i was working on a R Script, which uses gplots Library. Therefore at some point of the script
library(gplots)
is called. This works great using a 32 bit linux box (Linux an 3.2.0-33-generic-pae 52-Ubuntu SMP i686 GNU/Linux, Ubuntu 12.04).
However, I tried running the script on a 64 bit machine (Linux sim 2.6.38-15-server 66-Ubuntu SMP x86_64 GNU/Linux;Ubuntu 11.04) and now it throws errors:
Error in library(gplots) : there is no package called 'gplots'
Calls: generateHeatmap -> library
Execution halted
So when I try to install gplots it raises another error:
> install.packages('gplots', type="source", dependencies=T)
ERROR: dependency ‘gdata’ is not available for package ‘gplots’
* removing ‘/home/schaller/R/x86_64-pc-linux-gnu-library/2.12/gplots’
...
Thus, I am trying to install gdata:
>install.packages('gdata', type="source", dependencies=F)
Installing package(s) into ‘/home/schaller/R/x86_64-pc-linux-gnu-library/2.12’
(as ‘lib’ is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘gdata’ is not available
I've searched online for possible solutions. I Couldn't find any. However, I read that gdata is broken on current R versions in 64 bit mode. Someone posted a patched repo [1], but I couldn't use this a repo for installing gdata. So this means there is no possibility for using this package on a 64 bit machine for now?
[1] - https://stat.ethz.ch/pipermail/r-help/2010-April/236966.html
Further info: R version 2.12.1
ANSWER: Updating r-base to the current version fixed the problem.
You should be able to just do
after which both
gdata
andgplots
are installed from the Ubuntu repo.You can of course also use whichever package management frontend you prefer.