[pkg-bioc] Hello!

['Johannes Ranke']

Hi Andrew,

I hope your exams went fine! OK, Dirk and you convinced me to using perl
for a start. Dirk suggested to split tasks as follows:

	- updating the source mirror
	- updating the metadata
	- computing the mapping to Debian packages
	- publishing results
	- etc pp

If we take the last part out, is this list complete?

Johannes

* Andrew Dai <ad364 at hermes.cam.ac.uk> [060609 10:00]:
> Hi all,
> 
> My exams finally finished yesterday so I should be able to start work on
> this soonish. Personally I'd prefer to code at least at the moment in Perl,
> partly for the reason that R's supporting scripts are all in Perl themselves
> and partly because of all the pre-existing code. I'm happy with splitting
> the small tasks using Python.
> 
> 
> Andrew
> 
> -----Original Message-----
> From: Johannes Ranke [mailto:jranke at uni-bremen.de] 
> Sent: 09 June 2006 05:14
> To: Dirk Eddelbuettel
> Cc: pkg-bioc-devel at lists.alioth.debian.org; Andrew Dai
> Subject: Re: [pkg-bioc] Hello!
> 
> > On 8 June 2006 at 17:19, Johannes Ranke wrote:
> > | Thanks! I think the alioth pages really should be improved a little 
> > | bit (see my original mail).
> > 
> > Go right ahead :)
> 
> I can't, at least as far as
> 	
> 	http://alioth.debian.org/projects/pkg-bioc/
> 
> is concerned. In the summary text, CRAN is not even mentioned!
>  
> > | You mean the Wiki page AliothPkgBioc? Yes, this could be clarified.
> > 
> > Idem. I think Rafael may have made the wiki-page our home page. Not a bad
> idea.
> 
> Yes, that's nice!
>  
> > | Some related questions: Is somebody really using all these packages 
> > | that can be built? Do you use cran2deb.pl for your Debian packages? 
> > | It sounds like you use an improved version on your machine for this.
> > 
> > I used 'my' first version of Albrecht's / Detlef's script for an 
> > earlier Quantian build. Now for Quantian I just install into /usr/local.
> > 
> > So I don't think anybody uses the packages yet -- but it's a vicious 
> > circle because we also don't run the script regularly yet.
> 
> Maybe we should scale down the scope of the CRAN script to packages that
> actually build and are useful in Debian and that we care for. There is a lot
> of CRAN packages now that are probably only interesting for a very small
> number of people, as far as I can see.
>  
> > | So there would be two possibilities: 
> > | - Upload everything to Debian (which I would also be hesitant to do,
> > |   although this list could try to deal with the BTS).
> > | - Maintain a separate repository, maybe even on CRAN and BioC servers.
> > 
> > We don't yet. We also think 'all to Debian' is to massive. Maybe one 
> > day after we have a bit of a track record and more experience outside 
> > of it. I am sure we will find repo space somewhere -- as you said,
> possibly even on CRAN.
> 
> I can use my own repo for testing things in the meantime, but it's not split
> into stable, testing and unstable (yet).
>  
> > | <off-topic>
> > | I would prefer python, since I would like to learn it, as opposed to 
> > | perl, which seems outdated to me (although I have a strong 
> > | inclination to Debian, which is intimately tangled with perl, and 
> > | think it is a modern distribution. We had KDE 3.5.3 packages in sid 
> > | even before it was released!).
> > | </off-topic>
> > 
> > Even if you rewrote it all we had the problem that the current crew is 
> > using Perl -- there is some subtle self-selection going on.  But 
> > longer term maybe we can break the script into several smaller tasks 
> > (updating the source mirror, updating the metadata, computing the 
> > mapping to Debian packages, publishing results etc pp) some of which may
> well be Python-based.
> 
> I think splitting things up would be a good idea - maybe with a simple
> makefile to coordinate the smaller tasks.
>  
> > But for now Perl it is I'm afraid.  [ I have also meant to learn more 
> > Python, now for decade and counting ... Perl just "works" for me. ]
> 
> What about Andrew - what do you prefer?
> 
> Best,
> 
> Johannes

-- 
Dr. Johannes Ranke                 jranke at uni-bremen.de
UFT Bremen, Leobenerstr. 1         +49 421 218 8971 
D-28359 Bremen                     http://www.uft.uni-bremen.de/chemie/ranke