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

Vrakj [guest] guest at bioconductor.org
Tue Jun 10 23:33:05 CEST 2014


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 -----

----- 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")



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
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)

[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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