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

Bob Freeman bobfreemanma at speakeasy.net
Sun Nov 6 13:43:41 EST 2005


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?


At 1:07 PM -0500 11/6/05, Jason Stajich wrote:
>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 
>-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.
>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):
>>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.
>>Chris Papadopoulos
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>Jason Stajich
>Duke University
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org


Bob Freeman, Ph.D.
Bioinformatics consultant
90 Worcester St., #4
Boston, MA  02118
617/699.7057, vox

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