[Bioc-devel] Biobase dependencies
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