Your message dated Wed, 21 Dec 2022 14:49:36 +0000
with message-id <e1p80py-009z9z...@fasolo.debian.org>
and subject line Bug#1026742: fixed in kineticstools
0.6.1+git20220223.1326a4d+dfsg-2
has caused the Debian Bug report #1026742,
regarding kineticstools: FTBFS: dh_auto_test: error: pybuild --test
--test-pytest -i python{version} -p "3.11 3.10" returned exit code 13
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1026742: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1026742
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: kineticstools
Source-Version: 0.6.1+git20220223.1326a4d+dfsg-2
Done: Nilesh Patra <nil...@debian.org>
We believe that the bug you reported is fixed in the latest version of
kineticstools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1026...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nil...@debian.org> (supplier of updated kineticstools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 21 Dec 2022 19:59:38 +0530
Source: kineticstools
Architecture: source
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nil...@debian.org>
Closes: 1026742
Changes:
kineticstools (0.6.1+git20220223.1326a4d+dfsg-2) unstable; urgency=medium
.
* Team Upload.
* Test only for default python version as pysam is not
available for python3.11 (Closes: #1026742)
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Files:
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kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.debian.tar.xz
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--- End Message ---
