Package: src:python-pybedtools Version: 0.10.0-2 Severity: serious Tags: ftbfs
Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -------------------------------------------------------------------------------- [...] debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources [... snipped ...] Document: autodocs/pybedtools.bedtool.BedTool.field_count --------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.file_type ------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.filter ---------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.flank --------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage ------------------------------------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.groupby ----------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.head -------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta -------------------------------------------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.merge --------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.moveto ---------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.overlap ----------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.random ---------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.randomintersection ---------------------------------------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.randomstats --------------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid ------------------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.save_seqs ------------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.saveas ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.sequence ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes ------------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.shuffle ----------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.sort -------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.subtract ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.total_coverage ------------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.with_attrs -------------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.Interval ------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.create_interval_from_list ----------------------------------------------------------------- 1 items passed all tests: 1 tests in default 1 tests in 1 items. 1 passed and 0 failed. Test passed. Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions ----------------------------------------------------------------------------------- ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: iterator, n, extra = tag_bedpe(bedpe, queries) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[4]>", line 1, in <module> iterator, n, extra = tag_bedpe(bedpe, queries) ^^^^^^^^^ NameError: name 'tag_bedpe' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: for (label, group1, group2) in iterator: group1 = sorted(group1, key=lambda x: str(x)) group2 = sorted(group2, key=lambda x: str(x)) for i in group1: print(i, end='') # doctest: +NORMALIZE_WHITESPACE for i in group2: print(i, end='') # doctest: +NORMALIZE_WHITESPACE Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[5]>", line 1, in <module> for (label, group1, group2) in iterator: ^^^^^^^^ NameError: name 'iterator' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks}) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[1]>", line 1, in <module> iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks}) ^^^^^^^^^ NameError: name 'tag_bedpe' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: df = cis_trans_interactions(iterator, n, extra) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[2]>", line 1, in <module> df = cis_trans_interactions(iterator, n, extra) ^^^^^^^^^^^^^^^^^^^^^^ NameError: name 'cis_trans_interactions' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: print(df.sort_values(list(df.columns)).reset_index(drop=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[3]>", line 1, in <module> print(df.sort_values(list(df.columns)).reset_index(drop=True)) ^^ NameError: name 'df' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: print((df[df.target_label == 'tss']).sort_values(list(df.columns)).reset_index(drop=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[0]>", line 1, in <module> print((df[df.target_label == 'tss']).sort_values(list(df.columns)).reset_index(drop=True)) ^^ NameError: name 'df' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: assert set(df.loc[df.target_name == 'gene2', 'distal_name']).difference('.') == set([u'gene1', u'peak1']) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "<doctest default[0]>", line 1, in <module> assert set(df.loc[df.target_name == 'gene2', 'distal_name']).difference('.') == set([u'gene1', u'peak1']) ^^ NameError: name 'df' is not defined ********************************************************************** 1 items had failures: 7 of 18 in default 18 tests in 1 items. 11 passed and 7 failed. ***Test Failed*** 7 failures. Document: autodocs/pybedtools.contrib.plotting.Track ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.filenames.list_example_files ---------------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.helpers.chromsizes ------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.parallel.parallel_apply ----------------------------------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: default-arguments --------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: each -------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: filtering ------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: history ----------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: intersections ----------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: intervals ------------------- 1 items passed all tests: 50 tests in default 50 tests in 1 items. 50 passed and 0 failed. Test passed. Document: piping ---------------- 1 items passed all tests: 17 tests in default 17 tests in 1 items. 17 passed and 0 failed. Test passed. Document: save-results ---------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: topical-bam --------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-create-a-bedtool ---------------------------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-design-principles ----------------------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: topical-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 passed and 0 failed. Test passed. Document: topical-low-level-ops ------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: topical-random ------------------------ 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 passed and 0 failed. Test passed. Doctest summary =============== 387 tests 7 failures in tests 0 failures in setup code 0 failures in cleanup code build finished with problems, 126 warnings. make[1]: *** [Makefile:137: doctest] Error 1 make[1]: Leaving directory '/<<PKGBUILDDIR>>/docs' E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/docs ; make clean doctest dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 make: *** [debian/rules:30: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- The above is just how the build ends and not necessarily the most relevant part. If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202412/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you could not reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and affects, so that this is still visible in the BTS web page for this package. Thanks.
