Source: cyvcf2 Version: 0.30.22-1 Severity: important Tags: ftbfs upstream With the introduction of htslib 1.19 in experimental, cyvcf2 is experiencing test failures at package build time and autopkgtest time. The relevant part of the error looks like:
cyvcf2/tests/test_reader.py .....................Fatal Python error:
Aborted
Current thread 0x00007fa7874de040 (most recent call first):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cyvcf2/build/cyvcf2/tests/test_reader.py",
line 285 in test_writer_from_string
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 194 in
pytest_pyfunc_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in
_multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in
_hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in
__call__
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1792 in
runtest
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 169 in
pytest_runtest_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in
_multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in
_hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in
__call__
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 262 in
<lambda>
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341 in
from_call
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 261 in
call_runtest_hook
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 222 in
call_and_report
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 133 in
runtestprotocol
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 114 in
pytest_runtest_protocol
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in
_multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in
_hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in
__call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 350 in
pytest_runtestloop
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in
_multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in
_hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in
__call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 325 in
_main
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 271 in
wrap_session
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 318 in
pytest_cmdline_main
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 77 in
_multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 115 in
_hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 493 in
__call__
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 169 in main
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 192 in console_main
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 in
<module>
File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>
The affected test item looks like:
273 def test_writer_from_string():
274
275 header = """##fileformat=VCFv4.1
276 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
277 ##contig=<ID=chr2,length=249250621,assembly=hg19>
278 #CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT samplea
279 """
280
281 w = Writer.from_string("out.vcf", header)
282 w.write_header()
283 v =
w.variant_from_string("chr1\t234\t.\tA\tC\t40\tPASS\t.\tGT\t0/0")
284 w.write_record(v)
>285 w.close()
The test engine bails out after that, so this may not be the
single occurrence of the issue in the test suite.
From tests done locally, this does not look caused by the
disappearance of an internal htslib symbol that leaked to the
libhts3 package symbols table from version 1.16 to 1.18. That
could be a bug in cyvcf2, or one introduced in htslib 1.19, in
which case the bug may have to be reassigned accordingly. This
issue will become "serious" after htslib 1.19 is migrated to
unstable.
For information,
--
.''`. Étienne Mollier <emoll...@debian.org>
: :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/2, please excuse my verbosity
`- on air: Conception - In Your Multitude
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