Source: htslib, python-pysam Control: found -1 htslib/1.9-10 Control: found -1 python-pysam/0.15.1+ds-1 X-Debbugs-CC: [email protected] User: [email protected] Usertags: breaks needs-update
Dear maintainers,
With a recent upload of htslib the autopkgtest of python-pysam fails in
testing when that autopkgtest is run with the binary packages of htslib
from unstable. It passes when run with only packages from testing. In
tabular form:
pass fail
htslib from testing 1.9-10
python-pysam from testing 0.15.1+ds-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of htslib to testing
[1]. Due to the nature of this issue, I filed this bug report against
both packages. Can you please investigate the situation and reassign the
bug to the right package? If needed, please change the bug's severity.
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=htslib
https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-pysam/1739216/log.gz
=================================== FAILURES
===================================
_____________ TestIndexing.test_indexing_to_custom_location_works
______________
self = <tabix_test.TestIndexing
testMethod=test_indexing_to_custom_location_works>
def test_indexing_to_custom_location_works(self):
'''test indexing a file with a non-default location.'''
index_path = get_temp_filename(suffix='custom.tbi')
pysam.tabix_index(self.tmpfilename, preset="gff",
index=index_path, force=True)
> self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))
E AssertionError: False is not true
tests/tabix_test.py:89: AssertionError
____________ TestIndexing.test_indexing_with_explict_columns_works
_____________
self = <tabix_test.TestIndexing
testMethod=test_indexing_with_explict_columns_works>
def test_indexing_with_explict_columns_works(self):
'''test indexing via preset.'''
pysam.tabix_index(self.tmpfilename,
seq_col=0,
start_col=3,
end_col=4,
line_skip=0,
zerobased=False)
self.assertTrue(checkBinaryEqual(
> self.tmpfilename + ".tbi", self.filename_idx))
E AssertionError: False is not true
tests/tabix_test.py:102: AssertionError
_________________ TestIndexing.test_indexing_with_preset_works
_________________
self = <tabix_test.TestIndexing testMethod=test_indexing_with_preset_works>
def test_indexing_with_preset_works(self):
'''test indexing via preset.'''
pysam.tabix_index(self.tmpfilename, preset="gff")
self.assertTrue(checkBinaryEqual(
> self.tmpfilename + ".tbi", self.filename_idx))
E AssertionError: False is not true
tests/tabix_test.py:81: AssertionError
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