[Debian-med-packaging] Bug#749367: htslib: Is a solution available?

[Andreas Tille]

Hi Afif,

On Wed, Sep 23, 2015 at 11:17:38PM -0700, Afif Elghraoui wrote:
> Hi,
> Has anyone tested the patch that was applied upstream [1] regarding this
> issue? I'm asking because the corresponding upstream ticket is still
> open and the commit message on the patch describes it as a "partial fix".
> 
> I am not particularly interested in mips/mipsel, but this build failure
> is preventing testing migration (and therefore backporting) of samtools
> and several other dependencies because they are BD-uninstallable for
> these architectures.

[Slight warning:  This is the advise of an *experimental* phyiscist.]
Why not simply *trying* by uploading whether mips machines are able to
cope with this patch?  IMHO nobody will really use the package on mips
(yet - things might probably change in future) so I do not see any
danger that a user will be harmed by runtime problems (even so this user
should report the problem).

If your "experiment" fails excluding mips from builds (and asking
ftpmaster to remove the mips architecture) could be the next step to
deal with this blocker.

> If someone can confirm that the patch I referenced works, I am willing
> to backport it to the current htslib package to unblock the testing
> migrations.

The alternative would be that somebody logs in to one of the mips porter
machines[2] and try to build manually.  I did this procedure recently
for libfreecontact-perl which had simply timeout problems since the mips
autobuilders are really slow and were not able to finalise the test
suite.  In the end this procedure has stolen me some time and the outcome
was to remove the package for the mips architecture.
 
> If this is still a problem, the patch tag here should be removed and I
> will try to negotiate with the stable-backports team to allow rebuilding
> these packages (htslib, samtools, python-pysam, ...) on jessie despite
> their not having entered testing.

I think this negotiation is also more time consuming than the suggested
"experiment".

Kind regards

      Andreas.
 
> 1.
> https://github.com/samtools/htslib/commit/e8806c71f3408d2cbff8caa8df17eef848d33a02

[2] https://wiki.debian.org/MIPSPort 

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