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

[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

On May 16, 2013, at 5:42 AM, Miquel Ràmia <miquel.ramia at uab.cat> wrote:

> 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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