vcflib
vcflib copied to clipboard
Test failures on s390x prevent build from completing on Debian/Ubuntu
Hi,
libvcflib currently fails to build from source on s390x on Debian/Ubuntu because of testsuite failures:
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
I understand that having access to a s390x machine is not always feasible, so I can try to provide more details if needed.
Thanks.
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 [UTest::test.biwfa.score.affine.p1] Error [UTest::test.biwfa.score.affine.p2] Error [UTest::test.biwfa.score.affine.p3] Error [UTest::test.biwfa.score.affine.p4] Error [UTest::test.biwfa.score.affine.p5] Error [UTest::test.biwfa.score.affine.wfapt0] Error [UTest::test.biwfa.score.affine.wfapt1] Error [UTest::test.biwfa.score.affine2p] Error [UTest::test.biwfa.score.edit] Error [UTest::test.biwfa.score.indel] Error [UTest::test.edit] Error [UTest::test.indel] Error [UTest::test.pb.affine] Error [UTest::test.pb.affine.p0] Error [UTest::test.pb.affine.p1] Error [UTest::test.pb.affine.p2] Error [UTest::test.pb.affine.p3] Error [UTest::test.pb.affine.p4] Error [UTest::test.pb.affine.p5] Error [UTest::test.pb.affine.wfapt0] Error [UTest::test.pb.affine.wfapt1] Error [UTest::test.pb.affine2p] Error [UTest::test.pb.edit] Error [UTest::test.pb.indel] Error [UTest::test.score.affine] Error [UTest::test.score.affine.p0] Error [UTest::test.score.affine.p1] Error [UTest::test.score.affine.p2] Error [UTest::test.score.affine.p3] Error [UTest::test.score.affine.p4] Error [UTest::test.score.affine.p5] Error [UTest::test.score.affine.wfapt0] Error [UTest::test.score.affine.wfapt1] Error [UTest::test.score.affine2p] Error [UTest::test.score.edit] Error [UTest::test.score.indel] Error
Yes, you should take it up with the wfa2lib authors.
I remember this bug (https://github.com/smarco/WFA2-lib/issues/79). May it be a code regression. I double-checked, and the code for big-endian architectures is there. @vpa1977 Can you try running the latest release on WFA2lib (let us open a ticket at WFA2 repo if it doesn't work standalone). Thks
Yes, thank you!!! This update resolves the issue. The bug was raised against 2.3.3 release of WFA2 I believe.