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
[...]
I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build;
python3.12 -m pytest tests
============================= test session starts
==============================
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
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
_________________________
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
____________________ TestBamReader.test_small_buffersize[4]
____________________
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
____________________ TestBamReader.test_small_buffersize[8]
____________________
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
___________________ TestBamReader.test_small_buffersize[10]
____________________
self = <test_internal.TestBamReader object at 0x3ffb7c607d0>, buffersize
= 10
@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
___________________ TestBamReader.test_small_buffersize[20]
____________________
self = <test_internal.TestBamReader object at 0x3ffb7c60890>, buffersize
= 20
@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
___________________ TestBamReader.test_small_buffersize[40]
____________________
self = <test_internal.TestBamReader object at 0x3ffb7c60950>, buffersize
= 40
@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
____________________ TestBamReader.test_error_on_mapped_bam
____________________
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
_________________________ test_detect_bam_from_content
_________________________
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
________________________ test_detect_bam_from_filename
_________________________
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
=========================== 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
==============================
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
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
_________________________
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
____________________ TestBamReader.test_small_buffersize[4]
____________________
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
____________________ TestBamReader.test_small_buffersize[8]
____________________
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
___________________ TestBamReader.test_small_buffersize[10]
____________________
self = <test_internal.TestBamReader object at 0x3ff8f9f4a90>, buffersize
= 10
@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
___________________ TestBamReader.test_small_buffersize[20]
____________________
self = <test_internal.TestBamReader object at 0x3ff8f9f5450>, buffersize
= 20
@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
___________________ TestBamReader.test_small_buffersize[40]
____________________
self = <test_internal.TestBamReader object at 0x3ff8f992350>, buffersize
= 40
@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
____________________ TestBamReader.test_error_on_mapped_bam
____________________
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
_________________________ test_detect_bam_from_content
_________________________
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
________________________ test_detect_bam_from_filename
_________________________
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
=========================== 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
make: *** [debian/rules:11: binary-arch] Error 25
