Hi Dan,
On Fri, Apr 4, 2014 at 11:05 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > Hi Diego, > > ----- Original Message ----- >> From: "Diego Diez" <diego10r...@gmail.com> >> To: "bioc-devel" <bioc-de...@stat.math.ethz.ch> >> Sent: Friday, April 4, 2014 12:44:20 AM >> Subject: [Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9 >> >> Dear all, >> >> sorry if double posting this. I sent it two days ago using a >> different >> email not registered at bioc-devel and it seems (as for the archives) >> it has not reached destination. >> >> FYI, it seems the OSX build R 3.1.0 beta has split into snowleopard >> and mavericks builds: >> >> http://r.research.att.com >> >> When installing the later and trying to install Bioconductor I get >> the >> following: >> >> > source("http://bioconductor.org/biocLite.R";) >> Warning: unable to access index for repository >> http://www.bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1 >> >> package 'BiocInstaller' is available as a source package but not >> as a binary >> >> 'biocLite.R' failed to install 'BiocInstaller', use >> 'install.packages("BiocInstaller", >> repos="http://www.bioconductor.org/packages/2.14/bioc";)' >> Warning message: >> package 'BiocInstaller' is not available (for R version 3.1.0 beta) >> >> >> then did the following: >> >> >> > install.packages("BiocInstaller", >> + >> repos="http://www.bioconductor.org/packages/2.14/bioc",type="source";) >> trying URL >> 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz' >> Content type 'application/x-gzip' length 14183 bytes (13 Kb) >> opened URL >> ================================================== >> downloaded 13 Kb >> >> * installing *source* package 'BiocInstaller' ... >> ** R >> ** inst >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices >> ** testing if installed package can be loaded >> Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help >> * DONE (BiocInstaller) >> >> The downloaded source packages are in >> '/private/var/folders/dm/96krztk175d19vx9rcsgd2qc0000gn/T/RtmpMt3iRo/downloaded_packages' >> >> >> and after that did: >> >> > biocLite() >> Error: 'no packages in repository (no internet connection?)' while >> trying >> http://bioconductor.org/packages/2.14/bioc >> >> which failed, presumably because the new repository structure is not >> yet supported? > > > Yes, it's not yet supported. We just ordered some Mavericks machines > yesterday which we'll use to build BioC against the new R binary for > Mavericks. We'll announce on the Bioconductor and Bioc-devel mailing lists > when these builds are ready. > > Until then, you can run the R binary built on Snow Leopard. It will work fine > on Mavericks and you'll be able to download binary BioC packages. > Thank you. Also saw your other email sent to the list. What is the advantage then of having a mavericks build? I guess the problem is that Xcode 5 builds are not backward compatible. >> >> this did not work either: >> >> > biocLite(type="source") >> > > That's puzzling. What about installing an individual package from source with > biocLite()? Did not work either. > biocLite("Biobase",type="source") Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/2.14/bioc here include the output of traceback: > traceback() 11: stop(.msg(...), call. = call.) 10: .stop("'%s' while trying %s", conditionMessage(err), repos, call. = FALSE) 9: value[[3L]](cond) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 6: tryCatch({ .contribUrl(repos) }, error = function(err) { version <- getRversion() currentVersion <- sprintf("%d.%d", version$major, version$minor) lowerVersion <- .lowerRVersionString(version) oldRepos <- sub(currentVersion, lowerVersion, repos) if (oldRepos == repos) .stop("'%s' while trying %s", conditionMessage(err), repos, call. = FALSE) .message("'%s' while trying %s, trying %s", conditionMessage(err), repos, oldRepos) .contribUrl(oldRepos) }) 5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) 4: suppressWarnings(tryCatch({ .contribUrl(repos) }, error = function(err) { version <- getRversion() currentVersion <- sprintf("%d.%d", version$major, version$minor) lowerVersion <- .lowerRVersionString(version) oldRepos <- sub(currentVersion, lowerVersion, repos) if (oldRepos == repos) .stop("'%s' while trying %s", conditionMessage(err), repos, call. = FALSE) .message("'%s' while trying %s, trying %s", conditionMessage(err), repos, oldRepos) .contribUrl(oldRepos) })) 3: .getContribUrl(biocVersion()) 2: bioconductorPackageIsCurrent() 1: biocLite("Biobase", type = "source") this works (as it did with BiocInstaller) install.packages("Biobase",repos="http://www.bioconductor.org/packages/2.14/bioc",type="source";) Diego > Dan > > >> Best, >> Diego >> >> > sessionInfo() >> R version 3.1.0 beta (2014-03-31 r65343) >> Platform: x86_64-apple-darwin13.1.0 (64-bit) >> >> locale: >> [1] C/UTF-8/C/C/C/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.13.3 >> >> loaded via a namespace (and not attached): >> [1] tools_3.1.0 >> >> _______________________________________________ >> 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
