Your message dated Sat, 14 Jan 2023 19:19:41 +0000
with message-id <e1pgm45-005vzr...@fasolo.debian.org>
and subject line Bug#1028856: fixed in paleomix 1.3.7-3
has caused the Debian Bug report #1028856,
regarding paleomix: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i
python{version} -p 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.
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--
1028856: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028856
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: paleomix
Source-Version: 1.3.7-3
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
paleomix, 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 1028...@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 paleomix 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: Sat, 14 Jan 2023 19:29:03 +0100
Source: paleomix
Architecture: source
Version: 1.3.7-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1028856
Changes:
paleomix (1.3.7-3) unstable; urgency=medium
.
* d/salsa-ci.yml: disable i386 and reprotest; they always failed.
* python3.11.patch: add; fix test failure with python3.11. (Closes: #1028856)
* d/copyright: bump copyright year.
* Standards-Version: 4.6.2 (routine-update)
Checksums-Sha1:
09349853e05acc3fee197c3f1e69e0d806bdc680 2466 paleomix_1.3.7-3.dsc
8047d477cc6e851ab02d60459de1463939302f32 10940 paleomix_1.3.7-3.debian.tar.xz
Checksums-Sha256:
435e99760521e50cc8deb7f538b4a9fb285b8d9b5319ea86bb89d71ad73227d7 2466
paleomix_1.3.7-3.dsc
c0c37149ff9c29ec9e8fc49039a859eac0538a58ed1f03cb64586b1db53aaf9f 10940
paleomix_1.3.7-3.debian.tar.xz
Files:
e157fe82098e65783cbc67dc0b6fdd9d 2466 science optional paleomix_1.3.7-3.dsc
e8a35d561a8d97e38da9b80e8c813729 10940 science optional
paleomix_1.3.7-3.debian.tar.xz
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--- End Message ---
