[pkg-bioc] Re: Genetics Program

[Dirk Eddelbuettel]

Replying to both Steffen and Rafael here:

On 9 December 2005 at 10:41, Steffen Moeller wrote:
| > | Could we arrange a BioC repository for Alioth?
| >
| > Well we *do* have one in pkg-bioc [ which has refocussed on pkg-"CRAN and
| > BioC" but not been renamed ].
| Hm. We store the script there, but it was not yet decided if it was ok to 
| upload the .debs, so my understanding.

I am hesitant because I would not want packages of dubious quality to give a
bad first impression.  

Undoubtedly many of the CRAN/BioC packages would build and work just fine.
But the problem is that a fair number require hand-holding to, say, properly
translate CRAN dependencies into Debian dependencies, make sure those are all
present and installable, do some extra work to prevent building (for the
Windows only packages), do follow-up work (CIGwithR wants interaction with
webserver, gnomeGui ships as a package but is "only" a glade file that gets
installed somewhere else, RScaLAPACK needs a mess of library arrangements
(or, rather, an upstream autoconf patch) etc pp.  It should *really* work,
not *just work*.

So I'd rather test that at a lower key site for a bit and prove that we are
able to cope with it before unleashing it more broadly.

| From my perception the main work towards Debian quality is on the upstream 
| packages to document themselves better. My personal /etc/apt/sources.list

I could not disagree more. Debian is about doing the best we can with the
given packages: doing the best possible integration, the smoothest and most
coherence total package. I like blaming upstream just like everyone else :)
but seriously, it is about how we can value to the mix.  


On 10 December 2005 at 14:31, Rafael Laboissiere wrote:
| > Could we arrange a BioC repository for Alioth?
| 
| This is a no-brainer and any member of the pkg-bioc group should be able
| to upload files into the directory 
| /org/alioth.debian.org/chroot/home/groups/pkg-bioc/htdocs/<something> at
| the alioth.debian.org server.  The repository URL would then be
| http://pkg-bioc.alioth.debian.org/<something>.

Yes, but as I tried to say above, it is about a lot more that just throwing
the files out. You are keeping pretty buys with a two dozen (albeit more
complicated individually) Octave package, and we are talking 600 plus
packages for CRAN and BioC.

I would not like 600 packages to rot there.

| I see that the /org partition at alioth.debian.org has still 34 Gb free.
| I would though ask the Alioth admin people before setting up the
| repository.  We could also automate the creation of the repository
| through a cron job, although I guess that there will be limitations on
| using alioth.d.o's CPU time.
| 
| I can help you in setting this up, if you wish.  Drop me a note.

We would certainly like your help on infrastructure. I really like how the
Octave project at Alioth is set up. 

But I think we need to work a few more details out before we charge ahead. I
may be in the minority here and don't mean to block or veto this, but who
exactly would do the work?  You have your hands-full with Octave, Steffen
seems busy with his dozen plus packages, I have Quantian plus a few dozen
packages --- so who is going to run this? It will take one or two hours of
daily hand-holding.

Dirk

-- 
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