htslib: FTBFS on i386: 2 tests fail

[Michael Crusoe]

Andreas Tille, et al. I propose that we drop *-i386 for htslib, as it is
blocking a lot of packages.

Source: htslib
Version: 1.9-1
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the

past)

Hi,

https://buildd.debian.org/status/fetch.php?pkg=htslib&arch=i386&ver=1.9-1&stamp=1532825380&raw=0
CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 >
range.tmp

./compare_sam.pl range.tmp range.out

CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 >
range.tmp

./compare_sam.pl range.tmp range.out
/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/JMIB5wVvT_/test-vcf-api.bcf
bcf_get_format_float didn't produce the expected output.
.. failed ...
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/JMIB5wVvT_/test-vcf-api.bcf
/<<PKGBUILDDIR>>/test/test-vcf-sweep.out
/<<PKGBUILDDIR>>/test/test-vcf-sweep.out.new
.. failed ...
Andreas

[Andreas Tille]

Post by Michael Crusoe
Andreas Tille, et al. I propose that we drop *-i386 for htslib, as it is
blocking a lot of packages.

Fine for me - feel free to go for it, Andreas.

[Michael Crusoe]

I uploaded htslib 1.9-3 but now the "missing builds" are blocking its
migration. Can someone remind me how to fix the situation when
architectures are removed from a package?

Thanks,

Post by Andreas Tille

Post by Michael Crusoe
Andreas Tille, et al. I propose that we drop *-i386 for htslib, as it is
blocking a lot of packages.

Fine for me - feel free to go for it, Andreas.
--
http://fam-tille.de

[Andreas Tille]

Post by Michael Crusoe
I uploaded htslib 1.9-3 but now the "missing builds" are blocking its
migration. Can someone remind me how to fix the situation when
architectures are removed from a package?

File a bug report against ftpmaster (reportbug other - I think its item 10)

Hope this helps

Andreas.

[Sascha Steinbiss]

Hi all,

/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/JMIB5wVvT_/test-vcf-api.bcf
bcf_get_format_float didn't produce the expected output.
.. failed ...
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/JMIB5wVvT_/test-vcf-api.bcf
/<<PKGBUILDDIR>>/test/test-vcf-sweep.out
/<<PKGBUILDDIR>>/test/test-vcf-sweep.out.new
.. failed ...

I wonder if this is still https://github.com/samtools/htslib/issues/565
-- in this GitHub ticket Graham Inggs mentioned there was some kind of
workaround for it? Maybe it is enough to adjust this if it's just a
newer gcc version breaking the workarounds?

Cheers
Sascha

[Michael Crusoe]

Post by Sascha Steinbiss
Hi all,

/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/JMIB5wVvT_/test-vcf-api.bcf
bcf_get_format_float didn't produce the expected output.
.. failed ...
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/JMIB5wVvT_/test-vcf-api.bcf
/<<PKGBUILDDIR>>/test/test-vcf-sweep.out
/<<PKGBUILDDIR>>/test/test-vcf-sweep.out.new
.. failed ...

I wonder if this is still https://github.com/samtools/htslib/issues/565
-- in this GitHub ticket Graham Inggs mentioned there was some kind of
workaround for it? Maybe it is enough to adjust this if it's just a
newer gcc version breaking the workarounds?

https://github.com/samtools/htslib/issues/565#issuecomment-345821661

The suggested workaround was implemented last year, but the problem
remains:
https://salsa.debian.org/med-team/htslib/commit/020aa907e709125f31734c70687ba70c8cb3e98a

Post by Sascha Steinbiss
Cheers
Sascha