How does one configure rJava on OSX to select the right JVM -- .jinit() failing

Question

I installed rJava by calling install.packages("rJava") -- no problems seen

However when I call:

library(rJava)
.jinit()

I get:

JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Error in .jinit() : JNI_GetCreatedJavaVMs returned -1

I'm running OSX:

Darwin MBP-2 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

I have the following Sun JDK's installed:

$ ls /Library/Java/JavaVirtualMachines/
jdk1.7.0_79.jdk jdk1.8.0_65.jdk

Which Java is on my PATH:

$ which java
/Library/Java/JavaVirtualMachines/jdk1.7.0_79.jdk/Contents/Home//bin/Java

I also have JavaHome defined as:

$ echo $JAVA_HOME
/Library/Java/JavaVirtualMachines/jdk1.7.0_79.jdk/Contents/Home/

How did you configure R? Note that rJava will use whichever Java you configured in R - see `R CMD javareconf` and the R documentation. Also avoid setting `JAVA_HOME` by hand - you can only break things by setting it wrong. Finally, make sure you use rJava 0.9-8 or higher since you're on OS X and there are several bugs in Oracle Java there that need work-arounds. — Simon Urbanek, Jan 25 '16 at 18:53
@user1172468 did it finally work for you? I still have the issue — Dinesh, Apr 28 '16 at 17:26
@Dinesh, I fiexed it -- don't remember the fix unfortunately :-( — user1172468, May 10 '16 at 14:08

score 9 · Answer 1 · edited May 23 '17 at 11:54

9

The answer at https://stackoverflow.com/a/36045290/4351357 helped resolve this issue for me on MacOS Sierra Version 10.12. In particular, it provided the code in command 1, below.

The three Terminal commands I used are:

sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
sudo R CMD javareconf
install.packages("rJava",type='source')

edited May 23 '17 at 11:54

Community

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1

answered Oct 19 '16 at 22:13

Jonathan

125
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Worked for me in MacOS Sierra 10.12.1. Tks +1 – Murta Dec 15 '16 at 02:24
This seems to have worked for me too, OS Sierra Version 10.12.3. What does step one actually do? – DaveRGP Mar 22 '17 at 14:57
It seemed to work, in that the Java machine loaded, but since then there have been other issues – DaveRGP Apr 24 '17 at 16:03

score 6 · Answer 2 · edited May 23 '17 at 12:25

6

This solution Cannot load R xlsx package on Mac OS 10.11

sudo R CMD javareconf

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

Worked for me

edited May 23 '17 at 12:25

Community

1
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answered May 12 '16 at 23:06

Tim Child

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score 1 · Answer 3 · answered Jul 12 '16 at 18:09

While attempting to run this test on OSX 10.11.5 (El Capitan) http://www.r-bloggers.com/connecting-r-to-an-oracle-database-with-rjdbc/

I kept getting that same error. I attempted to just do the install as suggested by Tim Child. The thing I noticed was that my version of R Studio (Version 0.99.896 ) kept complaining about installing the 1.6 Legacy Java for OSX.

I installed the legacy Java from the website https://support.apple.com/kb/DL1572?locale=en_US

Then ran a simpler test in R Studio.

library(rJava)

.jinit()
print(.jcall("java/lang/System", "S", "getProperty", "java.version"))

My results:

 > library(rJava)
 > .jinit()
 > print(.jcall("java/lang/System", "S", "getProperty", "java.version"))
[1] "1.6.0_65"

Happy to see that I ran my other test (then that one that started me down this path). I still could not get it to set the most current Java version.

I did one more re-install of the package rJava

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

and things are working ok, using version of Java 1.6 for now, but at least I can get some work done. Hope some comes across a better fix :)

BioinfoNerd · Answer 4 · 2016-07-29T18:36:09.120

I struggled with this issue for a couple of hours. There was a really good thread with some background on rJava here: https://groups.google.com/forum/#!topic/r-sig-mac/eFSDrjphgGs

The following steps ended up working for me:
(1) Upgrade to the latest JDK

(2) Set the following environment variables in my ~/.bash_profile:
export JAVA_HOME=$(/usr/libexec/java_home)
export JAVA_CPPFLAGS=$(/usr/libexec/java_home)/include

(3) Re-install rJava from source as root:
sudo R CMD INSTALL rJava_0.9-8.tar.gz

(4) Re-configure Java as root:
sudo R CMD javareconf

Then I could properly install other libraries that depended on the correct configuration of rJava.

score 0 · Answer 5 · answered Nov 18 '20 at 16:27

0

This helped me:

sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home/jre/lib/server/libjvm.dylib /Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home/lib/libserver.dylib

answered Nov 18 '20 at 16:27

fycth

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How does one configure rJava on OSX to select the right JVM -- .jinit() failing

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