Bug#1067759: marked as done (python-dnaio ftbfs on s390x)

[Debian Bug Tracking System]

Your message dated Wed, 27 Mar 2024 09:07:15 +0000
with message-id <e1rppfb-005gbw...@fasolo.debian.org>
and subject line Bug#1067759: fixed in python-dnaio 1.2.0-2
has caused the Debian Bug report #1067759,
regarding python-dnaio ftbfs on s390x
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.)


-- 
1067759: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067759
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Package: src:python-dnaio
Version: 1.2.0-1
Severity: serious
Tags: sid trixie ftbfs

https://buildd.debian.org/status/fetch.php?pkg=python-dnaio&arch=s390x&ver=1.2.0-1&stamp=1711181830&raw=0

[...]

platform linux -- Python 3.12.2, pytest-8.1.1, pluggy-1.4.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
configfile: pyproject.toml
collected 640 items





self = <test_internal.TestBamReader object at 0x3ffb80b6ae0>

    def test_parse_bam(self):
        with dnaio.open(self.bam_file) as reader:
>           records = list(reader)

tests/test_internal.py:725:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


self = <test_internal.TestBamReader object at 0x3ffb7c60470>, buffersize = 4

    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


self = <test_internal.TestBamReader object at 0x3ffb7c60710>, buffersize = 8

    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError




    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError




    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError




    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


self = <test_internal.TestBamReader object at 0x3ffb7c60aa0>

    def test_error_on_mapped_bam(self):
        bam = TEST_DATA / (
            "project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878"
            ".bwa.markDuplicates.bam"
        )
        reader = BamReader(str(bam))
        it = iter(reader)
        with pytest.raises(NotImplementedError) as error:
>           next(it)

tests/test_internal.py:804:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


    def test_detect_bam_from_content() -> None:
        with dnaio.open("tests/data/simplebamnoextension") as f:
>           record = next(iter(f))

tests/test_open.py:187:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


    def test_detect_bam_from_filename() -> None:
        with dnaio.open("tests/data/simple.unaligned.bam") as f:
>           record = next(iter(f))

tests/test_open.py:193:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError

platform linux -- Python 3.11.8, pytest-8.1.1, pluggy-1.4.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build
configfile: pyproject.toml
collected 640 items





self = <test_internal.TestBamReader object at 0x3ff8f703090>

    def test_parse_bam(self):
        with dnaio.open(self.bam_file) as reader:
>           records = list(reader)

tests/test_internal.py:725:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


self = <test_internal.TestBamReader object at 0x3ff8f9f51d0>, buffersize = 4

    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


self = <test_internal.TestBamReader object at 0x3ff8f9f50d0>, buffersize = 8

    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError




    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError




    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError




    @pytest.mark.parametrize("buffersize", [4, 8, 10, 20, 40])
    def test_small_buffersize(self, buffersize):
        reader = BamReader(str(self.bam_file), buffer_size=buffersize)
>       assert len(list(reader)) == 3

tests/test_internal.py:794:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


self = <test_internal.TestBamReader object at 0x3ff8f990410>

    def test_error_on_mapped_bam(self):
        bam = TEST_DATA / (
            "project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878"
            ".bwa.markDuplicates.bam"
        )
        reader = BamReader(str(bam))
        it = iter(reader)
        with pytest.raises(NotImplementedError) as error:
>           next(it)

tests/test_internal.py:804:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


    def test_detect_bam_from_content() -> None:
        with dnaio.open("tests/data/simplebamnoextension") as f:
>           record = next(iter(f))

tests/test_open.py:187:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError


    def test_detect_bam_from_filename() -> None:
        with dnaio.open("tests/data/simple.unaligned.bam") as f:
>           record = next(iter(f))

tests/test_open.py:193:

src/dnaio/_core.pyx:807: in dnaio._core.BamIter.__next__
    ???


>   ???
E   EOFError: Incomplete record at the end of file

src/dnaio/_core.pyx:771: EOFError

make: *** [debian/rules:11: binary-arch] Error 25

I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; python3.12 -m pytest tests ============================= test session starts ============================== tests/test_chunks.py ........... [ 1%] tests/test_internal.py ................................................. [ 9%] ....................................................F................... [ 20%] ........................................................................ [ 31%] ........................................................................ [ 43%] ........................................................................ [ 54%] ........................................................................ [ 65%] FFFFFF [ 66%] tests/test_multiple.py ................................................. [ 74%] . [ 74%] tests/test_open.py ....................................................F [ 82%] F....................................................................... [ 93%] ..... [ 94%] tests/test_records.py ................................. [ 99%] tests/test_util.py . [100%] =================================== FAILURES =================================== _________________________ TestBamReader.test_parse_bam _________________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ____________________ TestBamReader.test_small_buffersize[4] ____________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ____________________ TestBamReader.test_small_buffersize[8] ____________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___________________ TestBamReader.test_small_buffersize[10] ____________________ self = <test_internal.TestBamReader object at 0x3ffb7c607d0>, buffersize = 10 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___________________ TestBamReader.test_small_buffersize[20] ____________________ self = <test_internal.TestBamReader object at 0x3ffb7c60890>, buffersize = 20 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___________________ TestBamReader.test_small_buffersize[40] ____________________ self = <test_internal.TestBamReader object at 0x3ffb7c60950>, buffersize = 40 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ____________________ TestBamReader.test_error_on_mapped_bam ____________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _________________________ test_detect_bam_from_content _________________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ________________________ test_detect_bam_from_filename _________________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ =========================== short test summary info ============================ FAILED tests/test_internal.py::TestBamReader::test_parse_bam - EOFError: Inco... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[4] - EOFE... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[8] - EOFE... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[10] - EOF... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[20] - EOF... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[40] - EOF... FAILED tests/test_internal.py::TestBamReader::test_error_on_mapped_bam - EOFE... FAILED tests/test_open.py::test_detect_bam_from_content - EOFError: Incomplet... FAILED tests/test_open.py::test_detect_bam_from_filename - EOFError: Incomple... ======================== 9 failed, 631 passed in 1.31s ========================= E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; python3.12 -m pytest tests I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests ============================= test session starts ============================== tests/test_chunks.py ........... [ 1%] tests/test_internal.py ................................................. [ 9%] ....................................................F................... [ 20%] ........................................................................ [ 31%] ........................................................................ [ 43%] ........................................................................ [ 54%] ........................................................................ [ 65%] FFFFFF [ 66%] tests/test_multiple.py ................................................. [ 74%] . [ 74%] tests/test_open.py ....................................................F [ 82%] F....................................................................... [ 93%] ..... [ 94%] tests/test_records.py ................................. [ 99%] tests/test_util.py . [100%] =================================== FAILURES =================================== _________________________ TestBamReader.test_parse_bam _________________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ____________________ TestBamReader.test_small_buffersize[4] ____________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ____________________ TestBamReader.test_small_buffersize[8] ____________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___________________ TestBamReader.test_small_buffersize[10] ____________________ self = <test_internal.TestBamReader object at 0x3ff8f9f4a90>, buffersize = 10 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___________________ TestBamReader.test_small_buffersize[20] ____________________ self = <test_internal.TestBamReader object at 0x3ff8f9f5450>, buffersize = 20 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___________________ TestBamReader.test_small_buffersize[40] ____________________ self = <test_internal.TestBamReader object at 0x3ff8f992350>, buffersize = 40 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ____________________ TestBamReader.test_error_on_mapped_bam ____________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _________________________ test_detect_bam_from_content _________________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ________________________ test_detect_bam_from_filename _________________________ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ =========================== short test summary info ============================ FAILED tests/test_internal.py::TestBamReader::test_parse_bam - EOFError: Inco... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[4] - EOFE... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[8] - EOFE... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[10] - EOF... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[20] - EOF... FAILED tests/test_internal.py::TestBamReader::test_small_buffersize[40] - EOF... FAILED tests/test_internal.py::TestBamReader::test_error_on_mapped_bam - EOFE... FAILED tests/test_open.py::test_detect_bam_from_content - EOFError: Incomplet... FAILED tests/test_open.py::test_detect_bam_from_filename - EOFError: Incomple... ======================== 9 failed, 631 passed in 1.17s ========================= E: pybuild pybuild:389: test: plugin pyproject 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 "3.12 3.11" returned exit code 13
--- End Message ---

--- Begin Message ---

Source: python-dnaio
Source-Version: 1.2.0-2
Done: Michael R. Crusoe <cru...@debian.org>

We believe that the bug you reported is fixed in the latest version of
python-dnaio, 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 1067...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe <cru...@debian.org> (supplier of updated python-dnaio 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: Wed, 27 Mar 2024 09:52:45 +0100
Source: python-dnaio
Architecture: source
Version: 1.2.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <cru...@debian.org>
Closes: 1067759
Changes:
 python-dnaio (1.2.0-2) unstable; urgency=medium
 .
   * Team upload.
   * d/control: stop building on big-endian architectures. Closes: #1067759
     All downstream packages are either architecture-independent or already
     aren't built on s390x, except for python3-cutadapt
   * d/tests/control: skip architectures that are not installable, see
     above.
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