Source: kineticstools Version: 0.6.1+git20220223.1326a4d+dfsg-1 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20221220 ftbfs-bookworm
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > cp kineticsTools/ipdSummary.py bin/ipdSummary > chmod +x bin/ipdSummary > PYTHONPATH=/<<PKGBUILDDIR>> PATH=$PATH:/<<PKGBUILDDIR>>/bin dh_auto_test > I: pybuild base:240: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build; python3.11 -m > pytest test > ============================= test session starts > ============================== > platform linux -- Python 3.11.1, pytest-7.2.0, pluggy-1.0.0+repack -- > /usr/bin/python3.11 > cachedir: .pytest_cache > rootdir: /<<PKGBUILDDIR>>, configfile: pytest.ini > plugins: xdist-3.1.0 > gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I > > [gw0] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw1] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw2] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw3] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw4] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw5] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw6] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw7] linux Python 3.11.1 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build > > [gw0] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw3] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw2] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw1] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw4] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw5] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw6] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > > [gw7] Python 3.11.1 (main, Dec 7 2022, 08:49:13) [GCC 12.2.0] > gw0 [11] / gw1 [11] / gw2 [11] / gw3 [11] / gw4 [11] / gw5 [11] / gw6 [11] / > gw7 [11] > > scheduling tests via LoadScopeScheduling > > test/test_outputs.py::TestOutputs::test_csv_output > [gw1] [ 9%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output > test/test_integration.py::TestKineticsTools::test_help > test/test_summarize_modifications.py::TestSummarizeModifications::test_integration > > [gw4] [ 18%] SKIPPED > test/test_summarize_modifications.py::TestSummarizeModifications::test_integration > > test/test_outputs.py::TestOutputs::test_bigwig > [gw1] [ 27%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig > test/test_loader.py::test_basic > [gw2] [ 36%] PASSED test/test_loader.py::test_basic > test/test_loader.py::test_path > [gw2] [ 45%] PASSED test/test_loader.py::test_path > test/test_loader.py::test_path_with_prefixed_chem > [gw2] [ 54%] PASSED test/test_loader.py::test_path_with_prefixed_chem > test/test_loader.py::test_getResourcePathSpec > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig > [gw0] [ 63%] SKIPPED > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli > [gw0] [ 72%] SKIPPED > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli > [gw2] [ 81%] PASSED test/test_loader.py::test_getResourcePathSpec > [gw3] [ 90%] PASSED test/test_integration.py::TestKineticsTools::test_help > test/test_integration.py::TestKineticsTools::test_ecoli_first_50k > [gw3] [100%] SKIPPED > test/test_integration.py::TestKineticsTools::test_ecoli_first_50k > > ==================================== ERRORS > ==================================== > _ ERROR collecting > .pybuild/cpython3_3.11_kineticstools/build/test/test_ReferenceUtils.py _ > ImportError while importing test module > '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build/test/test_ReferenceUtils.py'. > Hint: make sure your test modules/packages have valid Python names. > Traceback: > /usr/lib/python3.11/importlib/__init__.py:126: in import_module > return _bootstrap._gcd_import(name[level:], package, level) > test/test_ReferenceUtils.py:6: in <module> > from pbcore.io import AlignmentSet > /usr/lib/python3/dist-packages/pbcore/io/__init__.py:8: in <module> > from .align import * > /usr/lib/python3/dist-packages/pbcore/io/align/__init__.py:1: in <module> > from .BamIO import * > /usr/lib/python3/dist-packages/pbcore/io/align/BamIO.py:9: in <module> > from pysam.libcalignmentfile import AlignmentFile # pylint: > disable=no-name-in-module, import-error, fixme, line-too-long > /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module> > from pysam.libchtslib import * > E ModuleNotFoundError: No module named 'pysam.libchtslib' > _ ERROR collecting > .pybuild/cpython3_3.11_kineticstools/build/test/test_ipdModel.py _ > ImportError while importing test module > '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build/test/test_ipdModel.py'. > Hint: make sure your test modules/packages have valid Python names. > Traceback: > /usr/lib/python3.11/importlib/__init__.py:126: in import_module > return _bootstrap._gcd_import(name[level:], package, level) > test/test_ipdModel.py:5: in <module> > from pbcore.io import AlignmentSet > /usr/lib/python3/dist-packages/pbcore/io/__init__.py:8: in <module> > from .align import * > /usr/lib/python3/dist-packages/pbcore/io/align/__init__.py:1: in <module> > from .BamIO import * > /usr/lib/python3/dist-packages/pbcore/io/align/BamIO.py:9: in <module> > from pysam.libcalignmentfile import AlignmentFile # pylint: > disable=no-name-in-module, import-error, fixme, line-too-long > /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module> > from pysam.libchtslib import * > E ModuleNotFoundError: No module named 'pysam.libchtslib' > - generated xml file: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build/nosetests.xml - > ============================= slowest 20 durations > ============================= > 0.77s call > .pybuild/cpython3_3.11_kineticstools/build/test/test_integration.py::TestKineticsTools::test_help > > (19 durations < 0.005s hidden. Use -vv to show these durations.) > =========================== short test summary info > ============================ > ERROR test/test_ReferenceUtils.py > ERROR test/test_ipdModel.py > ==================== 5 passed, 6 skipped, 2 errors in 2.76s > ==================== > E: pybuild pybuild:386: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_kineticstools/build; python3.11 -m > pytest test > I: pybuild base:240: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build; python3.10 -m > pytest test > ============================= test session starts > ============================== > platform linux -- Python 3.10.9, pytest-7.2.0, pluggy-1.0.0+repack -- > /usr/bin/python3.10 > cachedir: .pytest_cache > rootdir: /<<PKGBUILDDIR>>, configfile: pytest.ini > plugins: xdist-3.1.0 > gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I > > [gw0] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw1] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw2] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw3] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw4] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw5] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw6] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw7] linux Python 3.10.9 cwd: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build > > [gw0] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw1] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw2] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw3] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw4] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw6] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw5] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > > [gw7] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0] > gw0 [19] / gw1 [19] / gw2 [19] / gw3 [19] / gw4 [19] / gw5 [19] / gw6 [19] / > gw7 [19] > > scheduling tests via LoadScopeScheduling > > test/test_summarize_modifications.py::TestSummarizeModifications::test_integration > > test/test_outputs.py::TestOutputs::test_csv_output > test/test_loader.py::test_basic > test/test_integration.py::TestKineticsTools::test_help > [gw5] [ 5%] SKIPPED > test/test_summarize_modifications.py::TestSummarizeModifications::test_integration > > test/test_ipdModel.py::TestIpdModel::test_refLength > [gw3] [ 10%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength > test/test_ipdModel.py::TestIpdModel::test_snippetFunc > [gw3] [ 15%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc > test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow > [gw3] [ 21%] SKIPPED > test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig > [gw1] [ 26%] SKIPPED > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli > [gw1] [ 31%] SKIPPED > test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli > [gw4] [ 36%] PASSED test/test_loader.py::test_basic > test/test_loader.py::test_path > [gw4] [ 42%] PASSED test/test_loader.py::test_path > test/test_loader.py::test_path_with_prefixed_chem > [gw4] [ 47%] PASSED test/test_loader.py::test_path_with_prefixed_chem > test/test_loader.py::test_getResourcePathSpec > [gw4] [ 52%] PASSED test/test_loader.py::test_getResourcePathSpec > [gw6] [ 57%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output > test/test_outputs.py::TestOutputs::test_bigwig > [gw6] [ 63%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig > test/test_ReferenceUtils.py::TestReferenceUtils::test_bam > [gw0] [ 68%] SKIPPED > test/test_ReferenceUtils.py::TestReferenceUtils::test_bam > test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset > [gw0] [ 73%] SKIPPED > test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset > test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow > [gw0] [ 78%] SKIPPED > test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow > test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows > [gw0] [ 84%] SKIPPED > test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows > test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks > [gw0] [ 89%] SKIPPED > test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks > [gw2] [ 94%] PASSED test/test_integration.py::TestKineticsTools::test_help > test/test_integration.py::TestKineticsTools::test_ecoli_first_50k > [gw2] [100%] SKIPPED > test/test_integration.py::TestKineticsTools::test_ecoli_first_50k > > - generated xml file: > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/nosetests.xml - > ============================= slowest 20 durations > ============================= > 0.73s call > .pybuild/cpython3_3.10_kineticstools/build/test/test_integration.py::TestKineticsTools::test_help > > (19 durations < 0.005s hidden. Use -vv to show these durations.) > ======================== 5 passed, 14 skipped in 2.34s > ========================= > dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 > 3.10" returned exit code 13 The full build log is available from: http://qa-logs.debian.net/2022/12/20/kineticstools_0.6.1+git20220223.1326a4d+dfsg-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221220;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.