This is because commits to this branch of Bioconductor has been disabled and it is intentional.
But it raises the larger question, recently touched upon in a lengthy thread on R-devel, on whether this is a good state of affairs for Bioconductor. Specifically the issue has to do with dependency of a Bioconductor package on a CRAN package and what happens when CRAN packages gets updated in a way that breaks backwards compability. Right now, we (Bioconductor) might get hosed. For example, we recently deployed a new computing cluster here at Hopkins. I maintain our R installation and some users have asked for an install of Bioconductor using the latest version of R-2.15, for reproducibility reasons. I have a number of scripts which installs a standard suite of packages we use here. The issue I am facing is that Rcpp has been updated and does not seem to be available for this version of R. This indirectly breaks crlmm, lumi, minfi, charm, methylumi, bead array, arrayQualityMetrics to mention but a few we use on our end. This seems somewhat undesirable from a reproducibility perspective - I cannot even install the packages! Best, Kasper On Tue, Apr 22, 2014 at 2:19 PM, Alejandro Reyes <alejandro.re...@embl.de>wrote: > Dear Dan, Dear developers list, > > Due a recent change in one cran package, DEXSeq 1.8.0 (for the R version > 3.0.*) stop working. I fixed this conflict in the release branch of > bioconductor and tried to commit my changes. But I don't seem to have write > access, e.g: > > $ svn ci --username a.reyes -m "fixed conflicts with newest version of > cran package" > Sending DESCRIPTION > svn: Commit failed (details follow): > svn: access to > '/bioconductor/!svn/ver/81643/branches/RELEASE_2_13/madman/Rpacks/DEXSeq/DESCRIPTION' > forbidden > > I also noticed that I also don't have read access... > > svn co --username a.reyes https://hedgehog.fhcrc.org/ > bioconductor/branches/RELEASE_2_13/madman/Rpacks/DEXSeq > svn: access to 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_ > 2_13/madman/Rpacks/DEXSeq' forbidden > > I was wondering if this intentional? If so, what would be the way to solve > this kind of problems (e.g. a dependency changing outside bioconductor that > breaks previous versions of a bioconductor package)? > > Best regards, > Alejandro > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
