On Apr 20, 2012, at 2:59 PM, [email protected] wrote: > > 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.
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? > But this returned the same error as before. > > What am I doing wrong? > 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 > 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. > >> sessionInfo() > 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 > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
