Background – time to upgrade to R 2.13.0
The news of the new release of is out, and the is buzzing. Bloggers about the new R compiler package that brings with it the hope to speed up our R code with and even a JIT compiler for R牵手常德棋牌官方下载. So it is time to upgrade, and bloggers are here to help. Some wrote how to upgrade R on and (based on ). And it is now my turn, with suggestions on how to upgrade R on windows 7.
Upgrading R on windows – the two strategies
The classic description of how to upgrade R can be found in (and also the )
There are basically two strategies for R upgrading on windows. The first is to install a new R version and copy paste all the packages to the new R installation folder. The second is to have a global R package folder, each time synced to the most current R installation (thus saving us the time of copying the package library each we upgrade R).
I described the second strategy in detail in a post I wrote a year ago titled: “How to upgrade R on windows XP – another strategy” which explains how to upgrade R using the simple two-liner code:
p.s: If this is the first time you are upgrading R using this method, then first run the following two lines on your old R installation (before 牵手常德棋牌官方下载running the above code in the new R intallation):
The above code should be enough. However, there are some common pitfalls you might encounter when upgrading R on windows 7, bellow I outline the ones I know about, and how they can be solved.
upgrade R on windows 7 – the issues
Ideally, we would simply run the code above and go on doing our statistics.
But for windows 7 users there are several common issues when upgrading to a new version of R (compared to when upgrading R in windows XP).
Issue 1 – folder location when upgrading from 32 bit to a 64 bit R version
The first issue is that the folder in which R is installed might be different if you have installed the 32 bit version on win 7 and now started using the 64 bit version, in which case you will need to run the following commands (notice the use of the “global.library.folder” paramater), I here assume you’ve installed R on D:R.
source("http://oi02img.icu/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt") # in the old R Old.R.RunMe(global.library.folder = "D:\R\library") # in the new R New.R.RunMe(global.library.folder = "D:\R\library")
Issue 2 – folder permissions
The second issue is problem with permissions. The default permissions of a regular user on windows 7 won’t let you create folders and files under the “c:program files” directory (and, if I am not mistaken, for some other directories as well). The result of this problem is that running the upgrade code I provided above, will often result with an error similar to this one:
 “The path to the Global library ( d:\R\library\ ) Didn’t exist – and was now created.”
Error in file(file, ifelse(append, “a”, “w”)) :
cannot open the connection
In addition: Warning messages:
1: In dir.create(global.library.folder) : ‘library’ already exists
2: In dir.create(global.library.folder) :
cannot create dir ‘library’, reason ‘No error’
3: In file(file, ifelse(append, “a”, “w”)) :
牵手常德棋牌官方下载 cannot open file ‘D:/R/R-213~1.0etcRenviron.site’: Permission denied
There are three solutions to this, the best one (I believe) is number 2 (maybe also combined with number 3):
Solution 1牵手常德棋牌官方下载: (which is easier to do, but I like less these days) is to run R with administrator privileges by following these steps:():
- Right click on the R shortcut
- Click on Properties
- Select the Compatibility tab
- At the bottom click “Change settings for all users”
- Again at the bottom select to “Run this program as an administrator”
The downside of this method is that every time you will start up R, you will get a nagging pop-up window asking you if you want to grant admin privileges to R, not a fun thing to deal with on a day to day basis. Also, some other programs might have a hard time “doing things to” R, if it is run as administrator while they are not.
Solution 2 (editors pick)牵手常德棋牌官方下载: Change (grant) your own user permissions to the relevant R folders (for example: “D:R”). In order to do this you can simply follow the steps described .
Solution 3: Install R in something like “D:R” instead of “C:program filesR” so to avoid permission problems.
Issue 3 – antivirus file access restrictions
One of the possible error massage you might come across when trying to upgrade (or install) your R packages is the following:
package ‘***’ successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation ‘C:Program FilesRR-2.13.0libraryfile70669f***’ to ‘C:Program FilesRR-2.13.0library***’
After (too much) pocking around, I suspect that the source of this error was two things. The first is my antivirus software. It appears that the “real time file system protection” was blocking R from copying the files between folders once they were downloaded. The second is the permission issues discussed above.
The solution is to add the R directory path to the exception list in the antivirus software + fixing the user permission as discussed above in “solution 2”.
p.s: I suspect that the reason this error happens with only some of the packages and not all of them is because of the *.dll the error prune packages have in them. But I am not sure of that.
Update牵手常德棋牌官方下载: After disabling the antivirus while updating, I still found that I need to use the update function twice until it is able to properly install the package. Another potential reason for this problem was by Sean O’Riordain suggesting that:
This is just an FYI documenting a conflict between R and
Google-Desktop. The solution was to click on the Google-Desktop icon
in the systray and click on “Pause Indexing”. I also temporarily
suspended anti-virus scanning before successfully
牵手常德棋牌官方下载 install.packages(“VR”) many times without getting an error message.
I was getting an intermittant failure when I tried to install a
package or update a package under Win-XP-Pro-sp2.
There is 5gb of free space on the drive and I’m an admistrator on this
machine and most times (but not every time) I tried to
upgrade.packages() or install.packages() I got the following error
message “unable to move temporary installation” message.
It appears to be a file-locking issue with the Google-Desktop search –
ie. during the few seconds that install.packages() creates a fileNNNN
directory tree, google-desktop starts reading these files and then
prevents this tree from being moved to its correct place under
I wish R will have an “automatic update” mechanism one day, but until then I hope the above code will make your R upgrading experience a tiny bit easier…