Tag Archives: windows 7

How to load the {rJava} package after the error “JAVA_HOME cannot be determined from the Registry”

In case you tried loading a package that depends on the {rJava} package (by Simon Urbanek), you might came across the following error:

Loading required package: rJava
library(rJava)
Error : .onLoad failed in loadNamespace() for ‘rJava’, details:
call: fun(libname, pkgname)
error: JAVA_HOME cannot be determined from the Registry

The error tells us that there is no entry in the Registry that tells R where Java is located. It is most likely that Java was not installed (or that the registry is corrupt).

This error is often resolved by installing a Java version (i.e. 64-bit Java or 32-bit Java) that fits to the type of R version that you are using (i.e. 64-bit R or 32-bit R). This problem can easily effect Windows 7 users, since they might have installed a version of Java that is different than the version of R they are using.

Note that it is necessary to ‘manually download and install’ the 64 bit version of JAVA. By default, the download page gives a 32 bit version .

You can pick the exact version of Java you wish to install from this link. If you might (for some reason) work on both versions of R, you can install both version of Java (Installing the “Java Runtime Environment” is probably good enough for your needs).
(Source: Uwe Ligges)

Other possible solutions is trying to re-install rJava.

If that doesn’t work, you could also manually set the directory of your Java location by setting it before loading the library:

Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre7') # for 64-bit version
Sys.setenv(JAVA_HOME='C:\\Program Files (x86)\\Java\\jre7') # for 32-bit version
library(rJava)

(Source: “nograpes” from Stackoverflow, which also describes the find.java in the rJava:::.onLoad function)

How to upgrade R on windows 7

Background – time to upgrade to R 2.13.0

The news of the new release of R 2.13.0 is out, and the R blogosphere is buzzing. Bloggers posting excitedly about the new R compiler package that brings with it the hope to speed up our R code with up to 4 times improvement and even a JIT compiler for R. So it is time to upgrade, and bloggers are here to help. Some wrote how to upgrade R on Linux and mac OSX (based on posts by Paolo). 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 the R project FAQ page (and also the FAQ on how to install R on windows)

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:

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

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 running the above code in the new R intallation):

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

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.

Continue reading How to upgrade R on windows 7

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

Update: This post has a follow-up for how to upgrade R on windows 7 explaining how to deal with permission issues.

Background – how I heard that there is more then one way to upgrade R

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.

Upgrading strategy – moving to a global R library

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:

  • download new R and install
  • copy the “library” content from the old R to the new R
  • 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 (thus, saving us time…).

For example, under windows XP, you might have R installed on:
C:\Program Files\R\R-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 Files\R\library

So in order to use this strategy, you will need to do the following steps (all of them are performed in an R code provided later in the post)-

  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. (Optional) 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:
Continue reading How to upgrade R on windows XP – another strategy (and the R code to do it)