[pkg-bioc] State of BioC autobuild

[Dirk Eddelbuettel]

Hi Steffen,

Thanks for pushing this sleeping project along another few inches!

On 5 February 2007 at 01:05, Steffen Moeller wrote:
| 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.

Yes, BioC was always a problem. At some point reposTools looks like a
solution and I packaged it -- but now that it is deprecated at BioC too, we
removed it from Debian.

| 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.

I probably won't have time to dig into this.  

Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison