[Bioperl-l] Update of bioperl-ext for modern environment

Chris Fields cjfields at illinois.edu
Wed Nov 26 10:34:37 EST 2008


We have partially accepted your patch (those specific for  
Ext::Align).  The Bio::SeqIO::staden::read patches didn't work,  
primarily b/c Bio::SeqIO::staden::read in subversion has already  
switched over a while ago to io_lib 1.11 compatibility and is now XS  
(no longer Inline::C).  However, since io_lib itself no longer carries  
abi/ztf by default (you need the full staden package) those modules no  
longer appear to work.

There are still some significant bugs that need to be worked out  
within bioperl-ext, particularly re: AlignStats, the alignment  
algorithm, etc.  The problem is the code has suffered some bit-rot  
over the years and isn't particularly well-supported; most bioperl-ext  
related bugs in Bugzilla have been around for a very long time.

What might be an alternative avenue to pursue is the BioLib  
initiative, which aims to make swig-based libraries available for all  
Bio* languages (and will likely have better support).



On Nov 20, 2008, at 7:04 AM, Thomas Jahns wrote:

> Hello everyone,
> I hope I  didn't duplicate anyone's work, but I couldn't find  
> anything on this in the archives and so I patched bioperl-ext-1.5.1  
> to work with
> - bioperl-1.5.2_102
> - staden io_lib 1.11.4
> and not crash perl.
> Please see attached patch, I hope someone reading here can integrate  
> it with the repository.
> There is one necessary externally visible change: instead of  
> specifiyng /foo/include/io_lib for the headers of the staden  
> package, one now needs to specify /foo/include, because read.h  
> includes other files with io_lib prefix.
> I hope I removed the double-free bug in the right place, if the  
> free'ing of a pointer passed into the function pgreen was  
> intentional, another strategy will be needed.
> Also I found make clean to be dysfunctional, but I don't know enough  
> about MakeMaker to fix that, thus for recompiles I used a script for  
> cleanup (also attached).
> Greetings,
> Thomas Jahns
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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