[pkg-bioc] State of BioC autobuild

[Steffen Moeller]

Dear all,

if I recall correctly then the BioC repository had the long lasting problem 
that wget does not work since it cannot read any index files. This was 
partially circumvented by having wget mirroring all the web pages that 
describe the packages. And ... somehow we never got too warm with that 
approach.

I have now updated our procedure by downloading the biocinstall.R script with 
wget that one is supposed to source for the installation on a local machine 
within R and sed-ed the install.packages to download.packages. The amazing 
bit is that is actually works.

Some further changes here and there guided me to the compilation of affy 
(first in alphabet) which fails since the dependency is not working. Though 
this I hope to a problem different than  the download. The current script 
likes using the description from the web pages. These are now downloaded 
dynamically from the cran2deb script. The description file that comes with 
the tar file though should be the ones that are parsed, not anything external 
to that. Resulting from the adaptation, the title of the package is not 
assigned correctly since it is assigned prior to the parsing of the 
descriptions.

Details are on the Wiki (http://wiki.debian.org/DebianBIOC) as "usual". It 
would be lovely should anybody find the time to investigate why affy was 
built without dependencies checked.

Many thanks.

Steffen
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 189 bytes
Desc: not available
Url : http://lists.alioth.debian.org/pipermail/pkg-bioc-devel/attachments/20070205/4846bddc/attachment.pgp