[pkg-bioc] Resume status of pkg-bioc

[David Vernazobres]

Dear all, 
I am considering the code on our SVN tools directory depreciated. I took the
decision to "rewrite" from scratch the code, to eliminate few design
flaw, and a lot of code, which were called 3 times, or action which
where done more than once time.
OK, some part are still the same, and did not changed a lot as CRAN2DEB.pm,
where some working-time are still need.
I reworked the build order and conception of the new code, in the optic 
of an automatic build daemon (a la vhffs[1]). The rewritten in 2 week-ends was
more for a proof of concept, and are still lacking some line of code. 
We have a build system, more robust and clean (in my opinion). Few code
part are still missing: There is not yet
* a storage.pm module: for reading, writing the data.
* a *sql*.pm module: the "low level" interface of storage.
* a web.pm: generation of the report build page.
*...
Well the full TODO list, try to enumerate the full lacking part.
I did not yet update the wiki, but most of the syntax did not change,
and a skim is provided at first in the README.

About the time need:
* the r_pkg_ordering for reading the file from the disk, took
about 150 seconds to build the dependencies graph of cran, bioc,
omegahat (on my old P4, with 2 SATA hard drive mount in raid 1, and the
filesystem in a LUKS, so it's definitely not the most powerful
architecture). So this part will be optimize as soon as the storage.pm exist.

2 builds mechanism are support: pbuilder[2], cowdancer[3].
Other build system could be support, it's just a matter of
 * cp PBuilder.pm mynewbuilder.pm
 * edit mynewbuilder.pm to correct the call done inside.
 * edit r_pkg_prepare to select the build install methods as mynewbuilder

Hope to get some participation on some small or big part of the code
which are need to have our automatic build daemon. Some part of the
TODOlist need some R experts, some other part need some perl guys, 
some need just common sense.

svn co
svn+ssh://developername@svn.debian.org/svn/pkg-bioc/trunk/tools-ng tools-ng

David

[1]: http://www.vhffs.org
[2]: http://packages.debian.org/sid/pbuilder
[3]: http://packages.debian.org/sid/cowdancer

-- 
Be realistic. Demand the Impossible.