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Re: BioCocoa


On Oct 12, 2008, at 10:54 PM, Charles Plessy wrote:


Le Sun, Oct 12, 2008 at 03:57:33PM -0700, Scott Christley a écrit :


So I got BioCocoa to produce a new source code release, and worked on
modifying the package files. The patch is not very big so I've attached it. This is my first attempt, so I welcome any comments. The resultant 
deb installs fine, and I compiled some code against the installed
BioCocoa, so it looks ok.


Dear Scott,

thanks a lot for the patch. Do you want write access to our Subversion
repository to ease your work ?
That would be nice. Though I would appreciate having my code reviewed while I'm still learning the process. 



I have two comments about your patch.

There is a surprisingly high number of users (relative to our other
packages) who seem to use the current biococoa.app package for the
sequence converter demo application. I think that it would be good that 
the updated biococoa source package would ship it in a binary package
that could be named sequenceconverter.app, and that could superseede
biococoa.app (in dpkg words: replace, provide and conflict).
Ok, need to think about this. I got involved with BioCocoa after it moved to version 2.X which was a complete re-architecture. The sequence converter code doesn't seem to compile with version 2.X, so I think it needs to either be rewritten or maybe functionality is missing from 2.X, I'm not sure which. But I guess if we split the old/ new biococoa into two packages, we can still provide the old application until its working in the new version. 





I tried to build the new "biococoa" Debian package, with objective C
compilers from the GCC version 4.3.2. It produced the attached error
messages and did not complete. Which version of your tools are you
using?


The problem starts with this error:
BCSequenceAlignment.h:29:34: warning: Foundation/Foundation.h: No such file or directory
This would seem to imply that either gnustep-base is not installed, or somehow the environment is not setup. The header files should reside under /usr/include/GNUstep. Maybe the dependencies for the package are not defined properly?
I'm actually using Lenny, for some reason I was getting internal errors with GCC on Sid. Lenny has GCC 4.3.1 


cheers
Scott
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