Bug 873025 – sci-biology/augustus-3.4.0-r2 fails tests (MUSL)

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Agostino Sarubbo 2022-09-26 09:21:45 UTC]

https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/augustus-3.4.0-r2 fails tests (MUSL).
Discovered on: amd64 (internal ref: tinderbox_musl)

NOTE:
This machine uses MUSL libc

[Comment 1 Agostino Sarubbo 2022-09-26 09:21:49 UTC]

Created attachment 814237 [details]
build.log

build log and emerge --info

[Comment 2 Agostino Sarubbo 2022-09-26 09:21:50 UTC]

Error(s) that match a know pattern:


' != ''
' != '' : *** expected_results/test_ab_initio_prediction/augustus.gff
' != '' : *** expected_results/test_format_and_error_out/augustus.gff3
' != '' : *** expected_results/test_training_new_species/test.out
AssertionError: '*** ../../tests/examples/expected_results[4451 chars]";
AssertionError: '*** ../../tests/examples/expected_results[5307 chars]";
AssertionError: '*** ../../tests/examples/expected_results[5421 chars]";
AssertionError: '*** expected_results/test_ab_initio_predi[405399 chars]";
AssertionError: '*** expected_results/test_format_and_erro[264026 chars]t1
AssertionError: '*** expected_results/test_training_new_sp[136692 chars]";
FAIL: test_ab_initio_prediction (__main__.TestAugustus)
FAIL: test_cgp (__main__.TestAugustus)
FAIL: test_cgp_sqlite (__main__.TestAugustus)
FAIL: test_cgp_sqlite_hints (__main__.TestAugustus)
FAIL: test_format_and_error_out (__main__.TestAugustus)
FAIL: test_training_new_species (__main__.TestAugustus)
FAILED (failures=6)

[Comment 3 Larry the Git Cow 2025-02-11 01:38:01 UTC]

The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7fdfd97f34314b9fb85bcbadb46efc07b94b67aa

commit 7fdfd97f34314b9fb85bcbadb46efc07b94b67aa
Author:     Alfred Wingate <[e-mail]>
AuthorDate: 2025-02-10 19:14:46 +0000
Commit:     Sam James <[e-mail]>
CommitDate: 2025-02-11 01:36:17 +0000

    sci-biology/augustus: add 3.5.0
    
    * Add missing dependency on python with tests.
    * Wire up unittests.
    * Disable test comparing on musl. This follows upstream with non-amd64 and
      non-linux environments.
    
    Bug: https://bugs.gentoo.org/868363
    Bug: https://bugs.gentoo.org/873025
    Signed-off-by: Alfred Wingate <[e-mail]>
    Closes: https://github.com/gentoo/gentoo/pull/40521
    Signed-off-by: Sam James <[e-mail]>

 sci-biology/augustus/Manifest              |  1 +
 sci-biology/augustus/augustus-3.5.0.ebuild | 93 ++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+)