[Debian-med-packaging] Bug#549427: [Samtools-devel] Samtools error on SPARC 32 bit processors.

[Heng Li]

Samtools uses unaligned memory, which does not do much harm on x86 and
x86_64 architectures, but will probably cause problems on others such as
sparc. I need to fix this issue.

Heng

On Sun, Oct 04, 2009 at 08:20:51PM +0900, Charles Plessy wrote:
> Dear SAMtools developers,
> 
> The C version of SAMtools is redistributed by the Debian project for multiple
> hadrware architectures. I included simple tests in the build process, where the
> non-interactive commands from examples/00README.txt are executed. This
> uncovered a ???Bus error??? error on the Sparc architecture:
> 
> > /usr/bin/make  -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS=""  -C examples all
> > make[1]: Entering directory `/build/buildd-samtools_0.1.6~dfsg-1-sparc-aGfAkY/samtools-0.1.6~dfsg/examples'
> > ../samtools faidx ex1.fa
> > ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
> > [sam_header_read2] 2 sequences loaded.
> > make[1]: *** [ex1.bam] Bus error
> > make[1]: *** Deleting file `ex1.bam'
> > make[1]: Leaving directory `/build/buildd-samtools_0.1.6~dfsg-1-sparc-aGfAkY/samtools-0.1.6~dfsg/examples'
> > make: *** [debian/stamp-makefile-check] Error 2
> > dpkg-buildpackage: error: debian/rules build gave error exit status 2
> > 
> > Please see
> > https://buildd.debian.org/fetch.cgi?&pkg=samtools&ver=0.1.6%7Edfsg-1&arch=sparc&stamp=1254564365&file=log
> > for the ful build log.
> 
> If you are interested in working out this problem, we can run further tests.
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> 
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