I am having a similar issue but I am logged in as Administrator (the only user on my computer). The result is that when I try to install a package like this:
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
biocLite("ShortRead") BioC_mirror: http://bioconductor.org
When the package(s) downloads, I get this:
The downloaded binary packages are in /var/folders/nb/09qklh116w558w77gcpn7zhm0000gp/T//RtmpX1P4OU/downloaded_packages
Warning message: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival'
A check of the library gives me this:
Error in library(Shortread) : there is no package called ‘Shortread’
I am using Bioconductor 3.0 in R 3.1.2 GUI 1.65 Mavericks build running in RStudio 0.98.1102.
Any suggestions would be most welcome!