[Bioperl-l] Update of bioperl-ext for modern environment
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).
> Thomas Jahns
> Sensationsangebot nur bis 30.11: GMX FreeDSL - Telefonanschluss + DSL
> für nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign
More information about the Bioperl-l