[help] Test of samtools breaks build on armel and sparc

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[help] Test of samtools breaks build on armel and sparc

Andreas Tille-5
Hi,

I realised that the samtools package is not build for armel and sparc[1]
in both cases since a test running at build time failed:

armel:

make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
Line 2, sequence length 35 vs 8960 from CIGAR
Parse error at line 2: CIGAR and sequence length are inconsistent


sparc:

make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/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


Any hint how to fix this would be welcome.

Kind regards

         Andreas.

[1] https://buildd.debian.org/status/package.php?p=samtools

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Re: [help] Test of samtools breaks build on armel and sparc

Patrick Baggett
Looks like SPARC is having a bus error, which almost always means unaligned data is being accessed. Running this test with gdb attached will break on the line where there is a problem and should give enough information to the original developer to resolve it.

Andreas -- can you send me (off-list) steps to reproduce this on my sparc/sid system?


On Mon, Aug 4, 2014 at 10:30 AM, Andreas Tille <[hidden email]> wrote:
Hi,

I realised that the samtools package is not build for armel and sparc[1]
in both cases since a test running at build time failed:

armel:

make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
Line 2, sequence length 35 vs 8960 from CIGAR
Parse error at line 2: CIGAR and sequence length are inconsistent


sparc:

make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/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


Any hint how to fix this would be welcome.

Kind regards

         Andreas.

[1] https://buildd.debian.org/status/package.php?p=samtools

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http://fam-tille.de


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