CODEWITHSUNDEEP
javarstdiorjava
Thijs van den Burg
Thijs van den Burg

Reputation: 41

sudo R CMD javareconf solution not working

I am trying to run rJava in RStudio but without success:

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/3.6/Resources/library/rJava/libs/rJava.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
  Reason: image not found

Using the common solution for rJava issues, 'sudo R CMD javareconf' doesn't work and gives me this ouput:

Java interpreter : /usr/bin/java
Java version     : 11.0.6
Java home path   : /Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar

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/jdk-11.0.6.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include/darwin  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c conftest.c -o conftest.o
clang-7: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]
In file included from conftest.c:1:
/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include/jni.h:39:10: fatal error: 
      'stdio.h' file not found
#include <stdio.h>
         ^~~~~~~~~
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

Did anyone come across this error before and knows how to tackle it?

Upvotes: 1

Views: 6994

Answers (2)

Thijs van den Burg
Thijs van den Burg

Reputation: 41

What did the trick in the end was to show Rstudio where to look as identified by user Rmadillo here:

github.com/rstudio/rstudio/issues/2254

Just run this each time before using the rJava package.

Upvotes: 0

Brandon Bertelsen
Brandon Bertelsen

Reputation: 44638

I had a problem like this with a coworker recently after they upgraded to Catalina. My solution was to install the offending version of JDK again. It looks like your system has confusion between 11.0.6 and 11.0.1.

  1. Go to this page: https://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase11-5116896.html

  2. Download and install 11.0.1

  3. sudo R CMD javareconf

  4. sudo Rstudio # elevate privs

  5. install.packages("rJava")

If that doesn't work, try again from step 2, but with 11.0.6 from https://www.oracle.com/technetwork/java/javase/overview/index.html

Upvotes: 1

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