Source: python-biopython Version: 1.81+dfsg-3 Severity: serious Tags: ftbfs Justification: ftbfs
While trying to pinpoint the root cause of test failures in the
packaging attempt of Biopython 1.83, I eventually realized that
the version 1.81 of Biopython is also affected by the same
issues. The relevant part of the test log looks like:
======================================================================
ERROR: test_embl7 (test_SeqIO.TestSeqIO.test_embl7)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 3388,
in test_embl7
self.perform_test(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626,
in perform_test
self.check_simple_write_read(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363,
in check_simple_write_read
records2 = list(SeqIO.parse(handle=handle, format=fmt))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line
72, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
447, in iterate
parser.close()
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
File "../Modules/pyexpat.c", line 416, in StartElement
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in
start_element_ns
self._cont_handler.startElementNS(pair, None,
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
163, in startEntryFieldElement
return self.startPropertyElement(attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
339, in startPropertyElement
record = self.records[-1]
~~~~~~~~~~~~^^^^
IndexError: list index out of range
======================================================================
ERROR: test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 2785,
in test_genbank8
self.perform_test(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626,
in perform_test
self.check_simple_write_read(
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363,
in check_simple_write_read
records2 = list(SeqIO.parse(handle=handle, format=fmt))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line
72, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
447, in iterate
parser.close()
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
File "../Modules/pyexpat.c", line 416, in StartElement
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in
start_element_ns
self._cont_handler.startElementNS(pair, None,
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
163, in startEntryFieldElement
return self.startPropertyElement(attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line
339, in startPropertyElement
record = self.records[-1]
~~~~~~~~~~~~^^^^
IndexError: list index out of range
I haven't checked but I heavily suspect that this is causing
also autopkgtest failures.
For information,
--
.''`. Étienne Mollier <[email protected]>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/0, please excuse my verbosity
`-
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