On Fri, Feb 21, 2025 at 11:26:11PM +0000, Santiago Vila wrote:
> Package: src:ariba
> Version: 2.14.7+ds-7
> Severity: serious
> Tags: ftbfs trixie sid
>...
> =================================== FAILURES
> ===================================
> ____________________ TestAssembly.test_assemble_with_spades
> ____________________
>
> self = <ariba.tests.assembly_test.TestAssembly
> testMethod=test_assemble_with_spades>
>
> @unittest.skipUnless(extern_progs.exe('spades'), "Spades assembler is
> optional and is not configured")
> def test_assemble_with_spades(self):
> '''test _assemble_with_spades'''
> reads1 = os.path.join(data_dir,
> 'assembly_test_assemble_with_spades_reads_1.fq')
> reads2 = os.path.join(data_dir,
> 'assembly_test_assemble_with_spades_reads_2.fq')
> tmp_dir = 'tmp.test_assemble_with_spades'
> tmp_log = 'tmp.test_assemble_with_spades.log'
> with open(tmp_log, 'w') as tmp_log_fh:
> print('First line', file=tmp_log_fh)
> common.rmtree(tmp_dir)
> #using spades_options=" --only-assembler" because error
> correction cannot determine quality offset on this
> #artificial dataset
> a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed',
> tmp_dir, 'not_needed_for_this_test.fa',
> 'not_needed_for_this_test.bam', tmp_log_fh,
> 'not needed',
> assembler="spades", spades_options="
> --only-assembler")
> a._assemble_with_spades()
> > self.assertTrue(a.assembled_ok)
> E AssertionError: False is not true
>
> ariba/tests/assembly_test.py:128: AssertionError
> ----------------------------- Captured stderr call
> -----------------------------
>...
Looking also at
https://tracker.debian.org/pkg/spades
Marked for autoremoval on 02 May: #1100877
Migration status for spades (3.15.5+dfsg-8 to 4.0.0+dfsg1-2): BLOCKED:
Rejected/violates migration policy/introduces a regression
Issues preventing migration:
∙ ∙ autopkgtest for shovill/1.1.0-9: amd64: Regression or new test ♻ (reference
♻)
∙ ∙ autopkgtest for unicycler/0.5.1+dfsg-3: amd64: Regression or new test ♻
(reference ♻)
I wonder whether spades 4.0.0+really3.15.5 might be the correct solution
for ariba/shovill/unicycler in trixie.
cu
Adrian
