Dear Kasper, regarding your issue with R-2.15: I was wondering whether using an older version of Rcpp from http://cran.r-project.org/src/contrib/Archive/Rcpp/ would help?
Cheers, Andrzej On Tue, Apr 22, 2014 at 2:46 PM, Kasper Daniel Hansen <kasperdanielhan...@gmail.com> wrote: > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
