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

Chris Papadopoulos papadop at uga.edu
Mon Nov 7 16:24:07 EST 2005

Thanks for the info. make clean, make and make install went OK but  
make test failed. bptutorial.pl was also looking for the t/ files.  
I'm looking for how CATFILE gets set in Bio::Root::IO.pm. I don't  
want to follow the entire trail but it's probably something more  
experienced folks would know. Worse case scenario, I just cp the  
files from the bioperl-ext source directory. Just need to know where to.

Thanks again,
Chris Papadopoulos

[Just as an aside, I really wish I kept notes on the whole process of  
bioperl and friends on OS 10.4. There were some minutiae that the  
online install tips didn't go over. Maybe if I'm feeling particularly  
masochistic after finals. I'll try to throw it on an older box I  
have. Folks on Darwin would benefit...]

On Nov 6, 2005, at 1:07 PM, 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/ 
> 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

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