Hi, I believe that the "R package ... is not available for R ..." message as produced by biocLite is a bit confusing for "new-ish" BioConductor users, and I have a suggestion how things could be improved.
Imagine that a brand new package is submitted to BioConductor and a related manuscript to some journal. Your typical reviewer as well as most other users that heard about the package will search for it and end up somewhere under http://bioconductor.org/packages/devel/bioc/..... From there, they will simply copy&paste source("http://bioconductor.org/biocLite.R";) biocLite("myFancyPackage") into their R 3.1 console, which will tell them that the package is not available for their version of R despite the fact that the actual package "depends" on, say, R >= 2.10.0. Your typical user may try several versions of R and than either give up, or contact the maintainer. Your manuscript reviewer will reject the manuscript as the "package is not available". Trust me, I have seen both happen, and I have answered several questions explaining how a package that is still just "a development version" can be installed. In order to make things less confusing, I would suggest that future versions of biocLite check also the development section of BioConductor (if a package cannot be found in the current release), and possibly produce a message that is more informative, e.g., "R package ... is still in development; you can either try again after the next BioConductor release in October|April 20xx, or you can follow these steps to install the development version now: ..." And (less important), if biocLite "knew" which packages are from CRAN rather than BioConductor (cache the names of the ~6,000 CRAN packages?), then it could also produce errors like "R package ... seems like a CRAN package; you may want to try install.packages to install it"). That may help some users as well. That's just my 2c :-). Cheers, Josef -- Josef Spidlen, Ph.D. Staff Scientist, Terry Fox Laboratory, BC Cancer Agency 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada Tel. +1 604-675-8000, ex. 7755 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
