[pkg-bioc] CVS %p

[Steffen Moeller]

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.

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



> 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

Steffen


-- 

Dr. Steffen Möller
University of Lübeck
Institute for Neuro- and Bioinformatics
Ratzeburger Allee 160
23538 Lübeck
Germany
T: +49 451 500 5504
F: +49 451 500 5502
moeller at inb.uni-luebeck.de
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