Getting R and Java 1.8 to work together on OSX

December 29, 2014
by Will
comments 24
Main

Hey Mac OSX users with Java 1.8 installed. Did R just request a Java 1.6 installation and then promptly crash your session?  If so, read on…

The Problem

A few days ago I was attempting to use the mallet package for topic models and I found that typing

> library(mallet)

caused two things to happen:

  1. The operating system launches a dialog asking whether I would like to download Java 1.6
  2. The R session crashes (regardless of what I did about the dialog)

This seems to be a general problem for packages that depends on the rJava package.

I’m running the latest Mac OSX (Yosemite 10.10.1) and have installed the latest Java

$ java -version
java version "1.8.0"
Java(TM) SE Runtime Environment (build 1.8.0-b132)
Java HotSpot(TM) 64-Bit Server VM (build 25.0-b70, mixed mode)

and the latest R

$ R --version
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

But for some reason with R, it’s Java 1.6 (which is no longer even being updated) or bust.

The fix (maybe)

The trail of bug reports starts here, but before you delve into those and bother Simon Urbanek as much as I did, try the following:

  1. Download and install Apple’s Java version 1.6 like you were asked to.
  2. Reconfigure your R installation by typing 
    sudo R CMD javareconf

    in a Terminal window. (Thanks to commenter Benjamin for pointing out that there shouldn’t have been a -n flag in this line)

  3. Trigger a recompile by reinstalling rJava by typing 
    install.packages('rJava', type='source')

Now if you relauch R and load your package it should use your shiny new Java 1.8 and not crash any R sessions.

[Late addition] For this to work you may have to set (or have something else set) some environment variables too. See the comments below for my settings.

 

24 Comments

  1. Rich H says

    Thanks, Will.

    I followed the steps but found sudo R CMD javareconf -n didn’t set 1.6 as the default Java for R.

    You can point R to 1.6’s direction by setting environment variables, like 

    Sys.setenv(JAVA_HOME = '/Library/Java//Home') 
# Java 1.6 will set up the 'Home' link under /Library/Java
Sys.setenv(LD_LIBRARY_PATH = '$LD_LIBRARY_PATH:$JAVA_HOME/lib')

    rJava can be loaded without any trouble after these.

    Cheers,
    Rich

    Reply
  2. Will says

    I was trying to get R to work with 1.8 not with the 1.6. When you followed the instructions did library(rJava) still fail, or did it just give you java 1.8?

    Your comment is reminding me that I have the lines

    export JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home"
export LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/lib/server

    in my ~/.bash_profile.

    Weirdly, launched from the command line

    Sys.getenv('JAVA_HOME')
[1] "/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home"
> Sys.getenv('LD_LIBRARY_PATH')
[1] "/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/lib/server"

    but from inside RStudio

    > Sys.getenv('JAVA_HOME')
[1] ""
> Sys.getenv('LD_LIBRARY_PATH')
[1] ":@JAVA_LD@"

    (still works in RStudio though.)

    Reply
  3. Benjamin says

    If you look closely, you should actually run

    sudo R CMD javareconf

    that is, without the -n flag, which triggers a dry run and prevents any actual configuration happening.

    You may have to fix the file permissions afterwards:

    sudo find /Library/Frameworks/R.framework/Resources/etc -type f -exec chmod 664 "{}" \;
    Reply
    • john doe says

      This worked for me. I am on os x yosemite and rJava problem when I tried to install RDAVIDWebservice. After following this step (and changing the permission as suggested), I was able to install it without problem. Thank you!

      Reply
  4. Dan Nguyen says

    Hello, thanks for writing this post…it’s one of the first that comes up when Googling for “rJava” and Yosemite…for future travelers, you might want to edit your post to reflect Benjamin’s comment:

    If you look closely, you should actually run

    sudo R CMD javareconf
    that is, without the -n flag, which triggers a dry run and prevents any actual configuration happening.

    That -n flag really threw me off for about an hour.

    Reply
  5. Lawrence says

    Sorry, for some reason the code snippets didn’t go through. One more try.

    Hi Will, I went through your instructions step-by-step to no avail. Worse, now rJava will no longer install. Hours later I still have no clue what is going on. I notice Sys.getenv(‘JAVA_HOME’) and Sys.getenv(‘LD_LIBRARY_PATH’) both return “” in R and RStudio. Below is the output from the reconfiguration showing the true ‘JAVA_HOME’ path. Any ideas? Thanks in advance. 

    Lawrences-MacBook-Air:~ LawrenceDeGeest$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.8.0_45
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_45.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 OS X

trying to compile and link a JNI progam 
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_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_45.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_45.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
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
    Reply
    • Will says

      Do you get the same result launching RStudio from the Finder as you do when you launch it from Terminal? That is, by typing: open -a RStudio

      Reply
  6. James says

    Hi, I followed the instruction listed and set the env variables JAVA_HOME and LD_LIBRARY_PATH. However, when running the last step which install.packages(‘rJava’, type=’source’), I got an error that 

    Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/bin/javac" (-1)

    Any suggestion for solution?

    I am using the same configuration of R and Java. Below is the screen shot of error

    *************************************
> install.packages('rJava', type='source')
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-6.tar.gz'
Content type 'application/x-gzip' length 567515 bytes (554 KB)
==================================================
downloaded 554 KB

* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether clang supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
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_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin'
java libs   : '-L/Library/Java/JavaVirtualMachines/jdk1.8.0_45.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... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether headless init is enabled... yes
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/private/var/folders/hm/4tgj4t6170bb9psty_sn1bl02hl9y4/T/Rtmp9hyY8o/R.INSTALL1e1cc9e4b0e/rJava/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
checking build system type... i386-apple-darwin14.4.0
checking host system type... i386-apple-darwin14.4.0
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking whether Java interpreter works... checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rglue.c -o Rglue.o
Rglue.c:838:13: warning: unused function 'new_jrectRef' [-Wunused-function]
static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) {
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c arrayc.c -o arrayc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c callJNI.c -o callJNI.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c callback.c -o callback.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fields.c -o fields.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c jri_glue.c -o jri_glue.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c loader.c -o loader.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c otables.c -o otables.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c rJava.c -o rJava.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c tools.c -o tools.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 rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o tools.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
(cd ../jri && make)
make -C src JRI.jar
/usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/bin/javac" (-1)
make[2]: *** [org/rosuda/JRI/Rengine.class] Error 2
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava’

The downloaded source packages are in
	‘/private/var/folders/hm/4tgj4t6170bb9psty_sn1bl02hl9y4/T/RtmpaLv6KZ/downloaded_packages’
Warning message:
In install.packages("rJava", type = "source") :
  installation of package ‘rJava’ had non-zero exit status
    Reply
  8. Stephen Houser says

    Thank you for getting me started solving this problem on El Capitan (10.11). While I was unable to use exactly what you had here. The following allowed me to install rJava successfully.

    JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home \
    JAVA_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers/ \
    r CMD javareconf

    Reply
  9. Jack Tanner says

    From StackOverflow: On OSX El Capitan 10.11, the user doesn’t have permission to write to /usr/lib. So instead, use the following command:

    sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
    Reply
    • Dusan says

      Tnx! This did the trick for me – I was getting

      unable to load shared object ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so’.

      while loading rJava or any package that depends on it – and this linking solved the problem.

      Thanks!

      Reply
    • Kami says

      Hi, Jack, I gave this a try, but am still getting this error when I use library(rJava):

      I am running RStudio1.0.143, OS X El Cap 10.11.6 and Java 8.

      Any help would be appreciated, I am out of my league here!

      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
      In addition: Warning message:
      package ‘rJava’ was built under R version 3.4.2

      Reply
    • AnKen says

      THANK YOU Jack!! This fixed my problem with loading rJava (after countless hours and hours of trying other methods, including other people’s suggestions for making this symlink). Legend! <3

      Reply
  10. Ken Benoit says

    It all seems to be working on OS X 10.11.3 now. I could install the rJava directly using install.packages("rJava") but also by installing the R-forge latest version using the R CMD INSTALL method.

    However I am going nuts trying to figure out what is happening here when I try to use the coreNLP package.


    R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
    Copyright (C) 2015 The R Foundation for Statistical Computing
    Platform: x86_64-apple-darwin13.4.0 (64-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY.
    You are welcome to redistribute it under certain conditions.
    Type 'license()' or 'licence()' for distribution details.

    Natural language support but running in an English locale

    R is a collaborative project with many contributors.
    Type 'contributors()' for more information and
    'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    > require(rJava)
    Loading required package: rJava
    > require(coreNLP)
    Loading required package: coreNLP
    > initCoreNLP()
    Error in rJava::.jnew("edu.stanford.nlp.pipeline.StanfordCoreNLP", basename(path)) :
    java.lang.UnsupportedClassVersionError: edu/stanford/nlp/pipeline/StanfordCoreNLP : Unsupported major.minor version 52.0
    > sessionInfo()
    R version 3.2.3 (2015-12-10)
    Platform: x86_64-apple-darwin13.4.0 (64-bit)
    Running under: OS X 10.11.3 (El Capitan)

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

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

    other attached packages:
    [1] coreNLP_0.4-1 rJava_0.9-9

    loaded via a namespace (and not attached):
    [1] plotrix_3.6-1 XML_3.98-1.3

    My Java setup:

    KBsMBP15:/ kbenoit$ sudo R CMD javareconf
    Password:
    Java interpreter : /usr/bin/java
    Java version : 1.8.0_74
    Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_74.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 OS X

    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 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_74.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_74.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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_74.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_74.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
    Updating Java configuration in /Library/Frameworks/R.framework/Resources
    Done.

    Reply
  11. Vivek Tiwari says

    Phew that really helped a lot !!! successfully got java 1.8 running with Rstudio was having trouble installing packages like rJava and RWeka otherwise. Thanks a lot !

    Reply

  12. Pingback: Java 1.8 Setup for R and R Studio | An Active Coder

  14. Dennis says

    Hi,

    I’m on MacBook Pro. I’m still getting the following errors. Can anybody help me?

    > library(“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
    > library(“xlsx”)
    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
    Error: package ‘rJava’ could not be loaded

    Reply
    • Will says

      No immediate thoughts on the Java side, but I can suggest using the readxl package instead of xlsx; it doesn’t require Java to run.

      Reply

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