Source: paleomix
Version: 1.3.7-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20230113 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> PATH=/<<PKGBUILDDIR>>/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
> dh_auto_test
> I: pybuild pybuild:307: cp -a README.rst
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build;
> I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build;
> python3.11 -m pytest tests
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.1, pytest-7.2.0, pluggy-1.0.0+repack
> rootdir: /<<PKGBUILDDIR>>, configfile: setup.cfg
> collected 1494 items
>
> tests/node_test.py ..................................................... [
> 3%]
> ......................................... [
> 6%]
> tests/nodegraph_test.py ......... [
> 6%]
> tests/atomiccmd_test/builder_test.py ................................... [
> 9%]
> ...................................................... [
> 12%]
> tests/atomiccmd_test/command_test.py ................................... [
> 15%]
> ............................................F........................... [
> 20%]
> ...........FF... [
> 21%]
> tests/atomiccmd_test/pprint_test.py .................................... [
> 23%]
> .. [
> 23%]
> tests/atomiccmd_test/sets_test.py ...................................... [
> 26%]
> ............ [
> 26%]
> tests/common_tests/bedtools_test.py ............................... [
> 29%]
> tests/common_tests/fileutils_test.py ................................... [
> 31%]
> ...................................................................... [
> 36%]
> tests/common_tests/makefile_test.py .................................... [
> 38%]
> ........................................................................ [
> 43%]
> ........................................................................ [
> 48%]
> ........................................................................ [
> 52%]
> ........................................................................ [
> 57%]
> ............................... [
> 59%]
> tests/common_tests/sampling_test.py ........................ [
> 61%]
> tests/common_tests/sequences_test.py ................................... [
> 63%]
> ............... [
> 64%]
> tests/common_tests/text_test.py ....................................... [
> 67%]
> tests/common_tests/utilities_test.py ................................... [
> 69%]
> ........................................................................ [
> 74%]
> .. [
> 74%]
> tests/common_tests/versions_test.py .................................... [
> 77%]
> ............................................................ [
> 81%]
> tests/common_tests/formats_tests/fasta_test.py ......................... [
> 82%]
> ............. [
> 83%]
> tests/common_tests/formats_tests/fastq_test.py ......................... [
> 85%]
> ........... [
> 86%]
> tests/common_tests/formats_tests/msa_test.py ........................... [
> 87%]
> ................... [
> 89%]
> tests/common_tests/formats_tests/newick_test.py ........................ [
> 90%]
> ........................................................................ [
> 95%]
> ...... [
> 95%]
> tests/common_tests/formats_tests/phylip_test.py ........ [
> 96%]
> tests/tools_test/factory_test.py xXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [
> 99%]
> XXXXXXXXXXXXX
> [100%]
>
> =================================== FAILURES
> ===================================
> __________________________ test_atomiccmd__paths__key
> __________________________
>
> self = PosixPath('/tmp/pytest-of-user42/pytest-8/test_atomiccmd__paths__key0')
> other_path = b'/tmp/pytest-of-user42/pytest-8/test_atomiccmd__paths__key0'
>
> def samefile(self, other_path):
> """Return whether other_path is the same or not as this file
> (as returned by os.path.samefile()).
> """
> st = self.stat()
> try:
> > other_st = other_path.stat()
> E AttributeError: 'bytes' object has no attribute 'stat'
>
> /usr/lib/python3.11/pathlib.py:923: AttributeError
>
> During handling of the above exception, another exception occurred:
>
> tmp_path =
> PosixPath('/tmp/pytest-of-user42/pytest-8/test_atomiccmd__paths__key0')
>
> def test_atomiccmd__paths__key(tmp_path):
> cmd = AtomicCmd(("echo", "-n", "%(TEMP_DIR)s"),
> OUT_STDOUT=AtomicCmd.PIPE)
> cmd.run(tmp_path)
> path = cmd._proc.stdout.read()
> > assert tmp_path.samefile(path), (tmp_path, path)
>
> tests/atomiccmd_test/command_test.py:374:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> _
> /usr/lib/python3.11/pathlib.py:925: in samefile
> other_st = self.__class__(other_path).stat()
> /usr/lib/python3.11/pathlib.py:872: in __new__
> self = cls._from_parts(args)
> /usr/lib/python3.11/pathlib.py:510: in _from_parts
> drv, root, parts = self._parse_args(args)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> _
>
> cls = <class 'pathlib.PosixPath'>
> args = (b'/tmp/pytest-of-user42/pytest-8/test_atomiccmd__paths__key0',)
>
> @classmethod
> def _parse_args(cls, args):
> # This is useful when you don't want to create an instance, just
> # canonicalize some constructor arguments.
> parts = []
> for a in args:
> if isinstance(a, PurePath):
> parts += a._parts
> else:
> a = os.fspath(a)
> if isinstance(a, str):
> # Force-cast str subclasses to str (issue #21127)
> parts.append(str(a))
> else:
> > raise TypeError(
> "argument should be a str object or an os.PathLike "
> "object returning str, not %r"
> % type(a))
> E TypeError: argument should be a str object or an
> os.PathLike object returning str, not <class 'bytes'>
>
> /usr/lib/python3.11/pathlib.py:499: TypeError
> _____________________ test_atomiccmd__cleanup_proc__commit
> _____________________
>
> tmp_path =
> PosixPath('/tmp/pytest-of-user42/pytest-8/test_atomiccmd__cleanup_proc__0')
>
> def test_atomiccmd__cleanup_proc__commit(tmp_path):
> > assert paleomix.atomiccmd.command._PROCS == set()
> E AssertionError: assert {<weakref at ...7f0441949d50>} == set()
> E Extra items in the left set:
> E <weakref at 0x7f04416dd670; to 'Popen' at 0x7f0441949d50>
> E Use -v to get more diff
>
> tests/atomiccmd_test/command_test.py:757: AssertionError
> _______________________ test_atomiccmd__cleanup_proc__gc
> _______________________
>
> tmp_path =
> PosixPath('/tmp/pytest-of-user42/pytest-8/test_atomiccmd__cleanup_proc__1')
>
> def test_atomiccmd__cleanup_proc__gc(tmp_path):
> > assert paleomix.atomiccmd.command._PROCS == set()
> E AssertionError: assert {<weakref at ...7f0441949d50>} == set()
> E Extra items in the left set:
> E <weakref at 0x7f04416dd670; to 'Popen' at 0x7f0441949d50>
> E Use -v to get more diff
>
> tests/atomiccmd_test/command_test.py:773: AssertionError
> =============================== warnings summary
> ===============================
> paleomix/atomiccmd/pprint.py:24
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py:24:
> DeprecationWarning: 'pipes' is deprecated and slated for removal in Python
> 3.13
> import pipes
>
> .pybuild/cpython3_3.11/build/tests/node_test.py::test_dir
> /usr/lib/python3/dist-packages/_pytest/python.py:199:
> PytestReturnNotNoneWarning: Expected None, but
> .pybuild/cpython3_3.11/build/tests/node_test.py::test_dir returned
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/tests', which will be an error
> in a future version of pytest. Did you mean to use `assert` instead of
> `return`?
> warnings.warn(
>
> .pybuild/cpython3_3.11/build/tests/node_test.py::test_file
> /usr/lib/python3/dist-packages/_pytest/python.py:199:
> PytestReturnNotNoneWarning: Expected None, but
> .pybuild/cpython3_3.11/build/tests/node_test.py::test_file returned
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/tests/data', which will be an
> error in a future version of pytest. Did you mean to use `assert` instead of
> `return`?
> warnings.warn(
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info
> ============================
> FAILED tests/atomiccmd_test/command_test.py::test_atomiccmd__paths__key -
> Typ...
> FAILED
> tests/atomiccmd_test/command_test.py::test_atomiccmd__cleanup_proc__commit
> FAILED tests/atomiccmd_test/command_test.py::test_atomiccmd__cleanup_proc__gc
> ====== 3 failed, 1439 passed, 1 xfailed, 51 xpassed, 3 warnings in 12.47s
> ======
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11
> returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/01/13/paleomix_1.3.7-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230113;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230113&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.
