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

[Dan Tenenbaum]

Hi,

----- Original Message -----
> From: "Vrakj [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, schlieysjunk at yahoo.com
> Sent: Tuesday, June 10, 2014 2:33:05 PM
> Subject: [BioC] error: 'BiocInstaller' package not in repository
> 
> 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")


Actually I wanted you to run 

R --vanilla

at your operating system's command prompt. 

Another thing to try is:

remove.packages("BiocInstaller")

and then:

source("http://bioconductor.org/biocLite.R")

Dan


> 
> 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.
> 
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