I am trying to get the R working environment on my mac. I just upgraded to Mac OS 10.11.1.
From rStudio, install.packages ("rJava") leads to this error:
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/../include/darwin'
java libs : '-L/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether JNI programs can be compiled... yes
checking JNI data types...
configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/local/lib/R/3.2/site-library/rJava’
R CMD javareconf output:
Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/bin/java
Java version : 1.8.0_66
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home
Java compiler : /Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/bin/jar
System Java on OS X
trying to compile and link a JNI program
detected JNI cpp flags : -I/System/Library/Frameworks/JavaVM.framework/Headers
detected JNI linker flags : -framework JavaVM
clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/System/Library/Frameworks/JavaVM.framework/Headers -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c conftest.c -o conftest.o
conftest.c:4:5: warning: 'JNI_CreateJavaVM' is deprecated [-Wdeprecated-declarations]
JNI_CreateJavaVM(0, 0, 0);
^
/System/Library/Frameworks/JavaVM.framework/Headers/jni.h:1937:1: note: 'JNI_CreateJavaVM' has been explicitly marked deprecated here
JNI_CreateJavaVM(JavaVM **pvm, void **penv, void *args);
^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress - L/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/lib - L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/usr/local/lib -o conftest.so conftest.o -framework JavaVM -F/usr/local/Cellar/r/3.2.2_1/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home
Java library path:
JNI cpp flags : -I/System/Library/Frameworks/JavaVM.framework/Headers
JNI linker flags : -framework JavaVM
Updating Java configuration in /usr/local/Cellar/r/3.2.2_1/R.framework/Resources
I have no clue. Any idea to fix this?
thanks
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