[Bioperl-l] Trouble installing BIo:DB:SAM tools

[Lincoln Stein]

>From the Bio::DB::SAM README:

TROUBLESHOOTING:
>
>
>> If you encounter problems during compiling, you may need to edit
>
> Build.PL so that extra_compiler_flags matches the CFLAGS and DFLAGS
>
> settings in the Samtools Makefile.  Here are some common problems:
>
>
>> 1. When building this module, you get an error like the following:
>
> relocation R_X86_64_32 against `a local symbol' can not be used when
>
> making a shared object; recompile with -fPIC
>
>
>> To fix this, edit the Makefile in the Samtools distribution by adding
>
> "-fPIC" to the CFLAGS line. It should look like this:
>
>
>>   CFLAGS=       -g -Wall -O2 -fPIC #-m64 #-arch ppc
>
>
>> Then do "make clean; make" in the Samtools directory to recompile the
>
> library. After this you should be able to build this module without
>
> errors.
>
>
>>
>>

On Tue, Apr 16, 2013 at 11:10 AM, Lalitha Viswanathan <
lalitha.viswanathan79 at gmail.com> wrote:

> Hi
> I am trying to install Bio::DB::SAM tools version 1.37 on ubuntu 12,10
> I have BioPerl 1.6 installed and working fine
> I installed samtools-0.1.19  as below
> a) make
>
> b) Then ran perl Build.PL in Bio::DB::SAM tools version 1.37
> c)  ./Build install throws below error
> /usr/bin/ld: /home/lalitha/Documents/samtools-0.1.19/libbam.a(bgzf.o):
> relocation R_X86_64_32S against `.rodata.str1.1' can not be used when
> making a shared object; recompile with -fPIC
> /home/lalitha/Documents/samtools-0.1.19/libbam.a: could not read symbols:
> Bad value
> collect2: error: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o
> c_bin/bam2bedgraph.o at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line
> 312.
>
> d) Same error is encountered when building through cpan
>
> Any help will be appreciated
>
> Thanks
> Lalitha
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-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>