Upgrade R on Mac OS 10.5.8

upgrade_R.R

# GET LIST OF INSTALLED PACKAGES
pkgs <- installed.packages(priority='NA')[,'Package']
save(pkgs, file="installed_pkgs.rda")

# Install the most recent version of R:
# Download the most recent version of R from The Comprehensive R Archive Network (CRAN)
# To wipe the old R version

rm -rf /Library/Frameworks/R.framework /Applications/R.app
rm -rf /Library/Receipts/R-*


# Build from source new R version (see this FAQ).
# From inside the decompressed R-?.?.? directory type:
# See Section 2.2 of RMacOSX FAQ for the flag description
./configure --with-blas='-framework vecLib' --enable-BLAS-shlib
make
sudo make install

# Install BioConductor packages using the biocLite.R installation script.
# In an R command window, type the following:
source("http://bioconductor.org/biocLite.R")
chooseBioCmirror()
biocLite()

# If you have other Bioconductor packages missing from the old installation:

load("installed_old.rda")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
for (i in 1:length(missing)) biocLite(missing[i])
Re-install the missing packages from CRAN:
load("installed_old.rda")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
install.packages(missing)
update.packages()

# If you use some package created by Henrik Bengtsson:
# source("http://www.braju.com/R/hbLite.R")
hbLite()