Source: seqmagick Version: 0.8.6-1 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20240313 ftbfs-trixie
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > debian/rules binary > dh binary --with python3 --buildsystem=pybuild > dh_update_autotools_config -O--buildsystem=pybuild > dh_autoreconf -O--buildsystem=pybuild > dh_auto_configure -O--buildsystem=pybuild > I: pybuild base:305: python3.12 setup.py config > /usr/lib/python3/dist-packages/setuptools/__init__.py:84: > _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are > deprecated. > !! > > > ******************************************************************************** > Requirements should be satisfied by a PEP 517 installer. > If you are using pip, you can try `pip install --use-pep517`. > > ******************************************************************************** > > !! > dist.fetch_build_eggs(dist.setup_requires) > WARNING: The wheel package is not available. > /usr/lib/python3/dist-packages/setuptools/dist.py:509: > SetuptoolsDeprecationWarning: Invalid version: ''. > !! > > > ******************************************************************************** > The version specified is not a valid version according to PEP 440. > This may not work as expected with newer versions of > setuptools, pip, and PyPI. > > This deprecation is overdue, please update your project and remove > deprecated > calls to avoid build errors in the future. > > See https://peps.python.org/pep-0440/ for details. > > ******************************************************************************** > > !! > self._validate_version(self.metadata.version) > running config > I: pybuild base:305: python3.11 setup.py config > /usr/lib/python3/dist-packages/setuptools/__init__.py:84: > _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are > deprecated. > !! > > > ******************************************************************************** > Requirements should be satisfied by a PEP 517 installer. > If you are using pip, you can try `pip install --use-pep517`. > > ******************************************************************************** > > !! > dist.fetch_build_eggs(dist.setup_requires) > WARNING: The wheel package is not available. > /usr/lib/python3/dist-packages/setuptools/dist.py:509: > SetuptoolsDeprecationWarning: Invalid version: ''. > !! > > > ******************************************************************************** > The version specified is not a valid version according to PEP 440. > This may not work as expected with newer versions of > setuptools, pip, and PyPI. > > This deprecation is overdue, please update your project and remove > deprecated > calls to avoid build errors in the future. > > See https://peps.python.org/pep-0440/ for details. > > ******************************************************************************** > > !! > self._validate_version(self.metadata.version) > running config > dh_auto_build -O--buildsystem=pybuild > I: pybuild base:305: /usr/bin/python3.12 setup.py build > /usr/lib/python3/dist-packages/setuptools/__init__.py:84: > _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are > deprecated. > !! > > > ******************************************************************************** > Requirements should be satisfied by a PEP 517 installer. > If you are using pip, you can try `pip install --use-pep517`. > > ******************************************************************************** > > !! > dist.fetch_build_eggs(dist.setup_requires) > WARNING: The wheel package is not available. > /usr/lib/python3/dist-packages/setuptools/dist.py:509: > SetuptoolsDeprecationWarning: Invalid version: ''. > !! > > > ******************************************************************************** > The version specified is not a valid version according to PEP 440. > This may not work as expected with newer versions of > setuptools, pip, and PyPI. > > This deprecation is overdue, please update your project and remove > deprecated > calls to avoid build errors in the future. > > See https://peps.python.org/pep-0440/ for details. > > ******************************************************************************** > > !! > self._validate_version(self.metadata.version) > running build > running build_py > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick > copying seqmagick/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick > copying seqmagick/fileformat.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick > copying seqmagick/transform.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/common.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/convert.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/quality_filter.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/backtrans_align.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/extract_ids.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/info.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > copying seqmagick/subcommands/mogrify.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/subcommands > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > copying seqmagick/test/test_subcommands_quality_filter.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > copying seqmagick/test/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > copying seqmagick/test/test_subcommands_common.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > copying seqmagick/test/test_subcommands_convert.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > copying seqmagick/test/test_transform.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > copying seqmagick/test/test_subcommands_backtrans_align.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/scripts > copying seqmagick/scripts/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/scripts > copying seqmagick/scripts/cli.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/scripts > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration > copying seqmagick/test/integration/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration > copying seqmagick/test/integration/test_extract_ids.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration > copying seqmagick/test/integration/test_mogrify.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration > copying seqmagick/test/integration/test_info.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration > copying seqmagick/test/integration/test_convert.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2.nex -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input5.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input3.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2_ungap_cut.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input6.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input2.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output3.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input2.fasta.gz -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input2.fasta.bz2 -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output4.nex -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input1.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output3.nex -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output4.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output5.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2.phy -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input4_ambig.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/seqmagick/test/integration/data > I: pybuild base:305: /usr/bin/python3 setup.py build > /usr/lib/python3/dist-packages/setuptools/__init__.py:84: > _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are > deprecated. > !! > > > ******************************************************************************** > Requirements should be satisfied by a PEP 517 installer. > If you are using pip, you can try `pip install --use-pep517`. > > ******************************************************************************** > > !! > dist.fetch_build_eggs(dist.setup_requires) > WARNING: The wheel package is not available. > /usr/lib/python3/dist-packages/setuptools/dist.py:509: > SetuptoolsDeprecationWarning: Invalid version: ''. > !! > > > ******************************************************************************** > The version specified is not a valid version according to PEP 440. > This may not work as expected with newer versions of > setuptools, pip, and PyPI. > > This deprecation is overdue, please update your project and remove > deprecated > calls to avoid build errors in the future. > > See https://peps.python.org/pep-0440/ for details. > > ******************************************************************************** > > !! > self._validate_version(self.metadata.version) > running build > running build_py > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick > copying seqmagick/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick > copying seqmagick/fileformat.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick > copying seqmagick/transform.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/common.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/convert.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/quality_filter.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/backtrans_align.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/extract_ids.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/info.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > copying seqmagick/subcommands/mogrify.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/subcommands > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > copying seqmagick/test/test_subcommands_quality_filter.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > copying seqmagick/test/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > copying seqmagick/test/test_subcommands_common.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > copying seqmagick/test/test_subcommands_convert.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > copying seqmagick/test/test_transform.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > copying seqmagick/test/test_subcommands_backtrans_align.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/scripts > copying seqmagick/scripts/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/scripts > copying seqmagick/scripts/cli.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/scripts > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration > copying seqmagick/test/integration/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration > copying seqmagick/test/integration/test_extract_ids.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration > copying seqmagick/test/integration/test_mogrify.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration > copying seqmagick/test/integration/test_info.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration > copying seqmagick/test/integration/test_convert.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration > creating > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2.nex -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input5.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input3.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2_ungap_cut.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input6.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input2.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output3.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input2.fasta.gz -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input2.fasta.bz2 -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output4.nex -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input1.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output3.nex -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output4.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output5.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/output2.phy -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > copying seqmagick/test/integration/data/input4_ambig.fasta -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/seqmagick/test/integration/data > dh_auto_test -O--buildsystem=pybuild > I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; > python3.12 -m pytest > ============================= test session starts > ============================== > platform linux -- Python 3.12.2, pytest-8.0.2, pluggy-1.4.0 > rootdir: /<<PKGBUILDDIR>> > collected 154 items > > seqmagick/test/integration/test_convert.py .ss.............. [ > 11%] > seqmagick/test/integration/test_extract_ids.py ..ss.. [ > 14%] > seqmagick/test/integration/test_info.py ...s [ > 17%] > seqmagick/test/integration/test_mogrify.py .s. [ > 19%] > seqmagick/test/test_subcommands_backtrans_align.py ....FFF.. [ > 25%] > seqmagick/test/test_subcommands_common.py ..................s..... [ > 40%] > seqmagick/test/test_subcommands_convert.py ...... [ > 44%] > seqmagick/test/test_subcommands_quality_filter.py ...................... [ > 59%] > .... [ > 61%] > seqmagick/test/test_transform.py ....................................... [ > 87%] > .................... > [100%] > > =================================== FAILURES > =================================== > __________________ AlignmentMapperTestCase.test_map_alignment > __________________ > > self = > <seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase > testMethod=test_map_alignment> > > def test_map_alignment(self): > nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF > SeqRecord(Seq('AAGGTCTTC'), id='2'), # KVF > SeqRecord(Seq('GGGGTTTTT'), id='3')] # GVF > prot = [SeqRecord(Seq('-K-F'), id='1'), > SeqRecord(Seq('-KVF'), id='2'), > SeqRecord(Seq('G-VF'), id='3')] > > result = self.instance.map_all(prot, nucl) > > result = [(s.id, str(s.seq)) for s in result] > > seqmagick/test/test_subcommands_backtrans_align.py:56: > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > seqmagick/subcommands/backtrans_align.py:148: in map_all > yield self.map_alignment(p, n) > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > > self = <seqmagick.subcommands.backtrans_align.AlignmentMapper object at > 0x7f5410093080> > prot_seq = SeqRecord(seq=Seq('-K-F'), id='1', name='<unknown name>', > description='<unknown description>', dbxrefs=[]) > nucl_seq = SeqRecord(seq=Seq('AAGTTT'), id='1', name='<unknown name>', > description='<unknown description>', dbxrefs=[]) > > def map_alignment(self, prot_seq, nucl_seq): > """ > Use aligned prot_seq to align nucl_seq > """ > if prot_seq.id != nucl_seq.id: > logging.warning( > 'ID mismatch: %s != %s. Are the sequences in the same order?', > prot_seq.id, nucl_seq.id) > > # Ungap nucleotides > > codons = batch(str(nucl_seq.seq.ungap('-')), 3) > E AttributeError: 'Seq' object has no attribute 'ungap' > > seqmagick/subcommands/backtrans_align.py:105: AttributeError > ___________ AlignmentMapperTestCase.test_map_alignment_excess_codons > ___________ > > self = > <seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase > testMethod=test_map_alignment_excess_codons> > > def test_map_alignment_excess_codons(self): > nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF > SeqRecord(Seq('AAGGTCTTC'), id='2')] # KVF > prot = [SeqRecord(Seq('K-F'), id='1'), > SeqRecord(Seq('KV-'), id='2')] > mapped = self.instance.map_all(prot, nucl) > > self.assertRaises(ValueError, list, mapped) > > seqmagick/test/test_subcommands_backtrans_align.py:76: > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > seqmagick/subcommands/backtrans_align.py:148: in map_all > yield self.map_alignment(p, n) > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > > def map_alignment(self, prot_seq, nucl_seq): > """ > Use aligned prot_seq to align nucl_seq > """ > if prot_seq.id != nucl_seq.id: > logging.warning( > 'ID mismatch: %s != %s. Are the sequences in the same order?', > prot_seq.id, nucl_seq.id) > > # Ungap nucleotides > > codons = batch(str(nucl_seq.seq.ungap('-')), 3) > E AttributeError: 'Seq' object has no attribute 'ungap' > > seqmagick/subcommands/backtrans_align.py:105: AttributeError > ________ AlignmentMapperTestCase.test_map_alignment_insufficient_codons > ________ > > self = > <seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase > testMethod=test_map_alignment_insufficient_codons> > > def test_map_alignment_insufficient_codons(self): > nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF > SeqRecord(Seq('AAGGTC'), id='2')] # KV > prot = [SeqRecord(Seq('K-F'), id='1'), > SeqRecord(Seq('KVF'), id='2')] > > mapped = self.instance.map_all(prot, nucl) > > self.assertRaises(ValueError, list, mapped) > > seqmagick/test/test_subcommands_backtrans_align.py:68: > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > seqmagick/subcommands/backtrans_align.py:148: in map_all > yield self.map_alignment(p, n) > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > > def map_alignment(self, prot_seq, nucl_seq): > """ > Use aligned prot_seq to align nucl_seq > """ > if prot_seq.id != nucl_seq.id: > logging.warning( > 'ID mismatch: %s != %s. Are the sequences in the same order?', > prot_seq.id, nucl_seq.id) > > # Ungap nucleotides > > codons = batch(str(nucl_seq.seq.ungap('-')), 3) > E AttributeError: 'Seq' object has no attribute 'ungap' > > seqmagick/subcommands/backtrans_align.py:105: AttributeError > =========================== short test summary info > ============================ > FAILED > seqmagick/test/test_subcommands_backtrans_align.py::AlignmentMapperTestCase::test_map_alignment > FAILED > seqmagick/test/test_subcommands_backtrans_align.py::AlignmentMapperTestCase::test_map_alignment_excess_codons > FAILED > seqmagick/test/test_subcommands_backtrans_align.py::AlignmentMapperTestCase::test_map_alignment_insufficient_codons > =================== 3 failed, 144 passed, 7 skipped in 1.01s > =================== > E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; python3.12 -m pytest > I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; > python3.11 -m pytest > ============================= test session starts > ============================== > platform linux -- Python 3.11.8, pytest-8.0.2, pluggy-1.4.0 > rootdir: /<<PKGBUILDDIR>> > collected 154 items > > seqmagick/test/integration/test_convert.py .ss.............. [ > 11%] > seqmagick/test/integration/test_extract_ids.py ..ss.. [ > 14%] > seqmagick/test/integration/test_info.py ...s [ > 17%] > seqmagick/test/integration/test_mogrify.py .s. [ > 19%] > seqmagick/test/test_subcommands_backtrans_align.py ....FFF.. [ > 25%] > seqmagick/test/test_subcommands_common.py ..................s..... [ > 40%] > seqmagick/test/test_subcommands_convert.py ...... [ > 44%] > seqmagick/test/test_subcommands_quality_filter.py ...................... [ > 59%] > .... [ > 61%] > seqmagick/test/test_transform.py ....................................... [ > 87%] > .................... > [100%] > > =================================== FAILURES > =================================== > __________________ AlignmentMapperTestCase.test_map_alignment > __________________ > > self = > <seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase > testMethod=test_map_alignment> > > def test_map_alignment(self): > nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF > SeqRecord(Seq('AAGGTCTTC'), id='2'), # KVF > SeqRecord(Seq('GGGGTTTTT'), id='3')] # GVF > prot = [SeqRecord(Seq('-K-F'), id='1'), > SeqRecord(Seq('-KVF'), id='2'), > SeqRecord(Seq('G-VF'), id='3')] > > result = self.instance.map_all(prot, nucl) > > result = [(s.id, str(s.seq)) for s in result] > > seqmagick/test/test_subcommands_backtrans_align.py:56: > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > seqmagick/test/test_subcommands_backtrans_align.py:56: in <listcomp> > result = [(s.id, str(s.seq)) for s in result] > seqmagick/subcommands/backtrans_align.py:148: in map_all > yield self.map_alignment(p, n) > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > > self = <seqmagick.subcommands.backtrans_align.AlignmentMapper object at > 0x7fb5bd176090> > prot_seq = SeqRecord(seq=Seq('-K-F'), id='1', name='<unknown name>', > description='<unknown description>', dbxrefs=[]) > nucl_seq = SeqRecord(seq=Seq('AAGTTT'), id='1', name='<unknown name>', > description='<unknown description>', dbxrefs=[]) > > def map_alignment(self, prot_seq, nucl_seq): > """ > Use aligned prot_seq to align nucl_seq > """ > if prot_seq.id != nucl_seq.id: > logging.warning( > 'ID mismatch: %s != %s. Are the sequences in the same order?', > prot_seq.id, nucl_seq.id) > > # Ungap nucleotides > > codons = batch(str(nucl_seq.seq.ungap('-')), 3) > E AttributeError: 'Seq' object has no attribute 'ungap' > > seqmagick/subcommands/backtrans_align.py:105: AttributeError > ___________ AlignmentMapperTestCase.test_map_alignment_excess_codons > ___________ > > self = > <seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase > testMethod=test_map_alignment_excess_codons> > > def test_map_alignment_excess_codons(self): > nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF > SeqRecord(Seq('AAGGTCTTC'), id='2')] # KVF > prot = [SeqRecord(Seq('K-F'), id='1'), > SeqRecord(Seq('KV-'), id='2')] > mapped = self.instance.map_all(prot, nucl) > > self.assertRaises(ValueError, list, mapped) > > seqmagick/test/test_subcommands_backtrans_align.py:76: > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > seqmagick/subcommands/backtrans_align.py:148: in map_all > yield self.map_alignment(p, n) > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > > def map_alignment(self, prot_seq, nucl_seq): > """ > Use aligned prot_seq to align nucl_seq > """ > if prot_seq.id != nucl_seq.id: > logging.warning( > 'ID mismatch: %s != %s. Are the sequences in the same order?', > prot_seq.id, nucl_seq.id) > > # Ungap nucleotides > > codons = batch(str(nucl_seq.seq.ungap('-')), 3) > E AttributeError: 'Seq' object has no attribute 'ungap' > > seqmagick/subcommands/backtrans_align.py:105: AttributeError > ________ AlignmentMapperTestCase.test_map_alignment_insufficient_codons > ________ > > self = > <seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase > testMethod=test_map_alignment_insufficient_codons> > > def test_map_alignment_insufficient_codons(self): > nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF > SeqRecord(Seq('AAGGTC'), id='2')] # KV > prot = [SeqRecord(Seq('K-F'), id='1'), > SeqRecord(Seq('KVF'), id='2')] > > mapped = self.instance.map_all(prot, nucl) > > self.assertRaises(ValueError, list, mapped) > > seqmagick/test/test_subcommands_backtrans_align.py:68: > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > seqmagick/subcommands/backtrans_align.py:148: in map_all > yield self.map_alignment(p, n) > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > _ > > def map_alignment(self, prot_seq, nucl_seq): > """ > Use aligned prot_seq to align nucl_seq > """ > if prot_seq.id != nucl_seq.id: > logging.warning( > 'ID mismatch: %s != %s. Are the sequences in the same order?', > prot_seq.id, nucl_seq.id) > > # Ungap nucleotides > > codons = batch(str(nucl_seq.seq.ungap('-')), 3) > E AttributeError: 'Seq' object has no attribute 'ungap' > > seqmagick/subcommands/backtrans_align.py:105: AttributeError > =========================== short test summary info > ============================ > FAILED > seqmagick/test/test_subcommands_backtrans_align.py::AlignmentMapperTestCase::test_map_alignment > FAILED > seqmagick/test/test_subcommands_backtrans_align.py::AlignmentMapperTestCase::test_map_alignment_excess_codons > FAILED > seqmagick/test/test_subcommands_backtrans_align.py::AlignmentMapperTestCase::test_map_alignment_insufficient_codons > =================== 3 failed, 144 passed, 7 skipped in 0.84s > =================== > E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest > dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 > 3.11" returned exit code 13 The full build log is available from: http://qa-logs.debian.net/2024/03/13/seqmagick_0.8.6-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&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.
