Upgrade to Feisty broke R package loading capabilities

After upgrading from Edgy eft to Feisty Fawn on my laptop and my desktop
independently (these systems are not synchronized), I started receiving errors when trying to load packages
in the R statistical language environment.

Tried running synaptic package manager, R not reported as broken.
Reinstalled the R base system using synaptic.
Completely removed R and all dependent packages then reinstalled the lot.

I also have the following in my .bashrc file for notifying R of the
location of my packages

R_LIBS=~/.lib/
export R_LIBS

> library(Biobase, lib.loc="~/.lib")
Loading required package: tools
Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) :
        in 'Biobase' methods for export not found: [, [[, $, abstract, addVarMetadataEntry, aggenv, aggfun, annotation, coerce, combine, content, convertVarLabels, description, dims, eList, experimentData, expinfo, exprs, exprs2excel, featureNames, geneNames, getExpData, getUnits, getVarMetadata, hybridizations, initfun, iter, length, locked, normControls, ncol, notes, otherInfo, pData, phenoData, preproc, sampleNames, samples, se.exprs, show, split, storageMode, update2MIAME, varLabels, varMetadata, reporterInfo, annotation<-, description<-, eList<-, experimentData<-, exprs<-, featureNames<-, geneNames<-, notes<-, pData<-, phenoData<-, sampleNames<-, varLabels<-, varMetadata<-, assayData<-, reporterInfo<-, se.exprs<-, storageMode<-, write.exprs, as.data.frame.exprSet, dim, assayData, reporterNames, pubMedIds, pubMedIds<-, initialize
Error: package/namespace load failed for 'Biobase'
> traceback()
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)),
       call. = FALSE, domain = NA)
1: library(Biobase, lib.loc = "~/.lib")
>

Another example

> loadNamespace(package="limma")
Error in loadNamespace(package = "limma") :
        in 'limma' methods specified for export, but none defined: show
> traceback()
2: stop(gettextf("in '%s' methods specified for export, but none defined: %s",
       package, paste(expMethods, collapse = ", ")), domain = NA)
1: loadNamespace(package = "limma")
>

Strangely, I can still load SOME packages
eg statmod.

> search()
[1] ".GlobalEnv" "package:stats" "package:graphics"
[4] "package:grDevices" "package:utils" "package:datasets"
[7] "package:methods" "Autoloads" "package:base"
> library(statmod)
> search()
 [1] ".GlobalEnv" "package:statmod" "package:stats"
 [4] "package:graphics" "package:grDevices" "package:utils"
 [7] "package:datasets" "package:methods" "Autoloads"
[10] "package:base"
>

I know this is as much an R help forum question as an Ubuntu question, but any help would be appreciated.

Cheers

Tom