Bio::DB::Sam installation problem

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Bio::DB::Sam installation problem

Rob Syme
On Ubuntu: 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC
2011 x86_64 x86_64 x86_64 GNU/Linux
During attempts at installation via both CPAN and manual, I get the
following error during compiltion:
$ ./Build
Building Bio-SamTools
cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o
blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o
-L/home/rob/src/samtools/current -lbam -lz
/usr/bin/ld: /home/rob/src/samtools/current/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/rob/src/samtools/current/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o
at /usr/local/share/perl/5.10.1/ExtUtils/CBuilder/Base.pm line 310.
I'm not sure why compilation is failing. Does anyone here have ideas
as to how I might compile Bio::DB::Sam?
-r
Rob Syme
PhD Student
Curtin University, Western Australia

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Re: Bio::DB::Sam installation problem

Fields, Christopher J
The hint is in this line:

"can not be used when making a shared object; recompile with -fPIC"

You need to compile Bio::DB::Sam with the -fPIC CFLAG.  See the README, under 'Troubleshooting':

http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.28/README

chris

On May 15, 2011, at 2:41 AM, Rob Syme wrote:

> On Ubuntu: 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC
> 2011 x86_64 x86_64 x86_64 GNU/Linux
> During attempts at installation via both CPAN and manual, I get the
> following error during compiltion:
> $ ./Build
> Building Bio-SamTools
> cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o
> blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o
> -L/home/rob/src/samtools/current -lbam -lz
> /usr/bin/ld: /home/rob/src/samtools/current/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/rob/src/samtools/current/libbam.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o
> at /usr/local/share/perl/5.10.1/ExtUtils/CBuilder/Base.pm line 310.
> I'm not sure why compilation is failing. Does anyone here have ideas
> as to how I might compile Bio::DB::Sam?
> -r
> Rob Syme
> PhD Student
> Curtin University, Western Australia
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: Bio::DB::Sam installation problem

Charles Plessy
Le Sun, May 15, 2011 at 06:45:34AM -0500, Chris Fields a écrit :
>
> You need to compile Bio::DB::Sam with the -fPIC CFLAG.  See the README, under 'Troubleshooting':

Dear Rob,

Alternatively, if the versions are suitable for you, you can install directly
from Ubuntu :

http://packages.ubuntu.com/libbam-dev (compiled with -fPIC).
http://packages.ubuntu.com/libbio-samtools-perl

The Debian Med project recently activated a personal package archive (PPA)
for Ubuntu, so please do not hesitate to tell us if some bacports would
be helpful there.

https://launchpad.net/~debian-med/+archive/ppa

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

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Re: Bio::DB::Sam installation problem

Rob Syme

Excellent. Thanks Chris, thanks Charles.
-r

On 15 May 2011 20:01, "Charles Plessy" <[hidden email]> wrote:
> Le Sun, May 15, 2011 at 06:45:34AM -0500, Chris Fields a écrit :
>>
>> You need to compile Bio::DB::Sam with the -fPIC CFLAG. See the README, under 'Troubleshooting':
>
> Dear Rob,
>
> Alternatively, if the versions are suitable for you, you can install directly
> from Ubuntu :
>
> http://packages.ubuntu.com/libbam-dev (compiled with -fPIC).
> http://packages.ubuntu.com/libbio-samtools-perl
>
> The Debian Med project recently activated a personal package archive (PPA)
> for Ubuntu, so please do not hesitate to tell us if some bacports would
> be helpful there.
>
> https://launchpad.net/~debian-med/+archive/ppa
>
> Have a nice day,
>
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan


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Re: Bio::DB::Sam installation problem

Lincoln Stein
In reply to this post by Fields, Christopher J
Actually, you need to recompile libbam.a (from the samtools distribution) with -fPIC. More instructions are in the README.

Lincoln

On Sun, May 15, 2011 at 7:45 AM, Chris Fields <[hidden email]> wrote:
The hint is in this line:

"can not be used when making a shared object; recompile with -fPIC"

You need to compile Bio::DB::Sam with the -fPIC CFLAG.  See the README, under 'Troubleshooting':

http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.28/README

chris

On May 15, 2011, at 2:41 AM, Rob Syme wrote:

> On Ubuntu: 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC
> 2011 x86_64 x86_64 x86_64 GNU/Linux
> During attempts at installation via both CPAN and manual, I get the
> following error during compiltion:
> $ ./Build
> Building Bio-SamTools
> cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o
> blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o
> -L/home/rob/src/samtools/current -lbam -lz
> /usr/bin/ld: /home/rob/src/samtools/current/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/rob/src/samtools/current/libbam.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o
> at /usr/local/share/perl/5.10.1/ExtUtils/CBuilder/Base.pm line 310.
> I'm not sure why compilation is failing. Does anyone here have ideas
> as to how I might compile Bio::DB::Sam?
> -r
> Rob Syme
> PhD Student
> Curtin University, Western Australia
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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Learn how Intel has extended the reach of its next-generation tools
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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 <[hidden email]>

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Learn how Intel has extended the reach of its next-generation tools
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http://p.sf.net/sfu/intel-dev2devmay
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Re: Bio::DB::Sam installation problem

Fields, Christopher J
Ah yes.  My mistake :)

chris

On May 16, 2011, at 11:13 AM, Lincoln Stein wrote:

> Actually, you need to recompile libbam.a (from the samtools distribution) with -fPIC. More instructions are in the README.
>
> Lincoln
>
> On Sun, May 15, 2011 at 7:45 AM, Chris Fields <[hidden email]> wrote:
> The hint is in this line:
>
> "can not be used when making a shared object; recompile with -fPIC"
>
> You need to compile Bio::DB::Sam with the -fPIC CFLAG.  See the README, under 'Troubleshooting':
>
> http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.28/README
>
> chris
>
> On May 15, 2011, at 2:41 AM, Rob Syme wrote:
>
> > On Ubuntu: 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC
> > 2011 x86_64 x86_64 x86_64 GNU/Linux
> > During attempts at installation via both CPAN and manual, I get the
> > following error during compiltion:
> > $ ./Build
> > Building Bio-SamTools
> > cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o
> > blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o
> > -L/home/rob/src/samtools/current -lbam -lz
> > /usr/bin/ld: /home/rob/src/samtools/current/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/rob/src/samtools/current/libbam.a: could not read symbols: Bad value
> > collect2: ld returned 1 exit status
> > error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o
> > at /usr/local/share/perl/5.10.1/ExtUtils/CBuilder/Base.pm line 310.
> > I'm not sure why compilation is failing. Does anyone here have ideas
> > as to how I might compile Bio::DB::Sam?
> > -r
> > Rob Syme
> > PhD Student
> > Curtin University, Western Australia
> >
> > ------------------------------------------------------------------------------
> > Achieve unprecedented app performance and reliability
> > What every C/C++ and Fortran developer should know.
> > Learn how Intel has extended the reach of its next-generation tools
> > to help boost performance applications - inlcuding clusters.
> > http://p.sf.net/sfu/intel-dev2devmay
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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 <[hidden email]>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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