After updating to R 3.1.0, I am unable to install Bioconductor packages. For example, > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help > biocLite("BiocUpgrade") 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc, using 'http://bioconductor.org/packages/2.12/bioc' Error: 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc This error occurs for anything that I try to install. It still works fine under R 3.0.0. I think that the problem is a mismatch between the version of R and the version of Bioconductor. However, I am unable to update the version of Bioconductor because of the above error. Here is the traceback: > traceback() 12: stop(.msg(...), call. = call.) 11: .stop("'BiocInstaller' package not in repository %s", repos, call. = FALSE) 10: .contribUrl(oldRepos) 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) .message("%s, using '%s'", conditionMessage(err), 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) .message("%s, using '%s'", conditionMessage(err), oldRepos) .contribUrl(oldRepos) })) 3: .getContribUrl(biocVersion()) 2: bioconductorPackageIsCurrent() 1: biocLite("BiocUpgrade") Thanks for any help -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.4 loaded via a namespace (and not attached): [1] tools_3.1.0 -- Sent via the guest posting facility at bioconductor.org.

Hi, ----- Original Message ----- > From: "Maintainer" <maintainer at="" bioconductor.org=""> > To: bioconductor at r-project.org, schlieysjunk at yahoo.com > Cc: "BiocInstaller Maintainer" <maintainer at="" bioconductor.org=""> > Sent: Tuesday, June 10, 2014 1:37:18 PM > Subject: [devteam-bioc] error: 'BiocInstaller' package not in repository > > After updating to R 3.1.0, I am unable to install Bioconductor > packages. For example, Start R with the --vanilla flag, like this: R --vanilla before running the command below. > > > source("http://bioconductor.org/biocLite.R") Dan > Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help > A newer version of Bioconductor is available for this version of R, > ?BiocUpgrade for help > > > biocLite("BiocUpgrade") > 'BiocInstaller' package not in repository > http://bioconductor.org/packages/2.12/bioc, using > 'http://bioconductor.org/packages/2.12/bioc' > Error: 'BiocInstaller' package not in repository > http://bioconductor.org/packages/2.12/bioc > > This error occurs for anything that I try to install. It still works > fine under R 3.0.0. I think that the problem is a mismatch between > the version of R and the version of Bioconductor. However, I am > unable to update the version of Bioconductor because of the above > error. > > Here is the traceback: > > traceback() > 12: stop(.msg(...), call. = call.) > 11: .stop("'BiocInstaller' package not in repository %s", repos, > call. = FALSE) > 10: .contribUrl(oldRepos) > 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) > .message("%s, using '%s'", conditionMessage(err), 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) > .message("%s, using '%s'", conditionMessage(err), oldRepos) > .contribUrl(oldRepos) > })) > 3: .getContribUrl(biocVersion()) > 2: bioconductorPackageIsCurrent() > 1: biocLite("BiocUpgrade") > > > Thanks for any help > > > > > > > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.10.4 > > loaded via a namespace (and not attached): > [1] tools_3.1.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >

Dan: Thanks for the input. I tried this, but it didn't help (output shown at end of message). Any more ideas? Thanks for your time ----- Original Message ----- >Hi, ----- Original Message ----- >> From: "Maintainer" <maintainer at="" bioconductor.org=""> >> To: bioconductor at r-project.org, schlieysjunk at yahoo.com >> Cc: "BiocInstaller Maintainer" <maintainer at="" bioconductor.org=""> >> Sent: Tuesday, June 10, 2014 1:37:18 PM >> Subject: [devteam-bioc] error: 'BiocInstaller' package not in repository >> >> After updating to R 3.1.0, I am unable to install Bioconductor >> packages. For example, >Start R with the --vanilla flag, like this: >R --vanilla >before running the command below. > > > source("http://bioconductor.org/biocLite.R") >Dan -------------------------------------------------------- Here is what happened: > system("R --vanilla") R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help > biocLite("BiocUpgrade") 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc, using 'http://bioconductor.org/packages/2.12/bioc' Error: 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc > -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.4 loaded via a namespace (and not attached): [1] tools_3.1.0 -- Sent via the guest posting facility at bioconductor.org.