Josef, The problems with reviewers you are describing sound very frustrating (for the author and the reviewer) but I suspect you think that biocLite is doing somethign that it is not (reimplementing the actual package installation machinery in R). Responses inline.
On Tue, Aug 19, 2014 at 4:40 PM, Josef Spidlen <jspid...@bccrc.ca> wrote: > 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. > This message is from install.packages, which biocLite calls, not biocLite itself. The message is the generic "the repository you pointed at doesn't have a version of the package you wanted installable on your system" (types of packages not withstanding). > > 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: ..." > You can't (safely) mix package versions from Bioc-devel and Bioc-release, so the instructions there would be "use bioc devel". I could easily be put in the availability section of a paper "it will be available as a devel package until X/Y/ZZZZ, after which it will be a fully released bioc package" > > 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. > biocLite does/can know where the packages come from, but again, it is just calling install.packages, and will happily install CRAN packages for you without any trouble. ~G > > 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 > -- Computational Biologist Genentech Research [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
