[pkg-bioc] NETTAB meeting in Pisa, Installation of local packages dated newer than repository

[Steffen Moeller]

Hi, 

I returned from Pisa last Saturday and think our presentation was 
well-perceived. There may be an adoption of our R packages or of our 
principles for a dynamic installation of packages (possibly also comprising 
our R packages) by the BioinfoGrid EU project people (that run Scientific 
Linux (still)) but this is too early to tell, really. I'll run into them in 
September again when we are planning for a workshop+conference
of our NorduGrid in Copenhagen 
(http://indico.hep.lu.se/conferenceDisplay.py?confId=318, some fancier web 
site is in preparation). Things will operationalise then. You are all invited 
to join in for that meeting, btw. It is a grid school plus workshop plus 
conference, no fees, there may be support for travel for students.

A major issue that the Grid people also run into is the synchronised update of 
bioinformatics databases, alike the issues recently discussed on Debian-Med 
and Debian-Devel.  I hope that we can think of some szenarios that allow for 
an active involvement of the community in this issue. There are differences 
between the packages we provided for R to those that represent databases only 
(or AnnotationData as BioConductor puts it of which we ignore the bigger full 
genome ones). I just need to make up my mind about what these differences 
are.

Back to the bits with quick tangible successes:

I just ran against the following bug:

Error: package 'Biobase' 1.12.2 was found, but >= 1.13.41 is required 
by 'affy'

for the compilation of affy a readily compiled version 1.4 of biobase was 
available but not installed since an earlier version was already installed.

I might fix this any time unless anybody of yours comes first. I just refrain 
from the building of packages just happening in the background.

Btw, how can we automatically sign the packages we compile without entering 
our keys all the time? Some gpg-agent magics?

Many greetings, particularly to the DD Andrea (of mplayer fame) who kindly 
signed my gpg key in Pisa

Steffen
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