How to upgrade R on windows – another strategy (and the R code to do it)

Update: In the end of the post I added simple step by step instruction on how to move to the new system. I STRONGLY suggest using the code only after you read the entire post.

Background

If you didn’t hear it by now – R 2.11.0 is out with a bunch of new features.

After Andrew Gelman recently lamented the lack of an easy upgrade process for R, a Stackoverflow thread (by JD Long) invited R users to share their strategies for easily upgrading R.

Strategy

In that thread, Dirk Eddelbuettel suggested another idea for upgrading R. His idea is of using a folder for R’s packages which is outside the standard directory tree of the installation (a different strategy then the one offered on the R FAQ).

The idea of this upgrading strategy is to save us steps in upgrading. So when you wish to upgrade R, instead of doing the following three steps:
1) download new R and install
2) copy the “library” content from the old R to the new R
3) upgrade all of the packages (in the library folder) to the new version of R.
You could instead just have steps 1 and 3, and skip step 2.

For example, under windows, you might have R installed on:
C:Program FilesRR-2.11.0
But (in this alternative model for upgrading) you will have your packages library on a “global library folder” (global in the sense of independent of a specific R version):
C:Program FilesRlibrary

So in order to use this strategy, you will need to do the following steps –

1. In the OLD R installation (in the first time you move to the new system of managing the upgrade):
   1. Create a new global library folder (if it doesn’t exist)
   2. Copy to the new “global library folder” all of your packages from the old R installation
   3. After you move to this system – the steps 1 and 2 would not need to be repeated. (hence the advantage)
2. In the NEW R installation:
   1. Create a new global library folder (if it doesn’t exist – in case this is your first R installation)
   2. Premenantly point to the Global library folder whenever R starts
   3. Delete from the “Global library folder” all the packages that already exist in the local library folder of the new R install (no need to have doubles)
   4. Update all packages. (notice that you picked a mirror where the packages are up-to-date, you sometimes need to choose another mirror)

Thanks to help from Dirk, David Winsemius and Uwe Ligges, I was able to write the following R code to perform all the tasks I described

So first you will need to run the following code:

Code for upgrading R

Old.R.RunMe <- function (global.library.folder = "C:/Program Files/R/library", quit.R = NULL)
{
# It will:
# 1. Create a new global library folder (if it doesn't exist)
# 2. Copy to the new "global library folder" all of your packages from the old R installation
 
 
	# checking that the global lib folder exists - and if not -> create it.
	if(!file.exists(global.library.folder))
	{	# If global lib folder doesn't exist - create it.
		dir.create(global.library.folder)
		print(paste("The path:" , global.library.folder, "Didn't exist - and was now created."))
	} else {
		print(paste("The path:" , global.library.folder, "already exist. (no need to create it)"))
	}
 
 
	print("-----------------------")
	print("I am now copying packages from old library folder to:")
	print(global.library.folder)
	print("-----------------------")
	flush.console()  # refresh the console so that the user will see the massage
 
	# Copy packages from current lib folder to the global lib folder
	list.of.dirs.in.lib <- paste( paste(R.home(), "\library\", sep = ""),
							list.files(paste(R.home(), "\library\", sep = "")),
							sep = "")
	folders.copied <- file.copy(from = list.of.dirs.in.lib, 	# copy folders
								to = global.library.folder,
								overwrite = TRUE,
								recursive =TRUE)		
 
	print("Success.")
	print(paste("We finished copying all of your packages (" , sum(folders.copied), "packages ) to the new library folder at:"))
	print(global.library.folder)
	print("-----------------------")
 
	# To quite R ?
	if(is.null(quit.R))
	{
		print("Can I close R?  y(es)/n(o)  (WARNING: your enviornment will *NOT* be saved)")
		answer <- readLines(n=1)
	} else {
		answer <- quit.R
	}
	if(tolower(answer)[1] == "y") quit(save = "no")
}
 
 
 
 
 
 
 
New.R.RunMe <- function (global.library.folder = "C:/Program Files/R/library", 
							quit.R = F,
							del.packages.that.exist.in.home.lib = T,
							update.all.packages = T)
{
# It will:
# 1. Create a new global library folder (if it doesn't exist)
# 2. Premenantly point to the Global library folder
# 3. Make sure that in the current session - R points to the "Global library folder"
# 4. Delete from the "Global library folder" all the packages that already exist in the local library folder of the new R install
# 5. Update all packages.
 
 
	# checking that the global lib folder exists - and if not -> create it.
	if(!file.exists(global.library.folder))
	{	# If global lib folder doesn't exist - create it.
		dir.create(global.library.folder)
		print(paste("The path to the Global library (" , global.library.folder, ") Didn't exist - and was now created."))
	} else {
		print(paste("The path to the Global library (" , global.library.folder, ") already exist. (NO need to create it)"))
	}
	flush.console()  # refresh the console so that the user will see the massage
 
 
	# Based on:
	# help(Startup)
	# checking if "Renviron.site" exists - and if not -> create it.
	Renviron.site.loc <- paste(R.home(), "\etc\Renviron.site", sep = "")
	if(!file.exists(Renviron.site.loc))
	{	# If "Renviron.site" doesn't exist (which it shouldn't be) - create it and add the global lib line to it.
		cat(paste("R_LIBS=",global.library.folder, sep = "") ,
				file = Renviron.site.loc)
		print(paste("The file:" , Renviron.site.loc, "Didn't exist - we created it and added your 'Global library link' (",global.library.folder,") to it."))
	} else {
		print(paste("The file:" , Renviron.site.loc, "existed!  make sure you add the following line by yourself:"))
		print(paste("R_LIBS=",global.library.folder, sep = "") )
		print(paste("To the file:",Renviron.site.loc))
	}
 
	# Setting the global lib for this session also
	.libPaths(global.library.folder)	# This makes sure you don't need to restart R so that the new Global lib settings will take effect in this session also
	# This line could have also been added to:
	# /etc/Rprofile.site
	# and it would do the same thing as adding "Renviron.site" did
	print("Your library paths are: ")
	print(.libPaths())	
	flush.console()  # refresh the console so that the user will see the massage
 
 
	if(del.packages.that.exist.in.home.lib)
	{
		print("We will now delete package from your Global library folder that already exist in the local-install library folder")
		flush.console()  # refresh the console so that the user will see the massage
		package.to.del.from.global.lib <- 		paste( paste(global.library.folder, "/", sep = ""),
													list.files(paste(R.home(), "\library\", sep = "")),
													sep = "")			
		number.of.packages.we.will.delete <- sum(list.files(paste(global.library.folder, "/", sep = "")) %in% list.files(paste(R.home(), "\library\", sep = "")))
		deleted.packages <- unlink(package.to.del.from.global.lib , recursive = TRUE)	# delete all the packages from the "original" library folder (no need for double folders)
		print(paste(number.of.packages.we.will.delete,"Packages where deleted."))
	}
 
	if(update.all.packages)
	{
		# Based on:
		# http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
		print("We will now update all your packges")
		flush.console()  # refresh the console so that the user will see the massage
 
		update.packages(checkBuilt=TRUE, ask=FALSE)
	}
 
	# To quite R ?
	if(quit.R) quit(save = "no")
}

Then you will want to run, on your old R installation, this:

Old.R.RunMe()

And on your new R installation, this:

New.R.RunMe()

Update – simple two line code to run when upgrading R

(Please do not try the following code before reading this post and understanding what it does)

In order to move your R upgrade to the new (simpler) system, do the following:
1) Download and install the new version of R
2) Open your old R and run –

source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
Old.R.RunMe()

(wait until it finishes)
3) Open your new R and run

source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
New.R.RunMe()

(wait until it finishes)

Once you do this, then from now on, whenever you will upgrade to a new R, all you will need to do only the following TWO (instead of three) steps:
1) Download and install the new version of R
2) Open your new R and run

source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
New.R.RunMe()

(wait until it finishes)

And that’s it.

If you have any more suggestions on how to make this code better – please do share.
(After some measure of review will be given to this code, I would upload it to a file for easy running through “source(…)” )