ubuntu1) ... 481s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 481s "graph [edge [ source u'u\4200' target u'u\4200' ] " 481s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 481s + "node [ id u'u\4200' label b ] ]" 481s Setting up libblas3:arm64 (3.12.0-3) ... 481s 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 481s Setting up python3-packaging (23.2-1) ... 482s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 482s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 482s Setting up python3-dateutil (2.8.2-3) ... 482s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 482s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 482s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 482s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 482s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 482s Setting up liblapack3:arm64 (3.12.0-3) ... 482s 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 482s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 482s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 482s Setting up ncbi-blast+ (2.12.0+ds-4) ... 482s Setting up python3-numpy (1:1.24.2-2) ... 487s Setting up libjs-sphinxdoc (7.2.6-4) ... 487s Setting up hmmer (3.4+dfsg-2) ... 487s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 487s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 497s Setting up macsyfinder (2.1.3-1) ... 497s /usr/lib/python3/dist-packages/macsypy/scripts/macsyconfig.py:282: SyntaxWarning: invalid escape sequence '\_' 497s """ 497s Setting up autopkgtest-satdep (0) ... 497s Processing triggers for man-db (2.12.0-3) ... 498s Processing triggers for libc-bin (2.39-0ubuntu6) ... 504s (Reading database ... 79977 files and directories currently installed.) 504s Removing autopkgtest-satdep (0) ... 505s autopkgtest [15:35:11]: test run-unit-test: [----------------------- 506s 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. 506s running test 506s /usr/lib/python3/dist-packages/setuptools/command/test.py:193: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 506s !! 506s 506s ******************************************************************************** 506s Requirements should be satisfied by a PEP 517 installer. 506s If you are using pip, you can try `pip install --use-pep517`. 506s ******************************************************************************** 506s 506s !! 506s ir_d = dist.fetch_build_eggs(dist.install_requires) 506s WARNING: The wheel package is not available. 506s /usr/lib/python3/dist-packages/setuptools/command/test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 506s !! 506s 506s ******************************************************************************** 506s Requirements should be satisfied by a PEP 517 installer. 506s If you are using pip, you can try `pip install --use-pep517`. 506s ******************************************************************************** 506s 506s !! 506s tr_d = dist.fetch_build_eggs(dist.tests_require or []) 506s WARNING: The wheel package is not available. 506s /usr/lib/python3/dist-packages/setuptools/command/test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 506s !! 506s 506s ******************************************************************************** 506s Requirements should be satisfied by a PEP 517 installer. 506s If you are using pip, you can try `pip install --use-pep517`. 506s ******************************************************************************** 506s 506s !! 506s er_d = dist.fetch_build_eggs( 506s WARNING: The wheel package is not available. 506s running egg_info 506s creating MacSyFinder.egg-info 506s writing MacSyFinder.egg-info/PKG-INFO 506s writing dependency_links to MacSyFinder.egg-info/dependency_links.txt 506s writing entry points to MacSyFinder.egg-info/entry_points.txt 506s writing requirements to MacSyFinder.egg-info/requires.txt 506s writing top-level names to MacSyFinder.egg-info/top_level.txt 506s writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' 506s reading manifest file 'MacSyFinder.egg-info/SOURCES.txt' 506s reading manifest template 'MANIFEST.in' 506s warning: no files found matching '*' under directory 'doc/build/html' 506s warning: no files found matching 'doc/build/latex/macsyfinder.pdf' 506s warning: no files found matching 'etc/macsyfinder.conf' 506s warning: no previously-included files matching '*' found under directory 'tests/__pycache__/' 506s warning: no previously-included files found matching 'tests/__init__.pyc' 506s warning: no previously-included files found matching '.coverage' 506s warning: no previously-included files found matching 'coverage_html/' 506s warning: no previously-included files found matching '.gitignore' 506s warning: no previously-included files found matching '.travis.yml' 506s warning: no previously-included files found matching '.github/' 506s warning: no files found matching 'CONTRIBUTORS' 506s warning: no files found matching 'NEWS' 506s adding license file 'COPYING' 506s writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' 506s running build_ext 506s /tmp/autopkgtest.H3FgLD/build.EJd/src/tests/__init__.py:128: SyntaxWarning: invalid escape sequence '\[' 506s red_pattern = "^\\x1b\[0?1;31m(.*)\\x1b\[0m$" 508s /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsyconfig.py:282: SyntaxWarning: invalid escape sequence '\_' 508s """ 508s test_Config (test_Config.TestConfig.test_Config) ... ok 508s test_Config_args (test_Config.TestConfig.test_Config_args) ... ok 508s test_Config_conf_file_virtualenv (test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok 508s test_Config_default_conf_file (test_Config.TestConfig.test_Config_default_conf_file) ... ok 508s test_Config_file_bad_values (test_Config.TestConfig.test_Config_file_bad_values) ... ok 508s test_Config_file_n_args (test_Config.TestConfig.test_Config_file_n_args) ... ok 508s test_bad_db_type (test_Config.TestConfig.test_bad_db_type) ... ok 508s test_bad_models_dir (test_Config.TestConfig.test_bad_models_dir) ... ok 508s test_bad_sequence_db (test_Config.TestConfig.test_bad_sequence_db) ... ok 508s test_bad_topology (test_Config.TestConfig.test_bad_topology) ... ok 508s test_bad_topology_file (test_Config.TestConfig.test_bad_topology_file) ... ok 508s test_bad_values (test_Config.TestConfig.test_bad_values) ... ok 508s test_cmd_config_file (test_Config.TestConfig.test_cmd_config_file) ... ok 508s test_config_file_2_dict (test_Config.TestConfig.test_config_file_2_dict) ... ok 508s test_cut_ga (test_Config.TestConfig.test_cut_ga) ... /tmp/autopkgtest.H3FgLD/build.EJd/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. 508s if filtering_node: 508s ok 508s test_e_value_search (test_Config.TestConfig.test_e_value_search) ... ok 508s test_hit_weights (test_Config.TestConfig.test_hit_weights) ... ok 508s test_hmmsearch (test_Config.TestConfig.test_hmmsearch) ... ok 508s test_hmmsearch_set_by_user (test_Config.TestConfig.test_hmmsearch_set_by_user) ... ok 508s test_model_conf (test_Config.TestConfig.test_model_conf) ... /tmp/autopkgtest.H3FgLD/build.EJd/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. 508s if weights_node: 508s ok 508s test_models_dir (test_Config.TestConfig.test_models_dir) ... ok 508s 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. 508s ok 508s test_out_dir (test_Config.TestConfig.test_out_dir) ... ok 508s test_previous_n_sequence_db (test_Config.TestConfig.test_previous_n_sequence_db) ... ignore sequence_db '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/base/test_1.fasta' use sequence_db from previous_run '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/data_set/results_1'. 508s ok 508s test_previous_wo_cfg (test_Config.TestConfig.test_previous_wo_cfg) ... ok 508s test_project_config_file (test_Config.TestConfig.test_project_config_file) ... ok 508s test_save (test_Config.TestConfig.test_save) ... ok 508s test_set_log_level (test_Config.TestConfig.test_set_log_level) ... ok 508s test_set_option (test_Config.TestConfig.test_set_option) ... ok 508s test_str_2_tuple (test_Config.TestConfig.test_str_2_tuple) ... ok 508s test_working_dir (test_Config.TestConfig.test_working_dir) ... ok 508s test_NoneConfig (test_Config.TestNoneConfig.test_NoneConfig) ... ok 508s test_bad_exchangeable_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... Models Parsing 508s Invalid model definition 'foo/bad_exchangeable_inter_gene_max_space': inter_gene_max_space must be an integer: 1.5 508s ok 508s 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 508s ok 508s test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... Models Parsing 508s Invalid model definition (/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/definitions/bad_inter_gene_max_space.xml): inter_gene_max_space must be an integer: 12.5 508s ok 508s Models Parsing 508s test_bad_max_nb_genes (test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... Models Parsing 508s Invalid model definition (/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/definitions/bad_max_nb_genes.xml): max_nb_genes must be an integer: HOHOHO 508s ok 508s test_bad_min_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... Models Parsing 508s 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 508s ok 508s test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... Models Parsing 508s Invalid model definition (/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/definitions/bad_min_genes_required_2.xml): min_genes_required must be an integer: 16.5 508s ok 508s test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... Models Parsing 508s 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 508s ok 508s test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... Models Parsing 508s ok 508s test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... Models Parsing 508s Invalid model definition (/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/definitions/bad_min_mandatory_genes_required_4.xml): min_mandatory_genes_required must be an integer: 12.5 508s ok 508s test_exchangeable_inheritance (test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... Models Parsing 508s ok 509s test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... ok 509s Models Parsing 509s test_gene_no_name (test_DefinitionParser.TestModelParser.test_gene_no_name) ... Models Parsing 509s Invalid model definition 'foo/gene_no_name': gene without name 509s ok 509s test_gene_w_unkown_attr (test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... Models Parsing 509s 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. 509s ok 509s test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... ok 509s Models Parsing 509s test_invalid_homolog (test_DefinitionParser.TestModelParser.test_invalid_homolog) ... Models Parsing 509s ok 509s test_invalid_homolog_2 (test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... Models Parsing 509s Invalid model definition 'foo/invalid_homolog_2': gene without name 509s ok 509s test_invalid_presence (test_DefinitionParser.TestModelParser.test_invalid_presence) ... Models Parsing 509s Invalid model 'foo/fail_invalid_presence' definition: presence value must be either: 'mandatory', 'accessory', 'neutral', 'forbidden' not foo_bar 509s ok 509s test_loner (test_DefinitionParser.TestModelParser.test_loner) ... Models Parsing 509s Models Parsing 509s ok 509s test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... Models Parsing 509s Models Parsing 509s ok 509s test_min_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... Models Parsing 509s ok 509s test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... Models Parsing 509s ok 509s test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... Models Parsing 509s 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 509s ok 509s test_model_w_unkown_attr (test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... 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. 509s ok 509s test_multi_loci_cfg (test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... Models Parsing 509s Models Parsing 509s ok 509s test_multi_model (test_DefinitionParser.TestModelParser.test_multi_model) ... Models Parsing 509s ok 509s test_multi_system (test_DefinitionParser.TestModelParser.test_multi_system) ... Models Parsing 509s ok 509s test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... Models Parsing 509s Invalid model definition (/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/definitions/no_inter_gene_max_space.xml): inter_gene_max_space must be defined 509s ok 509s test_only_one_accessory (test_DefinitionParser.TestModelParser.test_only_one_accessory) ... Models Parsing 509s model 'only_one_accessory' is not consistent: there is only one gene in your model. So its status should be 'mandatory'. 509s ok 509s test_parse_model_old_syntax (test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails' 509s test_parse_with_exchangeable (test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... Models Parsing 509s ok 509s test_wo_presence (test_DefinitionParser.TestModelParser.test_wo_presence) ... Models Parsing 509s Invalid model definition 'foo/fail_wo_presence': gene 'sctN_FLG' without presence 509s ok 509s test_add_exchangeable (test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok 509s test_alternate_of (test_Exchangeable.TestExchangeable.test_alternate_of) ... ok 509s test_is_exchangeable (test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok 509s test_loner (test_Exchangeable.TestExchangeable.test_loner) ... ok 509s test_model (test_Exchangeable.TestExchangeable.test_model) ... ok 509s test_multi_system (test_Exchangeable.TestExchangeable.test_multi_system) ... ok 509s test_add_get_gene (test_GeneBank.Test.test_add_get_gene) ... ok 509s test_contains (test_GeneBank.Test.test_contains) ... ok 509s test_genes_fqn (test_GeneBank.Test.test_genes_fqn) ... ok 509s test_get_uniq_object (test_GeneBank.Test.test_get_uniq_object) ... ok 509s test_iter (test_GeneBank.Test.test_iter) ... ok 509s test_fasta_iter (test_Indexes.TestFastaIter.test_fasta_iter) ... ok 509s 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. 509s ok 509s test_build_force (test_Indexes.TestIndex.test_build_force) ... ok 509s test_build_idx_gzip_seq (test_Indexes.TestIndex.test_build_idx_gzip_seq) ... MacSyFinder does not support 'bz2' compression (only gzip). 509s MacSyFinder does not support 'zip' compression (only gzip). 509s ok 510s test_build_idx_older_than_fasta (test_Indexes.TestIndex.test_build_idx_older_than_fasta) ... ok 510s 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 510s ok 510s 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 510s Traceback (most recent call last): 510s File "/tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/database.py", line 214, in _build_my_indexes 510s for seq_id, comment, length in f_iter: 510s File "/tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/database.py", line 53, in fasta_iter 510s _id = header[0] 510s ~~~~~~^^^ 510s IndexError: list index out of range 510s ok 510s test_build_no_idx (test_Indexes.TestIndex.test_build_no_idx) ... ok 510s test_build_not_writable (test_Indexes.TestIndex.test_build_not_writable) ... The '/tmp/test_macsyfinder_indexes' dir is not writable. 510s ok 510s 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. 510s The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building. 510s ok 510s test_empty_fasta (test_Indexes.TestIndex.test_empty_fasta) ... ok 510s test_find_my_indexes (test_Indexes.TestIndex.test_find_my_indexes) ... ok 510s test_index_dir (test_Indexes.TestIndex.test_index_dir) ... ok 510s test_iter (test_Indexes.TestIndex.test_iter) ... ok 510s test_allowed_hits (test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok 510s test_forbidden_hits (test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok 510s test_hits (test_LikelySystem.LikelySystemTest.test_hits) ... ok 510s test_init (test_LikelySystem.LikelySystemTest.test_init) ... ok 510s test_str (test_LikelySystem.LikelySystemTest.test_str) ... ok 510s test_hits (test_LikelySystem.UnlikelySystemTest.test_hits) ... ok 510s test_init (test_LikelySystem.UnlikelySystemTest.test_init) ... ok 510s test_reason (test_LikelySystem.UnlikelySystemTest.test_reason) ... ok 510s test_str (test_LikelySystem.UnlikelySystemTest.test_str) ... ok 510s test_MacsyDefaults_no_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok 510s test_MacsyDefaults_virtual_env (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok 510s test_ordered_match (test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok 510s test_sort_hits_by_status (test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... Gene 'fliE' not found in model 'foo/model_B' 510s ok 510s test_unordered_match (test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok 510s test_accessor_mutator (test_Model.TestModel.test_accessor_mutator) ... ok 510s test_eq (test_Model.TestModel.test_eq) ... ok 510s test_filter (test_Model.TestModel.test_filter) ... ok 510s test_fqn (test_Model.TestModel.test_fqn) ... ok 510s test_get_gene (test_Model.TestModel.test_get_gene) ... ok 510s test_gt (test_Model.TestModel.test_gt) ... ok 510s test_hash (test_Model.TestModel.test_hash) ... ok 510s test_inter_gene_max_space (test_Model.TestModel.test_inter_gene_max_space) ... ok 510s test_lt (test_Model.TestModel.test_lt) ... ok 510s test_max_nb_genes (test_Model.TestModel.test_max_nb_genes) ... ok 510s test_min_genes_required (test_Model.TestModel.test_min_genes_required) ... ok 510s test_min_mandatory_genes_required (test_Model.TestModel.test_min_mandatory_genes_required) ... ok 510s test_multi_loci (test_Model.TestModel.test_multi_loci) ... ok 510s test_str (test_Model.TestModel.test_str) ... ok 510s test_add_get_model (test_ModelBank.Test.test_add_get_model) ... ok 510s test_contains (test_ModelBank.Test.test_contains) ... ok 510s test_get_uniq_object (test_ModelBank.Test.test_get_uniq_object) ... ok 510s test_iter (test_ModelBank.Test.test_iter) ... ok 510s test_execute_hmm_protected_path (test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok 510s test_execute_hmm_w_GA_n_nocutga (test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok 510s test_execute_hmm_with_GA (test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping' 510s 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) 510s ok 510s 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) 510s an error occurred during Hmmer execution: command = "/tmp/hmmer_failed" --cpu 1 -o "/tmp/macsyfinder-20240323_15-35-16/hmmer_results/abc.search_hmm.out" -E 0.100000 "/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/profiles/abc.hmm" "/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240323_15-35-16/hmmer_results/abc.search_hmm.err 510s ok 510s 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) 510s an error occurred during Hmmer execution: command = "Nimportnaoik" --cpu 1 -o "/tmp/macsyfinder-20240323_15-35-16/hmmer_results/abc.search_hmm.out" -E 0.100000 "/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/profiles/abc.hmm" "/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240323_15-35-16/hmmer_results/abc.search_hmm.err 510s ok 510s 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''. 510s GA score will not used for gene 'bad_GA'. 510s bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''. 510s GA score will not used for gene 'bad_GA'. 510s bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'. 510s GA score will not used for gene 'bad_GA_2'. 510s bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'. 510s GA score will not used for gene 'bad_GA_2'. 510s ok 510s test_len (test_Profile.TestProfile.test_len) ... MacSyFinder does not support 'bz2' compression (only gzip). 510s MacSyFinder does not support 'zip' compression (only gzip). 510s Cannot read profile /tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/models/foo/profiles/bad_ext.hmm.gz: Not a gzipped file (b'BZ') 510s ok 510s test_str (test_Profile.TestProfile.test_str) ... ok 510s test_get_profile (test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok 510s test_get_uniq_object (test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok 510s test_unknow_profile (test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok 510s test_hits (test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok 510s test_init (test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok 510s test_str (test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok 510s test_fill_gembase_min_max_default_topology (test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok 510s test_fill_gembase_min_max_with_topology (test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok 510s test_fill_ordered_replicon_min_max (test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok 510s test_fill_topology (test_RepliconDB.Test.test_fill_topology) ... ok 510s test_get (test_RepliconDB.Test.test_get) ... ok 510s test_getitem (test_RepliconDB.Test.test_getitem) ... ok 511s test_guess_if_really_gembase (test_RepliconDB.Test.test_guess_if_really_gembase) ... ok 511s test_in (test_RepliconDB.Test.test_in) ... ok 511s test_items (test_RepliconDB.Test.test_items) ... ok 511s test_iteritems (test_RepliconDB.Test.test_iteritems) ... ok 511s test_names (test_RepliconDB.Test.test_names) ... ok 511s test_replicon_infos (test_RepliconDB.Test.test_replicon_infos) ... ok 511s test_extract (test_Report.TestGembaseHMMReport.test_extract) ... ok 511s test_extract_concurent (test_Report.TestGembaseHMMReport.test_extract_concurent) ... /tmp/autopkgtest.H3FgLD/build.EJd/src/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead 511s main_thread = threading.currentThread() 511s ok 511s test_extract (test_Report.TestGeneralHMMReport.test_extract) ... ok 511s test_extract_concurent (test_Report.TestGeneralHMMReport.test_extract_concurent) ... /tmp/autopkgtest.H3FgLD/build.EJd/src/tests/test_Report.py:541: DeprecationWarning: currentThread() is deprecated, use current_thread() instead 511s main_thread = threading.currentThread() 511s ok 511s test_HMMReport (test_Report.TestHMMReport.test_HMMReport) ... ok 511s test_best_hit (test_Report.TestHMMReport.test_best_hit) ... ok 511s test_build_my_db (test_Report.TestHMMReport.test_build_my_db) ... ok 511s test_fill_my_db (test_Report.TestHMMReport.test_fill_my_db) ... ok 511s test_hit_start (test_Report.TestHMMReport.test_hit_start) ... ok 511s test_parse_hmm_body (test_Report.TestHMMReport.test_parse_hmm_body) ... ok 511s test_parse_hmm_header (test_Report.TestHMMReport.test_parse_hmm_header) ... ok 511s test_save_extract (test_Report.TestHMMReport.test_save_extract) ... ok 511s test_str (test_Report.TestHMMReport.test_str) ... ok 511s test_extract (test_Report.TestOrderedHMMReport.test_extract) ... hit id 'NC_xxxxx_xx_056141' was not indexed, rebuild sequence 'test_base.fa' index 511s ok 511s test_extract_concurent (test_Report.TestOrderedHMMReport.test_extract_concurent) ... /tmp/autopkgtest.H3FgLD/build.EJd/src/tests/test_Report.py:461: DeprecationWarning: currentThread() is deprecated, use current_thread() instead 511s main_thread = threading.currentThread() 511s ok 511s test_HitSystemTracker (test_System.SystemTest.test_HitSystemTracker) ... ok 511s test_count (test_System.SystemTest.test_count) ... ok 511s test_fulfilled_function (test_System.SystemTest.test_fulfilled_function) ... ok 511s test_get_hits_encoding_multisystem (test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok 511s test_get_loners (test_System.SystemTest.test_get_loners) ... ok 511s test_get_multisystems (test_System.SystemTest.test_get_multisystems) ... ok 511s test_hits (test_System.SystemTest.test_hits) ... ok 511s test_init (test_System.SystemTest.test_init) ... ok 511s test_is_compatible (test_System.SystemTest.test_is_compatible) ... ok 511s test_loci_nb (test_System.SystemTest.test_loci_nb) ... ok 511s test_loci_num (test_System.SystemTest.test_loci_num) ... ok 511s test_multi_loci (test_System.SystemTest.test_multi_loci) ... ok 511s test_occurrence (test_System.SystemTest.test_occurrence) ... ok 511s test_position (test_System.SystemTest.test_position) ... ok 511s test_score (test_System.SystemTest.test_score) ... ok 511s test_wholeness (test_System.SystemTest.test_wholeness) ... ok 511s test_build_clusters (test_cluster.TestBuildCluster.test_build_clusters) ... ok 511s test_clusterize (test_cluster.TestBuildCluster.test_clusterize) ... ok 511s test_colocates (test_cluster.TestBuildCluster.test_colocates) ... ok 511s test_get_true_loners (test_cluster.TestBuildCluster.test_get_true_loners) ... ok 511s test_contains (test_cluster.TestCluster.test_contains) ... ok 511s test_fulfilled_function (test_cluster.TestCluster.test_fulfilled_function) ... ok 511s test_init (test_cluster.TestCluster.test_init) ... Cannot build a cluster from hits coming from different replicons 511s ok 511s test_len (test_cluster.TestCluster.test_len) ... ok 511s test_loner (test_cluster.TestCluster.test_loner) ... ok 511s test_merge (test_cluster.TestCluster.test_merge) ... ok 511s test_multi_system (test_cluster.TestCluster.test_multi_system) ... ok 511s test_replace (test_cluster.TestCluster.test_replace) ... ok 511s test_replicon_name (test_cluster.TestCluster.test_replicon_name) ... ok 511s test_score (test_cluster.TestCluster.test_score) ... ok 511s test_str (test_cluster.TestCluster.test_str) ... ok 511s 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'> 511s self.tearDown() 511s ResourceWarning: Enable tracemalloc to get the object allocation traceback 511s ok 511s test_cfg_n_previous_run (test_functional_test.Test.test_cfg_n_previous_run) ... ok 511s 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'> 511s self.tearDown() 511s ResourceWarning: Enable tracemalloc to get the object allocation traceback 511s ok 511s 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'> 511s self.tearDown() 511s ResourceWarning: Enable tracemalloc to get the object allocation traceback 511s ok 511s test_gembase (test_functional_test.Test.test_gembase) ... /tmp/autopkgtest.H3FgLD/build.EJd/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. 511s if filtering_node: 521s /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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s test_no_sequence (test_functional_test.Test.test_no_sequence) ... The sequence-db file '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/base/empty.fasta' does not contains sequences. 521s /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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 521s 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'> 521s self.tearDown() 521s ResourceWarning: Enable tracemalloc to get the object allocation traceback 521s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 522s 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'> 522s self.tearDown() 522s ResourceWarning: Enable tracemalloc to get the object allocation traceback 522s ok 528s test_timeout (test_functional_test.Test.test_timeout) ... Timeout is over. Aborting 528s The THHY002.0321.00001.C001 cannot be solved in time skip it! 528s The replicon THHY002.0321.00001.C001 cannot be solved before timeout. SKIP IT. 528s ok 528s 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'> 528s self.tearDown() 528s ResourceWarning: Enable tracemalloc to get the object allocation traceback 528s ok 528s 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'> 528s self.tearDown() 528s ResourceWarning: Enable tracemalloc to get the object allocation traceback 528s ok 528s 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'> 528s self.tearDown() 528s ResourceWarning: Enable tracemalloc to get the object allocation traceback 528s ok 528s 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'> 528s self.tearDown() 528s ResourceWarning: Enable tracemalloc to get the object allocation traceback 528s ok 528s test_working_dir_exists (test_functional_test.Test.test_working_dir_exists) ... ok 528s test_working_dir_exists_and_not_dir (test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok 528s test_core_gene (test_gene.TestCoreGene.test_core_gene) ... ok 528s test_str (test_gene.TestGeneStatus.test_str) ... ok 528s test_add_exchangeable (test_gene.TestModelGene.test_add_exchangeable) ... ok 528s test_alternate_of (test_gene.TestModelGene.test_alternate_of) ... ok 528s test_core_gene (test_gene.TestModelGene.test_core_gene) 528s test getter/setter for core_gene property ... ok 528s test_exhangeables (test_gene.TestModelGene.test_exhangeables) ... ok 528s test_hash (test_gene.TestModelGene.test_hash) ... ok 528s test_init (test_gene.TestModelGene.test_init) ... ok 528s test_inter_gene_max_space (test_gene.TestModelGene.test_inter_gene_max_space) 528s test getter for inter_gene_max_space property ... ok 528s test_is_Forbidden (test_gene.TestModelGene.test_is_Forbidden) 528s test if gene belong to model mandatory genes ... ok 528s test_is_accessory (test_gene.TestModelGene.test_is_accessory) 528s test if gene belong to model mandatory genes ... ok 528s test_is_exchangeable (test_gene.TestModelGene.test_is_exchangeable) ... ok 528s test_is_mandatory (test_gene.TestModelGene.test_is_mandatory) 528s test if gene belong to model mandatory genes ... ok 528s test_loner (test_gene.TestModelGene.test_loner) 528s test getter for loner property ... ok 528s test_model (test_gene.TestModelGene.test_model) 528s test getter/setter for model property ... ok 528s test_multi_model (test_gene.TestModelGene.test_multi_model) 528s test getter for multi_modelproperty ... ok 528s test_multi_system (test_gene.TestModelGene.test_multi_system) 528s test getter for multi_system property ... ok 528s test_str (test_gene.TestModelGene.test_str) ... ok 528s test_unknown_attribute (test_gene.TestModelGene.test_unknown_attribute) ... ok 528s test_cmp (test_hit.CoreHitTest.test_cmp) ... ok 528s test_eq (test_hit.CoreHitTest.test_eq) ... ok 528s test_get_position (test_hit.CoreHitTest.test_get_position) ... ok 528s test_hash (test_hit.CoreHitTest.test_hash) ... ok 528s test_str (test_hit.CoreHitTest.test_str) ... ok 528s test_compute_best_MSHit (test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok 528s test_get_best_hits (test_hit.GetBestHitTest.test_get_best_hits) ... ok 528s test_get_best_hits_4_func (test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok 528s test_sort_multisystem_hits (test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok 528s test_hit_weight_default (test_hit.HitWeightTest.test_hit_weight_default) ... ok 528s test_hit_weight_not_default (test_hit.HitWeightTest.test_hit_weight_not_default) ... ok 528s test_counterpart (test_hit.LonerMultiSystemTest.test_counterpart) ... Try to set counterpart for hit 'gspD' with non compatible hits: ['gspD', 'sctJ'] 528s ok 528s test_init (test_hit.LonerMultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system 528s ok 528s test_loner (test_hit.LonerMultiSystemTest.test_loner) ... ok 528s test_multi_system (test_hit.LonerMultiSystemTest.test_multi_system) ... ok 528s test_str (test_hit.LonerMultiSystemTest.test_str) ... ok 528s test_counterpart (test_hit.LonerTest.test_counterpart) ... ok 528s test_init (test_hit.LonerTest.test_init) ... hit_2 cannot be a loner gene_ref 'sctJ' not tag as loner 528s ok 528s test_len (test_hit.LonerTest.test_len) ... ok 528s test_loner (test_hit.LonerTest.test_loner) ... ok 528s test_multi_system (test_hit.LonerTest.test_multi_system) ... ok 528s test_str (test_hit.LonerTest.test_str) ... ok 528s test_delegation (test_hit.ModelHitTest.test_delegation) ... ok 528s test_eq (test_hit.ModelHitTest.test_eq) ... ok 528s test_hash (test_hit.ModelHitTest.test_hash) ... ok 528s test_init (test_hit.ModelHitTest.test_init) ... ok 528s test_loner (test_hit.ModelHitTest.test_loner) ... ok 528s test_multi_model (test_hit.ModelHitTest.test_multi_model) ... ok 528s test_multi_system (test_hit.ModelHitTest.test_multi_system) ... ok 528s test_counterpart (test_hit.MultiSystemTest.test_counterpart) ... ok 528s test_init (test_hit.MultiSystemTest.test_init) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system 528s ok 528s test_len (test_hit.MultiSystemTest.test_len) ... ok 528s test_loner (test_hit.MultiSystemTest.test_loner) ... ok 528s test_multi_system (test_hit.MultiSystemTest.test_multi_system) ... ok 528s test_str (test_hit.MultiSystemTest.test_str) ... ok 528s 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/tmp2drql9qu/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='UTF-8'> 528s self.tearDown() 528s ResourceWarning: Enable tracemalloc to get the object allocation traceback 528s ok 528s test_functional_split_out_error (test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... /tmp/tmpsnp47igr/macsyfinder_test_split/base is not a directory 528s ok 528s test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... /tmp/tmp129vis52/macsyfinder_test_split/base is not writable 528s Cannot create /tmp/tmp129vis52/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmp129vis52/macsyfinder_test_split/base' 528s ok 529s test_functional_merge (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv' 529s Merging 'best_solution.tsv' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_best_solution.tsv' 529s Merging 'all_systems.tsv' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_all_systems.tsv' 529s Merging 'best_solution_multisystems.tsv' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv' 529s Merging 'best_solution_loners.tsv' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv' 529s Merging 'rejected_candidates.tsv' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv' 529s Merging 'all_systems.txt' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_all_systems.txt' 529s Merging 'rejected_candidates.txt' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt' 529s Merging 'best_solution_summary' in to '/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv' 529s /usr/lib/python3.12/unittest/case.py:594: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp5u_qickp/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'> 529s self.tearDown() 529s ResourceWarning: Enable tracemalloc to get the object allocation traceback 529s ok 529s 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/tmpnvnchcly/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'> 529s self.tearDown() 529s ResourceWarning: Enable tracemalloc to get the object allocation traceback 529s ok 529s test_functional_merge_out_error (test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... /tmp/tmpl3m2z035/macsyfinder_test_merge/merged_results is not a directory 529s ok 529s test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... /tmp/tmpw7xne8br/macsyfinder_test_merge/merged_results is not writable 529s Cannot create /tmp/tmpw7xne8br/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmpw7xne8br/macsyfinder_test_merge/merged_results' 529s ok 530s 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/tmplozh8jlb/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'> 530s self.tearDown() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s ok 530s test_get_warning (test_macsy_merge_results.TestMerge.test_get_warning) ... ok 530s 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' 530s ok 530s test_add_comment (test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok 530s test_write (test_macsyconfig.TestConfigParserWithComment.test_write) ... ok 530s test_ask (test_macsyconfig.TestMacsyconfig.test_ask) ... ok 530s test_ask_bad_value (test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok 530s test_ask_default_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok 530s test_ask_use_default (test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok 530s test_ask_value_is_sequence (test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok 530s test_check_bool (test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok 530s test_check_choice (test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok 530s test_check_dir (test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok 530s test_check_exe (test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok 530s test_check_file (test_macsyconfig.TestMacsyconfig.test_check_file) ... ok 530s test_check_float (test_macsyconfig.TestMacsyconfig.test_check_float) ... ok 530s test_check_positive_int (test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok 530s test_check_str (test_macsyconfig.TestMacsyconfig.test_check_str) ... ok 530s test_functional_dark_theme (test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok 530s test_functional_file_already_exists (test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok 530s test_parse_args (test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok 530s test_set_base_options (test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok 530s test_set_general_options (test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok 530s test_set_hmmer_options (test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok 530s test_set_path_options (test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok 530s test_set_path_options_with_system_models_dir (test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok 530s test_set_score_options (test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok 530s test_set_section (test_macsyconfig.TestMacsyconfig.test_set_section) ... ok 530s test_set_section_use_defaults (test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok 530s test_available (test_macsydata.TestMacsydata.test_available) ... ok 530s test_build_argparser (test_macsydata.TestMacsydata.test_build_argparser) ... ok 530s test_check (test_macsydata.TestMacsydata.test_check) ... If everyone were like you, I'd be out of business 530s To push the models in organization: 530s cd /tmp/tmpwwynn0y3/fake_1 530s Transform the models into a git repository 530s git init . 530s git add . 530s git commit -m 'initial commit' 530s add a remote repository to host the models 530s for instance if you want to add the models to 'macsy-models' 530s git remote add origin https://github.com/macsy-models/ 530s git tag 0.0b2 530s git push origin 0.0b2 530s ok 530s test_check_with_errors (test_macsydata.TestMacsydata.test_check_with_errors) ... The package 'fake_1' have no 'definitions' directory. 530s The package 'fake_1' have no 'profiles' directory. 530s Please fix issues above, before publishing these models. 530s ok 530s 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. 530s The package 'fake_1' have not any README file. 530s 530s macsydata says: You're only giving me a partial QA payment? 530s I'll take it this time, but I'm not happy. 530s I'll be really happy, if you fix warnings above, before to publish these models. 530s ok 530s test_cite (test_macsydata.TestMacsydata.test_cite) ... Models 'nimportnaoik' not found locally. 530s ok 530s test_cmd_name (test_macsydata.TestMacsydata.test_cmd_name) ... ok 530s test_definition_all_def (test_macsydata.TestMacsydata.test_definition_all_def) ... /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpe_63s9ro/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='UTF-8'> 530s return open(path, 'r').read() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpe_63s9ro/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'> 530s return open(path, 'r').read() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s ok 530s test_definition_bad_def (test_macsydata.TestMacsydata.test_definition_bad_def) ... Model 'fake_1/niportnaoik' not found. 530s ok 530s test_definition_bad_pack (test_macsydata.TestMacsydata.test_definition_bad_pack) ... Package 'nimportnaoik' not found. 530s ok 530s test_definition_bad_subfamily (test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... 'niportnaoik' not found in package 'fake_1'. 530s ok 530s test_definition_models_dir (test_macsydata.TestMacsydata.test_definition_models_dir) ... /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbyj3ly9v/model_dir/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='UTF-8'> 530s return open(path, 'r').read() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbyj3ly9v/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'> 530s return open(path, 'r').read() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s ok 530s test_definition_one_def (test_macsydata.TestMacsydata.test_definition_one_def) ... /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpro2q47i7/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='UTF-8'> 530s return open(path, 'r').read() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s /tmp/autopkgtest.H3FgLD/build.EJd/src/macsypy/scripts/macsydata.py:623: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpro2q47i7/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='UTF-8'> 530s return open(path, 'r').read() 530s ResourceWarning: Enable tracemalloc to get the object allocation traceback 530s ok 530s test_download (test_macsydata.TestMacsydata.test_download) ... Downloading fake_1 1.0 530s Successfully downloaded packaging fake_1 in /tmp/tmput0f3jic/fake_1-1.0.tar.gz 530s No version that satisfy requirements '>2.0' for 'fake_1'. 530s Available versions: 1.0 530s Downloading fake_1 1.0 530s github limit error 530s ok 530s test_freeze (test_macsydata.TestMacsydata.test_freeze) ... ok 530s test_help (test_macsydata.TestMacsydata.test_help) ... Models 'nimportnaoik' not found locally. 530s ok 530s test_info (test_macsydata.TestMacsydata.test_info) ... Models 'nimportnaoik' not found locally. 530s ok 530s test_init_package_complete (test_macsydata.TestMacsydata.test_init_package_complete) ... The skeleton of complete_pack is ready. 530s The package is located at /tmp/tmpocrucofm/models/complete_pack 530s 530s - Edit metadata.yml and fill how to cite your package and where to find documentation about it. 530s - Add hmm profiles in /tmp/tmpocrucofm/models/complete_pack/profiles directory 530s - A skeleton of model definitions has been added in /tmp/tmpocrucofm/models/complete_pack/definitions. 530s For complete documentation about model grammar read https://macsyfinder.readthedocs.io/en/latest/modeler_guide/modeling.html 530s - A configuration file has been added (model_conf.xml) with default value tweak this file if needed. 530s (https://macsyfinder.readthedocs.io/en/latest/modeler_guide/package.html#model-configuration) 530s 530s Before to publish your package you can use `macsydata check` to verify it's integrity. 530s 530s Read macsyfinder modeler guide for further details: https://macsyfinder.readthedocs.io/en/latest/modeler_guide/index.html 530s ok 530s test_init_package_minimal (test_macsydata.TestMacsydata.test_init_package_minimal) ... Consider to add copyright to protect your rights. 530s 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 530s The skeleton of minimal_pack is ready. 530s The package is located at /tmp/tmpan__ccf6/models/minimal_pack 530s 530s - Edit metadata.yml and fill how to cite your package and where to find documentation about it. 530s - Add hmm profiles in /tmp/tmpan__ccf6/models/minimal_pack/profiles directory 530s - A skeleton of model definitions has been added in /tmp/tmpan__ccf6/models/minimal_pack/definitions. 530s For complete documentation about model grammar read https://macsyfinder.readthedocs.io/en/latest/modeler_guide/modeling.html 530s - A configuration file has been added (model_conf.xml) with default value tweak this file if needed. 530s (https://macsyfinder.readthedocs.io/en/latest/modeler_guide/package.html#model-configuration) 530s 530s Before to publish your package you can use `macsydata check` to verify it's integrity. 530s 530s Read macsyfinder modeler guide for further details: https://macsyfinder.readthedocs.io/en/latest/modeler_guide/index.html 530s ok 530s test_install_bad_target (test_macsydata.TestMacsydata.test_install_bad_target) ... ok 530s test_install_installed_package_corrupted (test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... Extracting fake_pack (0.0b2). 530s /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. 530s warnings.warn( 530s Installing fake_pack (0.0b2) in /tmp/tmp7bdmr9mb/models 530s Cleaning. 530s The models fake_pack (0.0b2) have been installed successfully. 530s fake_pack locally installed is corrupted. 530s You can fix it by removing '/tmp/tmp7bdmr9mb/models/fake_pack'. 530s ok 530s test_install_local (test_macsydata.TestMacsydata.test_install_local) ... Extracting fake_pack (3.0). 530s Installing fake_pack (3.0) in /tmp/tmpzas2x91q/models 530s Cleaning. 530s The models fake_pack (3.0) have been installed successfully. 530s ok 530s test_install_local_already_installed (test_macsydata.TestMacsydata.test_install_local_already_installed) ... Extracting fake_pack (0.0b2). 530s Installing fake_pack (0.0b2) in /tmp/tmpd4hey9cd/models 530s Cleaning. 530s The models fake_pack (0.0b2) have been installed successfully. 530s Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmpd4hey9cd/models/fake_pack. 530s To force installation use option -f --force-reinstall. 530s ok 531s test_install_local_already_installed_force (test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... Extracting fake_pack (0.0b2). 531s Installing fake_pack (0.0b2) in /tmp/tmprms0xpdp/models 531s Cleaning. 531s The models fake_pack (0.0b2) have been installed successfully. 531s Extracting fake_pack (0.0b2). 531s Installing fake_pack (0.0b2) in /tmp/tmprms0xpdp/models 531s Cleaning. 531s The models fake_pack (0.0b2) have been installed successfully. 531s ok 531s test_install_remote (test_macsydata.TestMacsydata.test_install_remote) ... Downloading fake_pack (0.0b2). 531s Extracting fake_pack (0.0b2). 531s Installing fake_pack (0.0b2) in /tmp/tmpt8v9rgmm/models 531s Cleaning. 531s The models fake_pack (0.0b2) have been installed successfully. 531s ok 531s test_install_remote_already_in_local (test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmp4at9al7n/models/fake_pack. 531s To force installation use option -f --force-reinstall. 531s ok 531s test_install_remote_already_in_local_force (test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... Downloading fake_pack (0.0b2). 531s Extracting fake_pack (0.0b2). 531s Installing fake_pack (0.0b2) in /tmp/tmp0a5dqztx/models 531s Cleaning. 531s The models fake_pack (0.0b2) have been installed successfully. 531s ok 531s 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. 531s To install it please run 'macsydata install --upgrade fake_pack' 531s ok 531s test_install_remote_permision_error (test_macsydata.TestMacsydata.test_install_remote_permision_error) ... Downloading fake_pack (0.0b2). 531s /tmp/tmp0jhcurof/models is not readable: [Errno 13] Permission denied: '/tmp/tmp0jhcurof/models' : skip it. 531s Extracting fake_pack (0.0b2). 531s Installing fake_pack (0.0b2) in /tmp/tmp0jhcurof/models 531s /tmp/tmp0jhcurof/models is not writable: [Errno 13] Permission denied: '/tmp/tmp0jhcurof/models/fake_pack' 531s Maybe you can use --user option to install in your HOME. 531s ok 531s 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' 531s ok 531s test_install_remote_upper_in_local (test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... fake_pack (0.0b2) is already installed. 531s To downgrade to 0.0b1 use option -f --force-reinstall. 531s ok 531s test_install_target (test_macsydata.TestMacsydata.test_install_target) ... Extracting fake_pack (3.0). 531s Installing fake_pack (3.0) in /tmp/tmpqrdfjncy/target 531s Cleaning. 531s The models fake_pack (3.0) have been installed successfully. 531s ok 531s test_list (test_macsydata.TestMacsydata.test_list) ... ok 531s test_list_long (test_macsydata.TestMacsydata.test_list_long) ... ok 531s test_list_outdated (test_macsydata.TestMacsydata.test_list_outdated) ... ok 531s test_list_uptodate (test_macsydata.TestMacsydata.test_list_uptodate) ... ok 531s test_list_verbose (test_macsydata.TestMacsydata.test_list_verbose) ... [Errno 2] No such file or directory: '/tmp/tmpzvh7lrws/models/fake_1/metadata.yml' 531s ok 531s test_no_subcommand (test_macsydata.TestMacsydata.test_no_subcommand) ... ok 532s test_search_in_pack_desc (test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok 532s test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok 532s test_search_in_pack_name (test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok 532s test_search_in_pack_name_match_case (test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok 532s test_search_reach_limit (test_macsydata.TestMacsydata.test_search_reach_limit) ... bla 532s ok 532s test_uninstall (test_macsydata.TestMacsydata.test_uninstall) ... models 'fake_1' in /tmp/tmpinvcgdsh/models/fake_1 uninstalled. 532s Models 'foo' not found locally. 532s ok 532s test_verbosity_to_log_level (test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok 532s test_db_type_set_to_gembase (test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... GA bit thresholds unavailable on profile T2SS_gspO. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilO. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilU. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilP. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilV. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilN. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilB. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilC. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilM. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile MSH_mshM. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilY. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilQ. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_fimT. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilX. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilA. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilW. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilE. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile ComM_comC. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilT. Switch to e-value threshold (-E 0.100000) 532s GA bit thresholds unavailable on profile T4P_pilD. Switch to e-value threshold (-E 0.100000) 532s Most of replicons contains only ONE sequence are you sure that '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/base/ordered_replicon_base.fasta' is a 'gembase'. 532s ok 532s test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok 532s test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok 532s test_list_models (test_macsyfinder.TestMacsyfinder.test_list_models) ... ok 532s test_loners_to_tsv (test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok 532s test_multisystem_to_tsv (test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok 532s test_parse_args (test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok 532s test_rejected_candidates_to_tsv (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok 532s test_rejected_candidates_to_txt (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok 551s test_search_systems (test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok 568s test_search_systems_unordered (test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok 568s test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok 568s test_summary_best_solution (test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok 568s test_summary_best_solution_empty (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok 568s test_summary_best_solution_lack_models (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok 568s test_summary_best_solution_lack_models_replicons (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok 568s test_summary_best_solution_lack_replicon (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok 568s test_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok 569s test_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok 569s test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok 569s test_LightHit (test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok 569s test_build_my_db (test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok 569s test_fill_my_db (test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok 569s test_functional (test_macsyprofile.TestMacsyprofile.test_functional) ... ok 569s test_functional_best_score (test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok 569s test_functional_coverage (test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok 569s test_functional_evalue (test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok 569s test_functional_no_hits (test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok 569s test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... nimportnaoik: No such directory. 569s ok 569s test_functional_out_exists (test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... The file /tmp/tmpfomrgh8v already exists. Remove it or specify a new output name --out or use --force option 569s ok 569s test_functional_pattern (test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok 569s test_getProfile_len (test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok 569s test_get_gene_name (test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok 569s test_header (test_macsyprofile.TestMacsyprofile.test_header) ... ok 569s test_hit_start (test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok 569s test_parse (test_macsyprofile.TestMacsyprofile.test_parse) ... ok 569s test_parse_hmm_body (test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok 569s test_parse_hmm_header (test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok 569s test_pasre_args (test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok 569s test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok 569s test_init_logger_default (test_macsypy.Test.test_init_logger_default) ... ok 569s 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/tmpq5i4002j' mode='a' encoding='UTF-8'> 569s self.tearDown() 569s ResourceWarning: Enable tracemalloc to get the object allocation traceback 569s ok 569s test_init_logger_no_out (test_macsypy.Test.test_init_logger_no_out) ... ok 569s test_logger_set_level_bad_level (test_macsypy.Test.test_logger_set_level_bad_level) ... ok 569s test_logger_set_level_default (test_macsypy.Test.test_logger_set_level_default) ... ok 569s test_logger_set_level_error (test_macsypy.Test.test_logger_set_level_error) ... ok 569s test_logger_set_level_handlers (test_macsypy.Test.test_logger_set_level_handlers) ... ok 569s test_parse (test_model_conf_parser.TestModelConfParser.test_parse) ... /tmp/autopkgtest.H3FgLD/build.EJd/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. 569s if weights_node: 569s /tmp/autopkgtest.H3FgLD/build.EJd/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. 569s if filtering_node: 569s ok 569s test_parse_bad_file (test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... unable to parse model configuration '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/conf_files/project.conf' : syntax error: line 2, column 0 569s ok 569s test_parse_filtering (test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... cannot parse 'cut_ga' element in '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/conf_files/model_conf.xml' expect True, 1, False, 0 got : 'FOO' 569s ok 569s test_parse_w_bad_value (test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... The model configuration file '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/conf_files/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO' 569s ok 569s test_parse_w_unkown_tag (test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... unknown element 'nimportnaoik' in '/tmp/autopkgtest.H3FgLD/build.EJd/src/tests/data/conf_files/model_conf.xml' ignore it. 569s ok 569s test_parse_weights (test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok 569s test_parse_wo_filtering (test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok 569s test_parse_wo_weights (test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok 569s test_init (test_package.TestLocalModelIndex.test_init) ... ok 569s test_init (test_package.TestModelIndex.test_init) ... ok 569s test_check (test_package.TestPackage.test_check) ... ok 569s test_check_metadata (test_package.TestPackage.test_check_metadata) ... ok 569s test_check_model_conf (test_package.TestPackage.test_check_model_conf) ... ok 569s 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' 569s ok 569s test_check_model_conf_no_conf (test_package.TestPackage.test_check_model_conf_no_conf) ... ok 569s test_check_model_consistency (test_package.TestPackage.test_check_model_consistency) ... ok 569s test_check_model_consistency_bad_definitions (test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok 569s test_check_model_consistency_extra_profile (test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok 569s test_check_model_consistency_lack_one_profile (test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok 569s test_check_no_readme_n_no_license (test_package.TestPackage.test_check_no_readme_n_no_license) ... ok 569s test_check_structure (test_package.TestPackage.test_check_structure) ... ok 569s test_check_structure_bad_path (test_package.TestPackage.test_check_structure_bad_path) ... ok 569s test_check_structure_no_def (test_package.TestPackage.test_check_structure_no_def) ... ok 569s test_check_structure_no_license (test_package.TestPackage.test_check_structure_no_license) ... ok 569s test_check_structure_no_metadata (test_package.TestPackage.test_check_structure_no_metadata) ... ok 569s test_check_structure_no_profiles (test_package.TestPackage.test_check_structure_no_profiles) ... ok 569s test_check_structure_no_readme (test_package.TestPackage.test_check_structure_no_readme) ... ok 569s test_find_readme (test_package.TestPackage.test_find_readme) ... ok 569s test_help (test_package.TestPackage.test_help) ... ok 569s test_info (test_package.TestPackage.test_info) ... ok 569s test_init (test_package.TestPackage.test_init) ... ok 569s test_metadata (test_package.TestPackage.test_metadata) ... ok 569s test_parse_arch_path (test_package.TestPackageFunc.test_parse_arch_path) ... ok 569s test_download (test_package.TestRemoteModelIndex.test_download) ... ok 569s test_get_metadata (test_package.TestRemoteModelIndex.test_get_metadata) ... ok 569s test_init (test_package.TestRemoteModelIndex.test_init) ... ok 569s test_list_package_vers (test_package.TestRemoteModelIndex.test_list_package_vers) ... ok 569s test_list_packages (test_package.TestRemoteModelIndex.test_list_packages) ... ok 570s test_remote_exists (test_package.TestRemoteModelIndex.test_remote_exists) ... ok 570s 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. 570s warnings.warn( 570s ok 570s test_url_json (test_package.TestRemoteModelIndex.test_url_json) ... ok 570s test_url_json_reach_limit (test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok 570s test_DefinitionLocationn (test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok 570s test_add_submodel (test_registries.DefinitionLocationTest.test_add_submodel) ... ok 570s test_all (test_registries.DefinitionLocationTest.test_all) ... ok 570s test_eq (test_registries.DefinitionLocationTest.test_eq) ... ok 570s test_family_name (test_registries.DefinitionLocationTest.test_family_name) ... ok 570s test_greater (test_registries.DefinitionLocationTest.test_greater) ... ok 570s test_hash (test_registries.DefinitionLocationTest.test_hash) ... ok 570s test_lesser (test_registries.DefinitionLocationTest.test_lesser) ... ok 570s test_root_name (test_registries.DefinitionLocationTest.test_root_name) ... ok 570s test_separator (test_registries.DefinitionLocationTest.test_separator) ... ok 570s test_split_fqn (test_registries.DefinitionLocationTest.test_split_fqn) ... ok 570s test_str (test_registries.DefinitionLocationTest.test_str) ... ok 570s test_ModelLocation (test_registries.ModelLocationTest.test_ModelLocation) ... ok 570s test_get_all_definitions (test_registries.ModelLocationTest.test_get_all_definitions) ... ok 570s test_get_definition (test_registries.ModelLocationTest.test_get_definition) ... ok 570s test_get_definitions (test_registries.ModelLocationTest.test_get_definitions) ... ok 570s test_get_profile (test_registries.ModelLocationTest.test_get_profile) ... ok 570s test_get_profiles_names (test_registries.ModelLocationTest.test_get_profiles_names) ... ok 570s test_str (test_registries.ModelLocationTest.test_str) ... ok 570s test_version (test_registries.ModelLocationTest.test_version) ... ok 570s 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. 570s ok 570s test_add_get (test_registries.ModelRegistryTest.test_add_get) ... ok 570s test_models (test_registries.ModelRegistryTest.test_models) ... ok 570s test_scan_models_dir (test_registries.ModelRegistryTest.test_scan_models_dir) ... ok 570s test_str (test_registries.ModelRegistryTest.test_str) ... ok 570s test_join_def_path (test_registries.RegitriesUtilsTest.test_join_def_path) ... ok 570s test_split_def_name (test_registries.RegitriesUtilsTest.test_split_def_name) ... ok 570s test_search (test_search_genes.TestSearchGenes.test_search) ... ok 570s test_search_fail (test_search_genes.TestSearchGenes.test_search_fail) ... ok 570s test_search_recover (test_search_genes.TestSearchGenes.test_search_recover) ... ok 570s test_worker_cpu (test_search_genes.TestSearchGenes.test_worker_cpu) ... ok 570s test_LikelySystemSerializer_txt (test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok 570s test_RejectedClusters_tsv (test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok 570s test_SolutionSerializer_tsv (test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok 570s test_SpecialHitSerializer_tsv (test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok 570s test_SystemSerializer_str (test_serialization.SerializationTest.test_SystemSerializer_str) ... ok 570s test_SystemSerializer_tsv (test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok 570s test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok 570s test_combine_clusters (test_solution.SolutionExplorerTest.test_combine_clusters) ... ok 570s test_combine_multisystems (test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok 570s test_find_best_solution (test_solution.SolutionExplorerTest.test_find_best_solution) ... ok 570s test_average_wholeness (test_solution.SolutionTest.test_average_wholeness) ... ok 570s test_gt (test_solution.SolutionTest.test_gt) ... ok 570s test_hits_number (test_solution.SolutionTest.test_hits_number) ... ok 570s test_hits_positions (test_solution.SolutionTest.test_hits_positions) ... ok 570s test_iteration (test_solution.SolutionTest.test_iteration) ... ok 570s test_lt (test_solution.SolutionTest.test_lt) ... ok 570s test_score (test_solution.SolutionTest.test_score) ... ok 570s test_sorting (test_solution.SolutionTest.test_sorting) ... ok 570s test_systems (test_solution.SolutionTest.test_systems) ... ok 570s test_get_def_to_detect (test_utils.TestUtils.test_get_def_to_detect) ... ok 570s test_get_replicon_names_bad_type (test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok 570s test_get_replicon_names_gembase (test_utils.TestUtils.test_get_replicon_names_gembase) ... ok 570s test_get_replicon_names_ordered (test_utils.TestUtils.test_get_replicon_names_ordered) ... ok 570s test_get_replicon_names_unordered (test_utils.TestUtils.test_get_replicon_names_unordered) ... ok 570s test_parse_time (test_utils.TestUtils.test_parse_time) ... ok 570s test_threads_available (test_utils.TestUtils.test_threads_available) ... ok 570s 570s ---------------------------------------------------------------------- 570s Ran 509 tests in 62.237s 570s 570s OK (skipped=2) 571s autopkgtest [15:36:17]: test run-unit-test: -----------------------] 572s autopkgtest [15:36:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 572s run-unit-test PASS 572s autopkgtest [15:36:18]: @@@@@@@@@@@@@@@@@@@@ summary 572s run-unit-test PASS 588s Creating nova instance adt-noble-arm64-macsyfinder-20240323-152646-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240323.img (UUID 5063c5cd-2683-4ea1-9e65-62351adfb1a7)...