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

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Hi Pierre,

I'm afraid I never managed to wrap my head around the SPAdes
version bump to 4.0.0 in the past year, and it seems it is going
to interfere with the availability of several tools in trixie if
the situation keeps going.

Adrian Bunk suggested, on 2025-04-10:

I wonder whether spades 4.0.0+really3.15.5 might be the correct solution
for ariba/shovill/unicycler in trixie.

Would that work for you to rollback to 3.15.5 for trixie, and
pursuing the upgrade effort in experimental in the meantime?

In hope this helps,
--
.''`. Étienne Mollier <emollier@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/1, please excuse my verbosity
`- on air: Ivory Tower - Blinded

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Hi Pierre,

Pierre Gruet, on 2025-04-12:

Le 10/04/2025 à 22:36, Étienne Mollier a écrit :

Adrian Bunk suggested, on 2025-04-10:

I wonder whether spades 4.0.0+really3.15.5 might be the correct solution for ariba/shovill/unicycler in trixie.

Would that work for you to rollback to 3.15.5 for trixie, and
pursuing the upgrade effort in experimental in the meantime?

I have just done so! The rdeps were tested locally with ratt, I will monitor the autopkgtests and close #1098530 if everything works as expected.

Great! Thank you for your work on this! :)

Have a nice day, :)
--
.''`. Étienne Mollier <emollier@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/1, please excuse my verbosity
`- on air: Fluctus Quadratum - Laplacian

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