[Debian-med-packaging] Bug#749367: htslib FTBFS on testing for mips/mipsel

[Aleksandar Zlicic]

Package: htslib
Version: 0.2.0~rc3-1
Tags: sid patch
Severity: important
Justification: FTBFS
User: debian-mips-dev-discuss at lists.alioth.debian.org
Usertags: mips-patch


While trying to build htslib on mips/mipsel, build fails on testing.

On mips, package fails with the following error:

>  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.cram.sam_
>  ./test_view -t xx.fa -C xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
>  ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
>  ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
>  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
>
>Successes 235
>
>Failures  5
>make[2]: *** [test] Error 1
>make[2]: Leaving directory `/«PKGBUILDDIR»'
>dh_auto_test: make -j1 test returned exit code 2
>make[1]: *** [override_dh_auto_test] Error 2
>make[1]: Leaving directory `/«PKGBUILDDIR»'
>make: *** [build-arch] Error 2


The reason for that are endianness related issues:
 - system endianness is not detected properly
 - function which converts multibyte data from big endian byte to little
endian byte order (and vice versa) has errors (this was partially fixed
in latest upstream release).

This is fixed in '01-fix-endianness.patch'.
After applying it, build fails with error:

>  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.cram.sam_
>  ./test_view -t xx.fa -C xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
>  ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
>  ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
>  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
>make[2]: *** [test] Error 1
>
>Successes 234
>
>Failures  6
>make[2]: Leaving directory `/«PKGBUILDDIR»'
>dh_auto_test: make -j1 test returned exit code 2
>make[1]: *** [override_dh_auto_test] Error 2
>make[1]: Leaving directory `/«PKGBUILDDIR»'
>make: *** [build-arch] Error 2

The same error appears on mipsel.

Reason for this is that unaligned memory access is not handled well
for achitectures that don't allow unaligned access, which causes bus errors
on both mips and mipsel.
This is fixed in '02-fix-alignment.patch'.


With these patches applied I have successfully built htslib on mips/mipsel.

Could you please consider including this patch?

Best regards,
Aleksandar Zlicic
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