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

Jason Stajich jason.stajich at duke.edu
Sun Nov 6 13:07:51 EST 2005

In os.h did you change
#include <config.h>

#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 - 
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.


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

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