[BioC] [devteam-bioc] error: 'BiocInstaller' package not in repository

[Dan Tenenbaum]

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.
> 
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