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!

I hate doing this, what do I type into the terminal to get this latest package of R? I'm trying deb cran.cnr.Berkeley.edu/bin/linux/ubuntu vivid/ but it says the command "deb" doesn't exist — kevluv93
If you have ubuntu 14.04 I suggest that you edit the file /etc/apt/sources.list and add the line deb https://cran.rstudio.com/bin/linux/ubuntu trusty/ at the end, provided that you can read/write the file. — RHertel
Once this is done, you can proceed with sudo apt-get update followed by sudo apt-get install r-base and sudo apt-get install r-base-dev. — RHertel
One more ?, how do you write in the sources.list file through the terminal? I've never done this before. I found the sources.list file, but can't write in it. — kevluv93
Probably a minimal editor such as gedit is installed. Try using sudo gedit /etc/apt/sources.list . If you are allowed to read and write the file, this should be easy because this is a standard editor, comparable to Windows' notepad. If you don't have the permission to modify the file, let me know and we'll try to find another solution. — RHertel

RHertel RHertel · Accepted Answer · 2015-08-14T17:36:22

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.

R Bioconductor: topGO Not Installing

2 Answers