[Bioc-devel] Biobase dependencies

[Sean Davis]

pingou wrote:
> 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
>
>   
Hello.  In general, you can install packages by using biocLite.  It 
would have found the ALL package.  It is an experiment data package and 
is available here:

http://bioconductor.org/packages/2.2/data/experiment/html/ALL.html

Sean