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

[Fields, Christopher J]

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

chris

On May 16, 2013, at 8:12 AM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> 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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> 
> 
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