--- Begin Message ---
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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1 items passed all tests:
13 tests in default
13 tests in 1 items.
13 passed and 0 failed.
Test passed.
Document: default-arguments
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1 items passed all tests:
13 tests in default
13 tests in 1 items.
13 passed and 0 failed.
Test passed.
Document: each
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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.
--- End Message ---
pgp2uRnHYrhP7.pgp
