[Bioperl-l] Bioperl-ext (staden::read) install issues

[Jason Stajich]

On Nov 6, 2005, at 1:43 PM, Bob Freeman wrote:

> Jason,
>
> I remember reading a past posting about the possibility of  
> commenting out the EVAL statement in Bio::SeqIO.pm (lines 315-317):
>
> sub BEGIN {
> #    eval { require Bio::SeqIO::staden::read; };
> }
>
> It certainly does eliminate the runtime error thrown by Perl about  
> Bio::SeqIO::staden::read not being installed correctly. Any  
> comments on whether or not this should be done?
>

I don't really have any knowledgeable comments about it --  disabling  
the eval hasn't been necessary for me with or without staden::read  
installed.  Someone who has been bitten by this will have to chime in.

> Bob
>
> At 1:07 PM -0500 11/6/05, Jason Stajich wrote:
>> In os.h did you change
>> #include <config.h>
>>
>> to
>> #include "config.h"
>>
>> This made a difference for me.
>> Make sure the the compile commands are actually point to the right  
>> include path.
>> i.e. make sure this is correct: -IPATH/TO/IOLIB/INCLUDE/io_lib in  
>> the gcc stmt below (for your system)
>>
>> gcc -c  -I/home/jes12/src/bioperl/bioperl-ext-1.5.1/Bio/SeqIO/ 
>> staden -IPATH/TO/IOLIB/INCLUDE/io_lib -D_REENTRANT -D_GNU_SOURCE - 
>> DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include - 
>> D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 - 
>> g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 - 
>> mtune=pentium4 -fasynchronous-unwind-tables   -DVERSION=\"1.51\" - 
>> DXS_VERSION=\"1.51\" -fPIC "-I/usr/lib/perl5/5.8.6/i386-linux- 
>> thread-multi/CORE"   read.c
>>
>>
>> There appears to be some complaints from Inline::C about version  
>> numbers not matching and not being parseable.  I just changed  
>> things to "1.50" instead of "1.5.1" and made sure that in read.pm
>> the code looks like this:
>>        use Inline (C => 'DATA',
>>                     VERSION => '1.51',
>>                     NAME => 'Bio::SeqIO::staden::read',
>>
>> instead of this:
>>        use Inline (C => 'DATA',
>>                     VERSION => '0.1',
>>                     NAME => 'Bio::SeqIO::staden::read',
>>
>> And further down I made this change
>> $VERSION = 1.51;
>>
>> instead of
>> $VERSION = 1.5;
>>
>>
>> All this to say the ext stuff needs some more TLC to work on  
>> different platforms and be more generally installable.
>>
>> -jason
>>
>> On Nov 4, 2005, at 10:08 AM, Chris Papadopoulos wrote:
>>> Hi all,
>>> Running bioperl 1.4 on Mac OS 10.4.2.
>>> Installed the Inline modules, copied .h files to /usr/local/ 
>>> include/io_lib/
>>> Here's the directory, probably has more than it needs (just got  
>>> frustrated and dumped 'em all):
>>> papadop:/usr/local/include/io_lib>ls
>>> Read.h            compression.h     open_trace_file.h tar_format.h
>>> abi.h             config.h          os.h              traceType.h
>>> acconfig.h        error.h           plain.h           translate.h
>>> alf.h             expFileIO.h       scf.h             xalloc.h
>>> array.h           fpoint.h          scf_extras.h      ztr.h
>>> calc_crc.h        mach-io.h         seqIOABI.h
>>> compress.h        misc.h            seqIOCTF.h
>>>
>>> For brevity's sake, please refer to the message dated Thu Apr 1  
>>> 13:02:01 EST 2004 from Barry Moore entitled:
>>> [Bioperl-l] Trouble installing bioperl-ext /  
>>> Bio::SeqIO::staden::read
>>>
>>> I'm having the exact same problem and my make output is virtually  
>>> identical. I specified the location of IOLIB_LIB and IOLIB_INC  
>>> for Makefile.PL as suggested.
>>>
>>> I would appreciate anyone's help here.
>>> Thanks,
>>> Chris Papadopoulos
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
> -- 
>
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> Bioinformatics consultant
> 90 Worcester St., #4
> Boston, MA  02118
> 617/699.7057, vox
>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12