Fwd: Problem compiling Bio::DB::Sam

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Fwd: Problem compiling Bio::DB::Sam

Fields, Christopher J
Not sure if anyone else has run into this yet.  I haven't confirmed it, but I wouldn't be surprised if the new samtools threading support is the problem (see 'undefined reference' errors below).  May just require an additional library requirement.

chris

Begin forwarded message:

> From: "Fields, Christopher J" <[hidden email]>
> Subject: Re: [Bioperl-l] Problem compiling Bio::DB::Sam
> Date: May 16, 2013 8:12:40 AM CDT
> To: Miquel Ràmia <[hidden email]>
> Cc: "<[hidden email]>" <[hidden email]>
>
> 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 <[hidden email]> 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)
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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Re: Problem compiling Bio::DB::Sam

Timothy Parnell
Curious,

I can compile Bio::DB::SamTools 1.37 (latest from CPAN) just fine with samtools-0.1.19 on Mac OS X 10.7.5 and 10.8.3.

But it will not compile on a  RedHat Linux system, same errors as below.

Unfortunately, I do not know enough to tell you why the GCC in Xcode can compile it ok, but on Linux it cannot.

Tim


On May 16, 2013, at 7:44 AM, "Fields, Christopher J" <[hidden email]> wrote:

> Not sure if anyone else has run into this yet.  I haven't confirmed it, but I wouldn't be surprised if the new samtools threading support is the problem (see 'undefined reference' errors below).  May just require an additional library requirement.
>
> chris
>
> Begin forwarded message:
>
>> From: "Fields, Christopher J" <[hidden email]>
>> Subject: Re: [Bioperl-l] Problem compiling Bio::DB::Sam
>> Date: May 16, 2013 8:12:40 AM CDT
>> To: Miquel Ràmia <[hidden email]>
>> Cc: "<[hidden email]>" <[hidden email]>
>>
>> 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 <[hidden email]> 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)
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> ------------------------------------------------------------------------------
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
> http://p.sf.net/sfu/alienvault_d2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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from a single console and one unified framework. Download a free trial.
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Re: Problem compiling Bio::DB::Sam

Lincoln Stein
Hi All,

I added the -lpthreads linker flag to Build.PL and the module now compiles and runs without the symbol definition errors. I've uploaded the fixed version to CPAN as Bio::DB::Sam version 1.38.

Lincoln


On Thu, May 16, 2013 at 10:27 AM, Timothy Parnell <[hidden email]> wrote:
Curious,

I can compile Bio::DB::SamTools 1.37 (latest from CPAN) just fine with samtools-0.1.19 on Mac OS X 10.7.5 and 10.8.3.

But it will not compile on a  RedHat Linux system, same errors as below.

Unfortunately, I do not know enough to tell you why the GCC in Xcode can compile it ok, but on Linux it cannot.

Tim


On May 16, 2013, at 7:44 AM, "Fields, Christopher J" <[hidden email]> wrote:

> Not sure if anyone else has run into this yet.  I haven't confirmed it, but I wouldn't be surprised if the new samtools threading support is the problem (see 'undefined reference' errors below).  May just require an additional library requirement.
>
> chris
>
> Begin forwarded message:
>
>> From: "Fields, Christopher J" <[hidden email]>
>> Subject: Re: [Bioperl-l] Problem compiling Bio::DB::Sam
>> Date: May 16, 2013 8:12:40 AM CDT
>> To: Miquel Ràmia <[hidden email]>
>> Cc: "<[hidden email]>" <[hidden email]>
>>
>> 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 <[hidden email]> 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)
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> ------------------------------------------------------------------------------
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
> http://p.sf.net/sfu/alienvault_d2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
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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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security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
http://p.sf.net/sfu/alienvault_d2d
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Re: Problem compiling Bio::DB::Sam

Fields, Christopher J
That fixed it on my Ubuntu server.  I can check it on RedHat as well.  Thanks Lincoln!  

chris

On May 16, 2013, at 2:30 PM, Lincoln Stein <[hidden email]>
 wrote:

> Hi All,
>
> I added the -lpthreads linker flag to Build.PL and the module now compiles and runs without the symbol definition errors. I've uploaded the fixed version to CPAN as Bio::DB::Sam version 1.38.
>
> Lincoln
>
>
> On Thu, May 16, 2013 at 10:27 AM, Timothy Parnell <[hidden email]> wrote:
> Curious,
>
> I can compile Bio::DB::SamTools 1.37 (latest from CPAN) just fine with samtools-0.1.19 on Mac OS X 10.7.5 and 10.8.3.
>
> But it will not compile on a  RedHat Linux system, same errors as below.
>
> Unfortunately, I do not know enough to tell you why the GCC in Xcode can compile it ok, but on Linux it cannot.
>
> Tim
>
>
> On May 16, 2013, at 7:44 AM, "Fields, Christopher J" <[hidden email]> wrote:
>
> > Not sure if anyone else has run into this yet.  I haven't confirmed it, but I wouldn't be surprised if the new samtools threading support is the problem (see 'undefined reference' errors below).  May just require an additional library requirement.
> >
> > chris
> >
> > Begin forwarded message:
> >
> >> From: "Fields, Christopher J" <[hidden email]>
> >> Subject: Re: [Bioperl-l] Problem compiling Bio::DB::Sam
> >> Date: May 16, 2013 8:12:40 AM CDT
> >> To: Miquel Ràmia <[hidden email]>
> >> Cc: "<[hidden email]>" <[hidden email]>
> >>
> >> 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 <[hidden email]> 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)
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> [hidden email]
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> [hidden email]
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > ------------------------------------------------------------------------------
> > AlienVault Unified Security Management (USM) platform delivers complete
> > security visibility with the essential security capabilities. Easily and
> > efficiently configure, manage, and operate all of your security controls
> > from a single console and one unified framework. Download a free trial.
> > http://p.sf.net/sfu/alienvault_d2d
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> ------------------------------------------------------------------------------
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
> http://p.sf.net/sfu/alienvault_d2d
> _______________________________________________
> 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]>
> ------------------------------------------------------------------------------
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
> http://p.sf.net/sfu/alienvault_d2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
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Re: Problem compiling Bio::DB::Sam

Charles Plessy
In reply to this post by Lincoln Stein
Le Thu, May 16, 2013 at 02:30:54PM -0500, Lincoln Stein a écrit :
> Hi All,
>
> I added the -lpthreads linker flag to Build.PL and the module now compiles
> and runs without the symbol definition errors. I've uploaded the fixed
> version to CPAN as Bio::DB::Sam version 1.38.

Dear all,

the update is "en route" to Debian and Ubuntu as well.

By the way, you may be interested (or not) to see logs of our experimental
builds with clang.

    http://buildd-clang.debian.net/fetch.php?pkg=libbio-samtools-perl&arch=amd64&ver=1.37-1&stamp=1366341542

Have a nice day,

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

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