BillPetti BillPetti - 27 days ago 8
Java Question

rJava loading error

Like a bunch of people, I am having trouble getting rJava to load in RStudio -- the same problem also reproduces itself when using the R GUI directly.

Here's the error:

> require(rJava)
Loading required package: rJava
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
Reason: image not found


I have tried a number of things, including reconfiguring from the command line:

sudo R CMD javareconf -n

Java interpreter : /usr/bin/java
Java version : 1.8.0_144
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on macOS

trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -fPIC -Wall -g -O2 -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm


When I check
options("java.home")
it was set to
NULL
, so I set it to the following:

> options("java.home"="/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre")


I also reinstalled Java SE Development Kit 8 and then resintalled
rJava
.

Regardless, I continue to get the same error.

Here is my session info:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] colorspace_1.3-2 scales_0.5.0 compiler_3.4.1 lazyeval_0.2.0
[5] plyr_1.8.4 tools_3.4.1 gtable_0.2.0 tibble_1.3.4
[9] Rcpp_0.12.12 ggplot2_2.2.1 grid_3.4.1 rlang_0.1.2
[13] munsell_0.4.3


Any thoughts would be appreciated.

Answer Source

I had a similar issue. Quickest solution was to manually load the dylib.

dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
require(rJava)

If the above solution works, a long term solution exists by adding this command to the terminal.

sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib

Found this solution here. You will no longer need to manually load the dylib each time.