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Whenever I try to install a new package I'm getting this error:

source("http://bioconductor.org/biocLite.R")  
Warning in install.packages :  
  package ‘BiocInstaller’ is not available (for R version 3.0.2 RC)  
Installing package into ‘/home/hd-master/R/x86_64-unknown-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)  
trying URL 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/BiocInstaller_1.12.0.tar.gz'  
Content type 'application/x-gzip' length 13509 bytes (13 Kb)  
opened URL  
==================================================  
downloaded 13 Kb  

Error in library(BiocInstaller) :   
  there is no package called 'BiocInstaller'  
Execution halted
Scott Ritchie
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on_the_shores_of_linux_sea
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  • Have you tried opening a new R session and running the command? If that doesn't work, can you post your `sessionInfo()`? – Scott Ritchie Oct 31 '13 at 08:29
  • Even re-installed R, still having the same problem. – on_the_shores_of_linux_sea Oct 31 '13 at 08:52
  • `R version 3.0.2 RC (2013-09-17 r63944)` Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.2 – on_the_shores_of_linux_sea Oct 31 '13 at 08:53
  • It doesn't appear to be a Bioconductor problem, it works on my R 3.0.2 – Scott Ritchie Oct 31 '13 at 09:00
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    What happens if you start with a blank `~/.Rprofile`? – Scott Ritchie Oct 31 '13 at 09:02
  • After removing RStudio is not working. But I'm able to install packages through R console. Any pointers what might be the issue? – on_the_shores_of_linux_sea Oct 31 '13 at 09:21
  • Just guessing at, from the command line, `R --vanilla` and then `install.packages("BiocInstaller", repos="http://bioconductor.org/packages/2.13/bioc")`. Also, `BiocInstaller` is a little special; what about installing a standard R package (you say you have problems when trying to install a new package). – Martin Morgan Oct 31 '13 at 20:13

1 Answers1

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  • Install R-3.0.2 (not RC).
  • Try starting R as follows: R --vanilla
  • See if you are pointing to a weird mirror. What is the output of getOption("repos")?
  • Try this: install.packages("BiocInstaller", repos="http://bioconductor.org/packages/2.13/bioc")
Waldir Leoncio
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Dan Tenenbaum
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