R Bioconductor: topGO Not Installing

Question

I've just finished downloading R and RStudios for use with Ubuntu 14.04. I have version R 3.0.2. I'm trying to install Bioconductor package topGO using RStudio. I used the code source(: http://bioconductor.org/biocLite.R ") and got the message: "Bioconductor version 2.13 ....a newer version of Bioconductor is available after installing newer version of R"

So I removed R from my computer and re-installed it. I think I have the newest version R version 3.0.2. I also ran biocLite("BiocUpgrade") on this new downmload of R and got the error message:

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R
  version 3.0.2.
Warning messages:
1: Bioconductor version 2.13 is the latest available for R
  version 3.0.0 
2: installed directory not writable, cannot update packages
  'boot', 'class', 'cluster', 'codetools', 'foreign',
  'KernSmooth', 'lattice', 'Matrix', 'mgcv', 'nlme', 'nnet',
  'rpart', 'spatial', 'survival' 

I have no clue what this means so I just tried to download topGO using biocLite("topGO"). It starts to download but then stops and gives the error message:

Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sprout/R/i686-pc-linux-gnu-library/3.0/GO.db’
ERROR: dependency ‘GO.db’ is not available for package ‘topGO’
* removing ‘/home/sprout/R/i686-pc-linux-gnu-library/3.0/topGO’

The downloaded source packages are in
    ‘/tmp/RtmpqFXYZT/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GO.db’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘topGO’ had non-zero exit status
3: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival' 

Any thoughts? Thank you for the help!

Answer 1

You don't have a recent version of R on your computer. Several packages require a more recent version. I suggest that you follow the instructions at https://cran.r-project.org/ on how to install the latest version of R (which is currently v3.2.1) and try again.

Answer 2

problem: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival'

solution:Run R as a root user IN TERMINAL

1,sudo R 2,biocLite("BiocUpgrade") 3,Update option:(type) a