[Debian-med-packaging] Bug#756780: [Help] Need help for architecture specific code (Was: Bug#756780: bowtie: FTBFS almost everywhere)

[Andreas Tille]

Hi Ben,

I recently updated the bowtie package in Debian to version 1.0.1.
Unfortunately this package failed to build on most of the architectures
in Debian.  When discussion this issue I've got the following response
which I would like to bring to your attention hereby.

On Mon, Aug 04, 2014 at 04:34:17PM +0800, Paul Wise wrote:
> On Mon, Aug 4, 2014 at 3:48 PM, Andreas Tille wrote:
> 
> > third_party/cpuid.h
> 
> No idea about this problem but here is what I could figure out based
> on the filename and the errors, using packages.d.o, codesearch.d.n and
> a quick look at wikipedia.
> 
> third_party/cpuid.h looks like an outdated copy of the cpuid.h header
> from gcc, please ask upstream to remove it and just use the normal
> one.

Do you have any specific reason to use this outdated copy of cpuid.h?
 
> The cpuid.h header seems to be only/mainly on x86 based platforms:
> 
> https://packages.debian.org/search?arch=any&searchon=contents&keywords=cpuid.h
> 
> If upstream was using autotools, they could detect if the header is
> present and only then enable the cpuid stuff.

It might make sense to use autotools to create the makefile and by doing
so simplify porting to different architectures.  Do you intend to do
something like this or would you appreciate help / patches to migrate
to autotools?
 
> The bowtie2 package appears to only be available on *-amd64 (same
> issue I guess, some code seems similar):
> 
> https://buildd.debian.org/status/package.php?p=bowtie2&suite=unstable
> 
> Looking at some valgrind code (thanks to codesearch) it seems you have
> to use popcntq on amd64 and popcnt on non-amd64 platforms.
> 
> http://sources.debian.net/src/valgrind/latest/none/tests/amd64/sse4-64.c#L2039

This remark boils down to the question whether it might be possible to
support bowtie2 also on other architectures.
 
> BTW, what is the difference between bowtie and bowtie2? Do we need
> both in the archive?

This question was asked by a non-biologist and I personally do also not
have any background in biology.  I guess that bowtie2 is not fully
replacing bowtie version 1 but it might be good to know your long term
plans for both versions.

Kind regards and thanks for providing bowtie as free software

       Andreas. 

-- 
http://fam-tille.de