[Debian-med-packaging] Bug#1058768: cyvcf2: ftbfs and autopkgtest regression with htslib 1.19

[Étienne Mollier]

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 <emollier at 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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