[Bioperl-l] Problem compiling Bio::DB::Sam

[Miquel Ràmia]

Hi all,

I get this message when compiling Bio::DB::Sam:

Building Bio-SamTools

gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o -L/var/lib/gbrowse2/databases/samtools/samtools-0.1.19 -lbam -lm -lz

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':

/var/lib/gbrowse2/databases/samtools/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'

collect2: ld returned 1 exit status

make: *** [bam2bedgraph] Error 1


Is this error related to the module or some dependencies? or maybe a
problem with my system?

Any help appreciated, thanks!


--
Miquel Ràmia Jesús
PhD. candidate (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)

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[Fields, Christopher J]

It may be due to the new samtools release (v 0.1.19). I know Heng Li has been working on the code over the last year for threading support (notice the undefined functions). Have you tried v 0.1.18?

chris

[Fields, Christopher J]

For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).

chris

[Miquel Ràmia]

On 17/05/13 06:16, Fields, Christopher J wrote:
> For the record, this is now fixed in the latest Bio::Samtools (via Lincoln).
>
> chris
>
>

Compiled correctly!

thank you