I could not get various packages to compile, until I installed
sudo apt-get install libxml2-dev libatlas-base-dev
This solved many build problems, including package XML, but I was still getting the following error when attempting to load library vsn:
> library(vsn)
Loading required package: lattice
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Error in inherits(x, "factor") : attempt to apply non-function
Error : .onLoad failed in 'loadNamespace' for 'vsn'
Error: package/namespace load failed for 'vsn'
Got it to work finally! I replaced the atlas lib mentioned above with libatlas3gf-sse2 (specific for newer processors) and also updated all of my bioconductor packages as follows:
source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)
-----------
references:
https://stat.ethz.ch/pipermail/r-help/2008-December/181390.html
http://ubuntuforums.org/showthread.php?t=717069
