[Debian-med-packaging] Bug#799698: Bug#799698: samtools: Unknown command "faidx" on (kfreebsd-)i386

[Vincent Danjean]

severity #799698 important
thanks

Le 21/09/2015 17:58, Aaron M. Ucko a écrit :
> Package: samtools
> Version: 1.2-2
> Severity: serious
> Justification: fails to build from source

If I understand correctly for bug report, samtools correctly builds
from source, but python-pysam fails.
  So, I'm downgrading the severity for the samtools package.
  A bug should probably be opened on python-pysam (with the whole
failed build log), severity serious as this package cannot be
build in Debian anymore.

  One someone will have to check if the bug is in samtool or if the
new samtools did not work with the old python-pysam.
  In the later case, this bug will be fixed by just adding a
Breaks: python-pysam (<< version-that-fixe-pysam-with-new-samtools)
in the samtools package. But, python-pysam will then need to be
fixed/updated in order to work with the new samtools.

> Builds of python-pysam for i386 and kfreebsd-i386 failed:
> 
>    samtools faidx ex1.fa
>    Unknown command "faidx".
> 
> This error appears to indicate a deficiency in samtools; could you
> please take a look?

deficiency or removal/change of a old tool ? I did not checked into
samtools changelog yet.

  Regards,
    Vincent

> Thanks!
> 
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