Bioperl: Re: bioperl-ext Patch for extension portability (fwd)

[James Gilbert]

Ewan,

Raphael Leplae found an unnecessary element in
Makefile.PL for bioperl-ext, which fixes the
compile on IRIX 6.5, and doesn't affect the
compilation on OSF or Linux.  But Allen has fixed
other things, and he is asking about the future
changes to the alignment packages in bioperl.  
This is rather outside my area of expertise, so
I'm posting this to the list.


Allen,

Do I understand that bioperl-ext doesn't compile
on DOS, but does with your fixes?

	James

James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

---------- Forwarded message ----------
Date: Tue, 9 May 2000 22:26:27 -0400
From: Allen Smith <easmith@beatrice.rutgers.edu>
To: James Gilbert <jgrg@sanger.ac.uk>
Subject: Re: bioperl-ext Patch for extension portability

On May 8,  9:29am, James Gilbert wrote:
> 
> 
> 
> Allen,
> 
> Thanks very much for your bug report and fix.

Quite welcome.

> I've been given a much smaller fix,

The fix wasn't just for IRIX; it was also to increase portability in
other respects (such as in which header files were imported, treatment 
of filenames for DOS machines, and in general using a subsidiary
Makefile.PL instead of a static makefile).

> which fixes the compile on our IRIX machines, but we're all
> running 6.5 here.

> Would you mind testing it on
> one of your machines?  I attatch the compressed
> archive.
>
> The fix just removes "CC=$(CC)" from:
> 
> sub MY::postamble{
> '
> $(MYEXTLIB): 
> DEFINE=\'$(DEFINE)\'; CC=\'$(PERLMAINCC)\'; export DEFINE INC CC; \
>         cd libs && $(MAKE) CC=$(CC) libsw$(LIB_EXT) -e
> 
> ';
> }

I'm afraid that that doesn't do the job fully... among other things,
there's a problem with the makefile when it tries to compile
wisefile.c, namely that it neglects to have a -o in the
compilation of an object file.

	-Allen

P.S. Incidentally, I realize that this extension is essentially a
direct port of part of WISE, without changes beyond those needed to
get it to run with Perl. It looks like my Ph.D. thesis is going to be
partially concerned with alignments and doing variations on how to run 
them. Would there be interest in my (heavily) revising the C code in
this to integrate it more fully with Perl (e.g., to have matrices
entered through perl instead of external files), and/or introducing another
alignment package module using C code from another public-domain source?

-- 
Allen Smith				easmith@beatrice.rutgers.edu
	


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