[Debian-med-packaging] Bug#1041451: gmap: FTBFS on all !amd64 archs

[Andreas Tille]

Control: tags -1 upstream
Control: forwarded -1 Thomas Wu <twu at gene.com>, Colin K. Watanabe <ckw at gene.com>


Hi Thomas and Colin,

the Debian packaged gmap fails to build since version 2023-06-01 for all
release architectures besides amd64.  You can read about this bug on our
bug tracker[1].  I think the analysis from Étienne below is a sensible
explanation for the issue.

It would be really helpful if you could clarify why you disabled SIMD?
Does this mean you suggest we should provide gmap for amd64 only?

Kind regards
    Andreas.


[1] https://bugs.debian.org/1041451

Am Tue, Aug 15, 2023 at 12:42:09PM +0200 schrieb Étienne Mollier:
> Hi,
> 
> The relevant part of the error message shows that the generic
> fully scalar gmap.nosimd executable is never built for any cpu
> architecture:
> 
> 	Note: /<<PKGBUILDDIR>>/build/src/gmap.avx2 does not exist.  For faster speed, may want to compile package on an AVX2 machine
> 	Note: /<<PKGBUILDDIR>>/build/src/gmap.sse42 does not exist.  For faster speed, may want to compile package on an SSE4.2 machine
> 	Note: /<<PKGBUILDDIR>>/build/src/gmap.sse41 does not exist.  For faster speed, may want to compile package on an SSE4.1 machine
> 	Note: /<<PKGBUILDDIR>>/build/src/gmap.ssse3 does not exist.  For faster speed, may want to compile package on an SSSE3 machine
> 	Note: /<<PKGBUILDDIR>>/build/src/gmap.sse2 does not exist.  For faster speed, may want to compile package on an SSE2 machine
> 	Note: /<<PKGBUILDDIR>>/build/src/gmap.nosimd does not exist.  For faster speed, may want to compile package on an non-SIMD machine
> 	Error: appropriate GMAP version not found
> 
> Looking into src/Makefile.am, indeed they seem disabled upstream
> for the current gmap versions:
> 
> 	# intersect-uint2.c requires SIMD
> 	#bin_PROGRAMS += gmap.nosimd
> 	#bin_PROGRAMS += gmapl.nosimd
> 	#bin_PROGRAMS += gsnap.nosimd
> 	#bin_PROGRAMS += gsnapl.nosimd
> 
> My quick attempts to bring the necessary support in the
> aforementioned intersect-uint2.c file were not very fruitful so
> far.  Something in there looks to prevent use of simde.
> 
> Anyways, in hope this helps further investigations,
> -- 
>   .''`.  Étienne Mollier <emollier at debian.org>
>  : :' :  gpg: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
>  `. `'   sent from /dev/pts/4, please excuse my verbosity
>    `-



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