Bug#1066772: marked as done (seqmagick: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

Debian Bug Tracking System Sun, 17 Mar 2024 11:18:24 -0700

Your message dated Sun, 17 Mar 2024 18:16:02 +0000
with message-id <e1rlv3c-00aqtn...@fasolo.debian.org>
and subject line Bug#1066772: fixed in seqmagick 0.8.6-2
has caused the Debian Bug report #1066772,
regarding seqmagick: FTBFS: dh_auto_test: error: pybuild --test --test-pytest 
-i python{version} -p "3.12 3.11" returned exit code 13
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1066772: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066772
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

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.

--- End Message ---

--- Begin Message ---

Source: seqmagick
Source-Version: 0.8.6-2
Done: Étienne Mollier <emoll...@debian.org>

We believe that the bug you reported is fixed in the latest version of
seqmagick, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1066...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated seqmagick package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sun, 17 Mar 2024 18:11:48 +0100
Source: seqmagick
Architecture: source
Version: 0.8.6-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1066772
Changes:
 seqmagick (0.8.6-2) unstable; urgency=medium
 .
   * replace-ungap.patch: new: fix test failure. (Closes: #1066772)
   * d/{rules,control}: activate autodep8-pybuild.
     This change increases autopkgtest coverage by running upstream test
     suite in such context.
Checksums-Sha1:
 9e94c4a1cab3ee534c049fe02d94f2e899f41900 2262 seqmagick_0.8.6-2.dsc
 bd083a3329df9905afc5a3b59920857829b0291e 5684 seqmagick_0.8.6-2.debian.tar.xz
Checksums-Sha256:
 a7f3133e280f7b47270e45ec1f66472c8bf6847b5badbc1104b6e021fb69f220 2262 
seqmagick_0.8.6-2.dsc
 0928428c9540ec6c3326c27ced9509c09db45438a03951e5e79d3e6dfa69b15b 5684 
seqmagick_0.8.6-2.debian.tar.xz
Files:
 cde92bf8d6db0df22e3cc20aabfb1bf2 2262 science optional seqmagick_0.8.6-2.dsc
 2ba652f926db9a5c5c74751225f574f8 5684 science optional 
seqmagick_0.8.6-2.debian.tar.xz

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--- End Message ---

Bug#1066772: marked as done (seqmagick: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

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