[BioC] error: 'BiocInstaller' package not in repository

Vrakj [guest] guest at bioconductor.org
Tue Jun 10 22:37:18 CEST 2014


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


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