problems updating biomaRt in R version 3.0

Question

[Max]

I recently upgraded R on our servers to version 3.0, and when I attempted to to access biomaRt with library("biomaRt"), I get the error message

Error: package 'biomaRt' was built before R 3.0.0: please re-install it

However, executing the standard command

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

fails to reinstall/update biomaRt, as I get the same error the next time I attempt to access the biomaRt library. What do I need to do in order to reinstall biomaRt for compatibility with R 3.0.0?

Answer 1

[Neilfws]

1. Check that there is not another biomaRt build somewhere on your system (e.g. in a system-wide location)

2. If you've upgraded R version, you probably need to upgrade Bioconductor too:

   biocLite("BiocUpgrade")
   

[Max]

It seems as though there's a whole host of dependencies that need to be upgraded, e.g.

Error : package 'RCurl' was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package 'biomaRt'
* removing '/usr/local/lib/R/site-library/biomaRt'
* restoring previous '/usr/local/lib/R/site-library/biomaRt'

[Neilfws]

In that case try:

update.packages(check.built = TRUE, ask = FALSE)

but be aware, it is difficult to provide advice since we cannot know the precise history and state of your system.