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

Chris Fields cjfields at illinois.edu
Wed Nov 26 09:29:38 EST 2008


Just to keep you updated, I'm check on the attached patch and script  
against main trunk code and will post back how it works out.


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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> <bioperl-ext-update.patch><clean-bioperl- 
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