CODEWITHSUNDEEP
javarrstudiorjavamacos-high-sierra
eipi10
eipi10

Reputation: 93761

rJava load error in RStudio/R after "upgrading" to OSX Yosemite

I recently "upgraded" from OSX Mountain Lion to Yosemite and from R 3.1.3 to 3.2. Immediately after the upgrade, when I opened R or RStudio I got a pop-up message saying that I needed to install Java 6. In addition, loading rJava or any package that depends on rJava (e.g., xlsx) caused RStudio to crash (R also crashed when I tried this by opening R.app directly).

After trying a few fixes found on Stack Overflow and elsewhere (more details below), I am at a point where loading rJava or any package that depends on rJava no longer causes R to crash, but results in the following error:

library(rJava)
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so
  Reason: image not found
Error: package or namespace load failed for ‘rJava’

However, if I invoke R from the command line and then load rJava or any package that depends on rJava, it seems to work (or at least I don't get any error messages).

I've tried a number of different attempted fixes, some of them a few times, and can't quite remember exactly what I did in what order (didn't realize this would be such a morass and wasn't really keeping track), but here's the gist of it:

At some point while trying all of these, I was able to load rJava without crashing R, but instead got the error message posted above. In addition, when I quit RStudio, it would seem to close normally, but then an "RStudio quit unexpectedly" message would pop up, indicating that the program had crashed while trying to close.

I finally decided to install Java for OS X 2014-001 (Java 6), as I seemed to be running out of options. Now, when I opened R or RStudio the "This software needs Java 6" pop-up message no longer appeared. However, I was still getting the .onLoad failed in loadNamespace() for 'rJava' error message posted above.

In reviewing some of the posts I'd already looked at, I noticed another SO answer that I'd missed before, which recommended opening RStudio with the following command line code that gives RStudio the correct path to java:

LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio

That opened an RStudio window and I was also able to load rJava and packages that depend on it without getting an error.

Lastly, I tried running R from the command line (which I hadn't done before). It turns out that on the command line, loading rJava or any package that depends on rJava works and does not throw any errors.

So, I can now get rJava to work if I open RStudio from the command line with the code that gives RStudio the java path (as noted above). However, I'd like to find a way to fix the underlying problem, whatever it may be, so that RStudio can be opened in the usual Mac way, without needing a command line kludge. I'm also concerned that having an old version of Java installed could cause problems down the road.

Does anyone have any ideas about how to diagnose and solve this issue?

Upvotes: 125

Views: 82071

Answers (19)

Peter N. Steinmetz
Peter N. Steinmetz

Reputation: 1252

For Rstudio, the best way to set an environment variable, like JAVA_HOME, upon launch from Spotlight or the dock, in other words, a GUI launch, is to use launchctl. That is described in this answer generally - Setting environment variables on OS X

For my system the following two commands worked for jdk21

launchctl setenv JAVA_HOME /Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home
sudo launchctl config user path JAVA_HOME /Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home

In general, hacking the symlinks as in a lot of other proposed answers here will lead to troubles, often very hard to diagnose, down the road.

Upvotes: 0

Si Kh
Si Kh

Reputation: 1

You can change the reference in R by using the following command:

sudo install_name_tool -change /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server/libjvm.dylib /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so

Upvotes: 0

speleo
speleo

Reputation: 123

I noticed that 'rJava' is pretty strict about JDK version while loading in Rstudio.
In my case (Mac OS. 10.14.6 - Mojave) I had installed jdk-13 which was tested against jdk-11.
I have linked my JDK version to a non-existent directory that was assumed to be valid by Rstudio (JDK 11):

sudo ln -sf /Library/Java/JavaVirtualMachines/jdk-13.jdk/ /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk

and suprisingly it works like a charm...
BTW., there was no problem to run 'rJava' following the previous instructions in native R.

Upvotes: 1

iainhunter
iainhunter

Reputation: 487

I went through all the troubleshooting I could find, then installed jdk-11.0.1_osx-x64_bin.dmg from: Oracle downloads

Everything worked perfectly after that.

Check the version of the library that was not loaded when you run library('rJava') and match it to the java version you need installed.

Upvotes: 1

Endre
Endre

Reputation: 802

On macOS High Sierra (10.13.1) and Java Version 9 you have to use a slightly different JVM path (notice the missing jre folder in the path compared to the instructions for earlier Java versions):

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

You also have to notify R about the JVM:

MY_R_VERSION=$(Rscript -e "cat(with(R.version, sprintf('%s.%s', major, substring(minor, 1, 1))))")
ln -s /usr/local/lib/libjvm.dylib /Library/Frameworks/R.framework/Versions/$MY_R_VERSION/Resources/lib/

Upvotes: 27

Galen
Galen

Reputation: 21

The image not found issue exists with a brand-new install on OSX High Sierra with the latest Java SE 10 JDK.

I was able to solve the path issue with rJava using the fix found on the rJava Github issues page: https://github.com/s-u/rJava/issues/78

R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers

Upvotes: 2

Megatron
Megatron

Reputation: 17079

Run the following on the command line: sudo R CMD javareconf

Several solutions above have mentioned this, but they also suggest that one remove and subsequently re-install the rJava package. I found those additional steps to be unnecessary.

Upvotes: 0

ishonest
ishonest

Reputation: 483

Check the location of libjvm.dylib file.

Try this, in my case this worked:

dyn.load('/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/lib/server/libjvm.dylib')
library(rJava)

Upvotes: 1

Süleyman
Süleyman

Reputation: 11

This line below has solved the same problem I was having with rJava package as some others in this discussion did. I'm sure there are more than one solution to this problem and I sincerely thank them all for their contributions because sometimes one line like the one below saves a lot of time from going to trash! 

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

Upvotes: 0

Jim
Jim

Reputation: 4767

You should be able to use the CRAN rJava, without needing to recompile rJava or do any additional steps by linking the shared library to the R frameworks library directory.

sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /Library/Frameworks/R.framework/Libraries

Upvotes: 7

mokjpn
mokjpn

Reputation: 11

Maybe another simple answer which does not touch your filesystem:

$ install_name_tool -add_rpath /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so

(Substitute jdk1.8.0_131.jdk with your JDK path.)

Upvotes: 1

Gregory R. Warnes
Gregory R. Warnes

Reputation: 565

This is how I configured it working properly on two Macs running Mac OS X El Capitan (10.11.6):

  1. Uninstall 'rJava' by issuing the following commands in a terminal window:

    Rscript -e 'remove.packages("rJava")'
sudo Rscript -e 'remove.packages("rJava")'

  2. Download and install the Java software from Oracle: https://www.java.com/en/download/mac_download.jsp

  3. Add the following lines to /Users/<userid>/.bashrc using your favorite editor:

    # Set JAVA_HOME so rJava package can find it
export JAVA_HOME=$(/usr/libexec/java_home -v 1.8)/jre

  4. Close and restart any terminal, R, and RStudio windows (to pick up the changes to .bashrc).

  5. Run the following command in a Terminal window:

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

  6. Run the following command in a Terminal window: 

    sudo Rscript -e 'install.packages("rJava", repos="http://rforge.net", type="source")'

Upvotes: 6

Sander W. van der Laan
Sander W. van der Laan

Reputation: 790

Following command works:

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

After that, in RStudio, loading rJava works through loading of the "xlsx" package.

library("xlsx")

P.S. #1 Environment: Mac OS X El Capitan 10.11.3+ with RStudio 0.99.491+ and R 3.2.3+. (I've now tested this also on macOS Sierra (10.12) and R.3.3.1.)

P.S. #2 I find that openxlsx is much faster and doesn't rely on Java to work, so I'm now using that package. Hope that helps others.

Upvotes: 16

Nasser
Nasser

Reputation: 11

Here what worked for me on MAC:

  1. in your ~/.profile or ~/.bashrc add this line: %export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home

    1.1 % source .profile (or % source .bashrc)

  2. % sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
  3. remove.packages(rJava)
  4. remove.packages(Rweka)
  5. From the terminal enter this command: %sudo R CMD javareconf
  6. install.packages("rJava", dependencies = TRUE, type = "source")
  7. install.packages("rJava", dependencies = TRUE, type = "source")
  8. Load your library("rJava", "RWeka")

Best of luck.

Upvotes: 1

Hamidreza Ahady Dolatsara
Hamidreza Ahady Dolatsara

Reputation: 291

Here is the easy steps for it:

  1. remove the rJava package: remove.packages(rJava)
  2. close R
  3. install latest Java on you mac
  4. open terminal and type this command: sudo R CMD javareconf

  5. Open R and install rJava with this command:

    install.packages("rJava", dependencies=TRUE, type="source")

Upvotes: 5

Alex Seidlitz
Alex Seidlitz

Reputation: 3736

I had the same problem and went through the same steps as you. The final step to allow starting RStudio through Finder/Spotlight was to link libjvm.dylib to /usr/local/lib:

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

-f flag is added to force overwriting existing file/link

Upvotes: 280

yuan
yuan

Reputation: 391

You can load the libjvm.dylib explictly, by run like

dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
library(rJava)

Upvotes: 29

ignazw
ignazw

Reputation: 129

Here you can download the legacy Java version 6 for El Capitan: https://support.apple.com/kb/DL1572?viewlocale=en_US&locale=en_US After doing so, the rJava package works for me.

Upvotes: 0

lalas
lalas

Reputation: 763

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

Upvotes: 53

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