[Debian-med-packaging] Bug#1026742: kineticstools: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 3.10" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Tue Dec 20 17:28:43 GMT 2022
Source: kineticstools
Version: 0.6.1+git20220223.1326a4d+dfsg-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&fusertaguser=lucas@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.
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