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configuration failed for package ‘rJava’

2 messages · bugreport19621012 at fastmail.fm, Simon Urbanek

#
I am on a Mac Lion.  sessionInfo() is below my signature.

I attempted to install GGally and its dependencies. This led to the following error:

ERROR: configuration failed for package ?rJava?

and the following piece of advice:

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

So I ran "R CMD javareconf" as root. This seemed to work fine:

BEGIN QUOTE

/Volumes/spin/SoftwareDownload/R> whoami
root
/Volumes/spin/SoftwareDownload/R> R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_31
Java home path   :
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path: 
JNI linker flags : -framework JavaVM
JNI cpp flags    : -I$(JAVA_HOME)/include

Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

END QUOTE

I closed and reopened R and again attempted

install.packages("rJava", type="source")

since the binary is not available for Mac. But this returned the same error as before.

What am I doing wrong?

Jacob A. Wegelin
Assistant Professor
Department of Biostatistics
Virginia Commonwealth University
830 E. Main St., Seventh Floor
P. O. Box 980032
Richmond VA 23298-0032
U.S.A.
R version 2.14.2 Patched (2012-02-29 r58604)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] psych_1.1.11 tools_2.14.2
#
On Apr 20, 2012, at 2:59 PM, bugreport19621012 at fastmail.fm wrote:

            
That is not true - it is available on CRAN:

http://cran.r-project.org/bin/macosx/leopard/contrib/2.15/rJava_0.9-3.tgz
http://cran.r-project.org/bin/macosx/leopard/contrib/2.14/rJava_0.9-3.tgz

are you using some incomplete mirror?
Make sure you have Java Developer package installed.
On Lion Apple no longer includes headers in the JVM home, so you have to set JAVA_CPPFLAGS to point inside the JavaVM framework:

JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers R CMD javareconf

That said, I'd still recommend you use the binary.

Cheers,
Simon