Updating an R installation
update.packages() function can be used to download and install the most recent version of a contributed package.
The installed.packages() function is used to save a list of packages to a location outside of the R director y tree, and then the list is used with the install.packages() function to download and install the latest contributed packages into the new R installation.
Here are the steps:
1 If you have a customized Rprofile.site file (see appendix B), save a copy outside of R.
2 Launch your current version of R and issue the following statements
oldip <- installed.packages()[,1]
save(oldip, file="path/installedPackages.Rdata")
where path is a director y outside of R.
3 Download and install the newer version of R.
4 If you saved a customized version of the Rprofile.site file in step 1, copy it into the new installation.
5 Launch the new version of R, and issue the following statements
load("path/installedPackages.Rdata")
newip <- installed.packages()[,1]
for(i in setdiff(oldip, newip))
install.packages(i)
eg:
oldip <- installed.packages()[,1]
save(oldip, file="D:\\app\\rlib\\installedPackages.Rdata")
# down load from http://cran.r-project.org/
load("D:\\app\\rlib\\installedPackages.Rdata")
newip <- installed.packages()[,1]
for(i in setdiff(oldip, newip))
install.packages(i)
where path is the location specified in step 2.
6 Delete the old installation (optional).
source(http://bioconductor.org/biocLite.R)
biocLite("globaltest")
biocLite("Biobase")
