Ubuntu
freebayes package

FTBFS on s390x (testsuite failures)

Bug #2024021 reported by Sergio Durigan Junior
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
vcflib
New
Unknown
freebayes (Debian)
Fix Released
Unknown
freebayes (Ubuntu)
New
Undecided
Unassigned
libvcflib (Debian)
Fix Released
Unknown
libvcflib (Ubuntu)
New
Undecided
Unassigned
libwfa2 (Ubuntu)
New
Undecided
Unassigned

Bug Description

libvcflib is currently FTBFSing on s390x:

make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp obj-s390x-linux-gnu/CTestTestfile.cmake test/
ln -sf obj-s390x-linux-gnu/ build
cd test && ctest .
Test project /<<PKGBUILDDIR>>/test
    Start 1: realign
1/9 Test #1: realign ..........................***Failed 0.05 sec
    Start 2: pyvcflib
2/9 Test #2: pyvcflib ......................... Passed 0.05 sec
    Start 3: vcflib-api
3/9 Test #3: vcflib-api ....................... Passed 0.05 sec
    Start 4: vcf2tsv
4/9 Test #4: vcf2tsv .......................... Passed 0.08 sec
    Start 5: vcfallelicprimitives
5/9 Test #5: vcfallelicprimitives .............***Failed 0.53 sec
    Start 6: vcfwave
6/9 Test #6: vcfwave ..........................***Failed 0.47 sec
    Start 7: vcffilter
7/9 Test #7: vcffilter ........................ Passed 0.14 sec
    Start 8: vcfnulldotslashdot
8/9 Test #8: vcfnulldotslashdot ............... Passed 0.06 sec
    Start 9: doc/vcfintersect
9/9 Test #9: doc/vcfintersect ................. Passed 0.05 sec

67% tests passed, 3 tests failed out of 9

Total Test time (real) = 1.54 sec

The following tests FAILED:
   1 - realign (Failed)
   5 - vcfallelicprimitives (Failed)
   6 - vcfwave (Failed)
Errors while running CTest

https://launchpadlibrarian.net/672424300/buildlog_ubuntu-mantic-s390x.libvcflib_1.0.9+dfsg-1_BUILDING.txt.gz

Bug Watch Updater (bug-watch-updater)
Changed in vcflib:
status: Unknown → New
Revision history for this message
Vladimir Petko (vpa1977) wrote :
Download full text (4.4 KiB)

The realign test fail due to libwfa2 library issue

Running integration tests for libwfa2 via `./tests/wfa.utest.sh` produces the following results on amd64 platform:

-----------------------
> Comparing ./tests vs ./tests/wfa.utest.check
 [UTest::test.affine2p] OK
[UTest::test.affine] OK
[UTest::test.affine.p0] OK
[UTest::test.affine.p1] OK
[UTest::test.affine.p2] OK
[UTest::test.affine.p3] OK
[UTest::test.affine.p4] OK
[UTest::test.affine.p5] OK
[UTest::test.affine.wfapt0] OK
[UTest::test.affine.wfapt1] OK
[UTest::test.biwfa.affine2p] OK
[UTest::test.biwfa.affine] OK
[UTest::test.biwfa.affine.p0] OK
[UTest::test.biwfa.affine.p1] OK
[UTest::test.biwfa.affine.p2] OK
[UTest::test.biwfa.affine.p3] OK
[UTest::test.biwfa.affine.p4] OK
[UTest::test.biwfa.affine.p5] OK
[UTest::test.biwfa.affine.wfapt0] OK
[UTest::test.biwfa.affine.wfapt1] OK
[UTest::test.biwfa.edit] OK
[UTest::test.biwfa.indel] OK
[UTest::test.biwfa.score.affine2p] OK
[UTest::test.biwfa.score.affine] OK
[UTest::test.biwfa.score.affine.p0] OK
[UTest::test.biwfa.score.affine.p1] OK
[UTest::test.biwfa.score.affine.p2] OK
[UTest::test.biwfa.score.affine.p3] OK
[UTest::test.biwfa.score.affine.p4] OK
[UTest::test.biwfa.score.affine.p5] OK
[UTest::test.biwfa.score.affine.wfapt0] OK
[UTest::test.biwfa.score.affine.wfapt1] OK
[UTest::test.biwfa.score.edit] OK
[UTest::test.biwfa.score.indel] OK
[UTest::test.edit] OK
[UTest::test.indel] OK
[UTest::test.pb.affine2p] OK
[UTest::test.pb.affine] OK
[UTest::test.pb.affine.p0] OK
[UTest::test.pb.affine.p1] OK
[UTest::test.pb.affine.p2] OK
[UTest::test.pb.affine.p3] OK
[UTest::test.pb.affine.p4] OK
[UTest::test.pb.affine.p5] OK
[UTest::test.pb.affine.wfapt0] OK
[UTest::test.pb.affine.wfapt1] OK
[UTest::test.pb.edit] OK
[UTest::test.pb.indel] OK
[UTest::test.score.affine2p] OK
[UTest::test.score.affine] OK
[UTest::test.score.affine.p0] OK
[UTest::test.score.affine.p1] OK
[UTest::test.score.affine.p2] OK
[UTest::test.score.affine.p3] OK
[UTest::test.score.affine.p4] OK
[UTest::test.score.affine.p5] OK
[UTest::test.score.affine.wfapt0] OK
[UTest::test.score.affine.wfapt1] OK
[UTest::test.score.edit] OK
[UTest::test.score.indel] OK
+ grep 'Exit status:' ./tests/wfa.utest.log

------------------------------

S390x tests:
--------------------------------
> Comparing ./tests vs ./tests/wfa.utest.check
 [UTest::test.affine] Error
[UTest::test.affine.p0] Error
[UTest::test.affine.p1] Error
[UTest::test.affine.p2] Error
[UTest::test.affine.p3] Error
[UTest::test.affine.p4] Error
[UTest::test.affine.p5] Error
[UTest::test.affine.wfapt0] Error
[UTest::test.affine.wfapt1] Error
[UTest::test.affine2p] Error
[UTest::test.biwfa.affine] Error
[UTest::test.biwfa.affine.p0] Error
[UTest::test.biwfa.affine.p1] Error
[UTest::test.biwfa.affine.p2] Error
[UTest::test.biwfa.affine.p3] Error
[UTest::test.biwfa.affine.p4] Error
[UTest::test.biwfa.affine.p5] Error
[UTest::test.biwfa.affine.wfapt0] Error
[UTest::test.biwfa.affine.wfapt1] Error
[UTest::test.biwfa.affine2p] Error
[UTest::test.biwfa.edit] Error
[UTest::test.biwfa.indel] Error
[UTest::test.biwfa.score.affine] Error
[UTest::test.biwfa.score.affine.p0] Error
...

Read more...

Revision history for this message
Vladimir Petko (vpa1977) wrote :

Raise issue upstream:
https://github.com/smarco/WFA2-lib/issues/79

Revision history for this message
Graham Inggs (ginggs) wrote :

f.y.i. libvcflib s390x binaries were removed from Debian testing on 2023-03-24, along with 32-bit architectures.

Revision history for this message
Vladimir Petko (vpa1977) wrote :

Retested https://github.com/smarco/WFA2-lib/issues/79 - there are some test failures.

Bug Watch Updater (bug-watch-updater)
Changed in freebayes (Debian):
status: Unknown → Fix Released
Bug Watch Updater (bug-watch-updater)
Changed in libvcflib (Debian):
status: Unknown → Fix Released
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