[pkg-bioc] CVS %p

[David Vernazobres]

On Tue, Feb 27, 2007 at 04:44:45PM +0100, Steffen Moeller wrote :
> Hi David,
> 
> On Tuesday 27 February 2007 15:45:50 David Vernazobres wrote:
> > > All changes that I have done to the script took care not to break
> > > anything that is already existing. I do not exactly grasp how your plan
> > > will work out since you will need a root directory to install the
> > > packages anyway, but if it work and does not break anything, please go
> > > ahead.
> >
> > I do not want to break something, I just would like to have a clean
> > build directory. When the list think that we must not change a single
> > things from the past, ok, but I think that some cleaning from time to
> > time is also good.
> >
> > >>From cran2deb.pl when there is some declaration like :
> >
> >  @dirs=("contrib/main","pub/R/contrib/main");
> > And we will add more directories in this search path each time someone
> > used a different kind of mirrors ?
> > Why not making directly a wget which is taking care of writing
> > in the sources directory with
> >
> >   wget -N --retr-symlinks -I"contrib/main/Descriptions" -nH \
> >     -m "ftp://cran.us.r-project.org/contrib/main/*.tar.gz" \
> >     --cut-dirs=2 -P sources
> >
> > or
> >   wget -N --retr-symlinks -I"pub/R/contrib/main/Descriptions" -nH \
> > 	-m "ftp://cran.de.r-project.org/pub/R/contrib/main/*.tar.gz" \
> >     --cut-dirs=4 -P sources
> 
> while I would not mind to add directories, this solution is indeed fine. I 
> discussed this another day with Dirk. The information should not be on the 
> Wiki page but in a cran_update.sh script or so, in analogy to the bioc 
> (interim-?)solution. The Wiki page could then give a quick description of the 
> process and link to the CVS web interface for whoever has interest in the 
> nitty gritty.

bioc_update, cran_update.sh, omegahat_update.sh,...
well I choose the solution r_pkg_prepare.sh who is modular, and give the
possibility to do just 1 repository, or all repository in one shoot.

 
> For the selection of an EU or US mirror, I just found out that the netselect 
> script does not work since .de. does not answer it. Maybe this is of a rescue 
> for you:
> 
> for i in de us; do ping -c 2 cran.$i.r-project.org -q -W 1|tail -1|
> cut -f2 -d= |cut -f2 -d/; done
> 35.508
> 123.650

Well, I am not really for automating the mirror localisation. By
experience, I have seen roaming ubuntu laptop using netselect for apt. 
They were handing-up using the Australian mirror when they were
sitting in Germany, just because the Australian was quicker to answer
to the ping.... So I will add a switch Europe/US (-en/-us).



> > So we removed part of the complexity by having an homogeneous
> > bioc/cran/omegahat directories.
> > Each of these directories will have the following subdirectories :
> > builds html sources changelogdb.
> >
> > I am thinking that it's also part of what you mean with
> > "a reference build environment setup for CRAN,BioC and Omeghat all
> > together." Or are you referring just to the build part ?
> 
> I was referring to the build part, but for that to be homogenous so should be 
> the underlying directory structure. I personally would want to allow the bioc 
> and cran directories to be just about anywhere relative to each other. I need 
> to investigate myself more to learn why I think so :o)
> 
> > > > > The next two big steps in the development of cran2deb remain (to me):
> > > > > * make %repositoryOf persistent - should be fairly trivial
> > > > > * create a decent build-dependencies tree and derive a same-as decend
> > > > > build order from it. I have no idea about how difficult this is - not
> > > > > toooo difficult I'd have thought but why have I not just done it?
> > > >
> > > > Using the recent graph theory ?
> > >
> > > Indeed, my latest submission uses the Graph::directed class to model the
> > > dependencies and knows how to use Graph::traverse::DFS to run through it.
> >
> > Well, ok, I updated my directory and looked at your last changed.
> 
> I am fairly confident that you like it. As time permits, I will add the proper 
> readout of the description files.
> 
Best regards
 
david


-- 
David VERNAZOBRES, PhD student                     | dv at uni-muenster.de
Division of Bioinformatics, University of Muenster | Schlossplatz 4
(+49)(251)8321635                                  | D48149 Muenster
http://www.uni-muenster.de/Evolution.ebb/          | Germany