[Bioc-devel] Biobase dependencies

pingou pingoufc4 at yahoo.fr
Thu Oct 25 12:47:14 CEST 2007

Dear all,

Trying to do the RPM of Bioconductor for Fedora and CentOs, I am
updating my package to the last version.

In the case of Biobase [1] I met a problem.
To do a good installation through RPM, the packaging guide lines [2]
require to run the R CMD check command.
But Biobase, seems to need a library called "ALL", I have been looking 
for a library called ALL in the Bioconductor repository, on the CRAN 
website, through google and I could not find any.

So my question is then, does this library exist ?
If not why is it present on the DESCRIPTION file as 'R CMD check' check
for the required library *but also* for the suggest library.

When I try to package it, it returns me
 >Namespace dependencies not required:
 >  ALL

This question in fact create some problems of circular dependencies to
create the RPM
For example BSgenome [3] needs Biostring [4] which need BSgenome...

Should we not try to avoid this kind of dependencies so that the R CMD
check can be apply without problem ?

My two questions, and my two cents to this project,

Thanks in advance,
Best regards,
P.Yves Chibon

[1] http://bioconductor.org/packages/2.2/bioc/html/Biobase.html
[2] http://fedoraproject.org/wiki/Packaging/R
[3] http://bioconductor.org/packages/2.2/bioc/html/BSgenome.html
[4] http://bioconductor.org/packages/2.2/bioc/html/Biostrings.html

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