[pkg-bioc] CVS %p

[David Vernazobres]

On Sun, Feb 25, 2007 at 11:01:23PM +0100, Steffen Moeller wrote :
> On Sunday 25 February 2007 22:12:15 Dirk Eddelbuettel wrote:
> > On 25 February 2007 at 21:25, CVS User smoe-guest wrote:
> > | Update of /cvsroot/pkg-bioc/tools
> > | In directory alioth:/tmp/cvs-serv388
> > |
> > | Modified Files:
> > | 	CRAN2DEB.pm cran2deb.pl
> > | Log Message:
> > | Find the right .deb for r-cran-ggobi|r-omegahat-ggobi and other
> > | dependencies with ambiguities.
> 
> > I think the former is clearly deprecated:
> 
> It was just the only (while bad) example that sprang to mind. Those R packages 
> in DESCRIPTIONS' depends line that we could not yet assign to a particular 
> repository are denoted in the "|"-separated alternatives list. The routine 
> that attempts to install the packages (sudo at the moment, should be 
> happening automagically in pbuilder w/ apt-proxy) finds the correct .deb now 
> rather than interpreting the |-savvy string literally.
> 
> > (URLs are short as run apt-proxy here to cache for pbuilder and my
> > benefit.)
> 
> When the scripts produces a new .deb file, pr when it is uploaded with 
> mini-dinstall, is the apt-proxy internal information system automagically 
> updated? If so, then there would be no need for the script to use dpkg -i, 
> indeed. Otherwise the script should initiate the update of the apt-proxy 
> somehow. Sadly, I have updated my apt to the one from experimental and cannot 
> install apt-proxy or mini-dinstall due to some totally unnecessary conflict.  
>    python-apt: Depends: libapt-pkg-libc6.3-6-3.11
> and refrain from contributing at this front for the moment.

May need to do it a bit of apt "magic", so we just update the local
repository, and not the full computer sources.list.

mkdir -p /path/pkgbiocdevel/lists/partial/
apt-get -o Dir::Etc::SourceList=/path/sources.list.pkgbiocdevel -o
Dir::State::Lists=/path/pkgbiocdevel/lists/ update
and we could install with the same command line :
apt-get -o Dir::Etc::SourceList=/path/sources.list.pkgbiocdevel -o
Dir::State::Lists=/path/pkgbiocdevel/lists/ install pkg-to-install

the resulting part is that we need to somehow, fix the directory
structure: 
.../
.../tools   <- the cvs part
.../bioc 
.../cran
.../omegahat



> 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 ?

> * a reference build environment setup for CRAN,BioC and Omeghat all together. 
> Dirk suggests using pbuilder for it all, possibly helped with apt-proxy and 
> mini-dinstall. The current sudo should be skipped for security concerns and 
> exists only for the direct (and fairly easy) evaluation of the prior two 
> tasks.
I am starting to work on this part.
I think that apt-proxy is not necessary, and should not be necessary. We
should not extend too much the requiered architecture, in my point of
view.

Best regards

David