[Debian-med-packaging] Bug#806675: hmmer: nhmmer fails with fatal exception on armhf

[Andreas Tille]

Hi Sean,

thanks for the fast clarification.  It would be great if you could keep
me informed in case you would enhance the number of architectures to
make sure we will follow this move.

Kind regards

      Andreas.

On Wed, Dec 02, 2015 at 01:21:25AM +0000, Eddy, Sean wrote:
> HMMER3 is currently only supported on Intel or PPC compatible platforms because it makes use of vector parallelization using SSE or Altivec/VMX. ARM and PPC64le platforms are currently not supported.
> 
> Sean
> 
> 
> > On Dec 1, 2015, at 9:22 PM, Andreas Tille <andreas at an3as.eu> wrote:
> > 
> > Hi Sean,
> > 
> > I'd like to forward this issue to you as the hmmer author.  Since in
> > Debian packages are usually build on several different architectures
> > sometimes hidden bugs are detected.  Since arm64 and ppc64el might
> > become relevant in bioinformatics in the not to distant future I'd
> > consider this issue important.
> > 
> > Any hint would be welcome.
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> > On Tue, Dec 01, 2015 at 09:10:30PM +0000, Edmund Grimley Evans wrote:
> >> A lot of the test failures seen in
> >> https://buildd.debian.org/status/fetch.php?pkg=hmmer&arch=arm64&ver=3.1b2-1&stamp=1436134634
> >> are not easily reproducible.
> >> 
> >> For example, when I tried
> >> 
> >>    cd testsuite/
> >>    touch tmp ; rm tmp* ; ./i9-optional-annotation.pl .. .. tmp
> >> 
> >> it gave "ok" most of the time, but every now and then it gave
> >> "FAIL: on line 0 target name, dtbl1".
> >> 
> >> One of the few easily reproducible failures I found on arm64 was this:
> >> 
> >>    touch tmp1 ; rm tmp1* ; ./i8-nonresidues.pl .. .. tmp1
> >> 
> >> I didn't see that test ever produce a different output from
> >> "FAIL: expected one line in domtbl; saw 2". The "nonresidues"
> >> test also failed on ppc64el. Perhaps you should look at that
> >> one first. Or perhaps you're more worried about the general
> >> non-determinism that affects many of the tests. The obvious question
> >> to ask is: does this non-determinism only exist in the test suite,
> >> or does it also exist in the packaged programs?
> >> 
> >> _______________________________________________
> >> Debian-med-packaging mailing list
> >> Debian-med-packaging at lists.alioth.debian.org
> >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> >> 
> > 
> > -- 
> > http://fam-tille.de
> 
> 

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