R CMD javareconf not finding jni.h

Question

I'm trying to install rJava in a docker container based on debian (jessie) with Anaconda.

As root, I did

$ apt-get update  && apt-get install -y --no-install-recommends \   default-jdk default-jre libicu-dev  

Then

$ R CMD javareconf  Java interpreter : /usr/lib/jvm/jdk1.8.0_121/jre/bin/java Java version     : 1.8.0_121 Java home path   : /usr/lib/jvm/jdk1.8.0_121 Java compiler    : /usr/lib/jvm/jdk1.8.0_121/bin/javac Java headers gen.: /usr/lib/jvm/jdk1.8.0_121/bin/javah Java archive tool: /usr/lib/jvm/jdk1.8.0_121/bin/jar  trying to compile and link a JNI program  detected JNI cpp flags    : -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm gcc -std=gnu99 -I/opt/conda/lib/R/include -DNDEBUG -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/opt/conda/include    -fpic  -I/opt/conda/include  -c conftest.c -o conftest.o conftest.c:1:17: fatal error: jni.h: No such file or directory  #include <jni.h>                  ^ compilation terminated. /opt/conda/lib/R/etc/Makeconf:133: recipe for target 'conftest.o' failed make: *** [conftest.o] Error 1 Unable to compile a JNI program   JAVA_HOME        : /usr/lib/jvm/jdk1.8.0_121 Java library path:  JNI cpp flags    :  JNI linker flags :  Updating Java configuration in /opt/conda/lib/R Done. 

But jni.h is right in the JDK:

# find /usr/lib/jvm/jdk1.8.0_121/ -name jni.h /usr/lib/jvm/jdk1.8.0_121/include/jni.h 

It just doesn't look like javareconf is finding it. And, if I look at all the variables I could set with javareconf, like JAVA_HOME, I don't see the ability to set JNI cpp flags, which would need the right includes.

I've seen various posts around the Internet of this problem, but no solutions.

Answer 1

I'm not sure if an answer has been confirmed here, but I would point everyone to this article by Andrew Collier.

What he recommends:

(1) Updating all repositories

sudo apt update -y 

(2) Being sure JRE and JDK 8 are installed

sudo apt install -y openjdk-8-jdk openjdk-8-jre 

(3) Then, as many users have said already, pointing R to java with an explicit path to JDK 8

sudo R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/ 

The specific Java package does not matter too much as long as it has all the necessary compiled contents within the /include directory.

user@laptop:~$ ls /usr/lib/jvm/java-8-openjdk-amd64/include/ classfile_constants.h  jdwpTransport.h  jvmticmlr.h  linux jawt.h                 jni.h            jvmti.h 

For more on this, I would recommend how to make jni.h be found? for going about locating/compiling this directory correctly.

Answer 2

R is looking at different location:

detected JNI cpp flags    : -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux 

I experienced similar problem, but everything is fine after installing jdk:

sudo apt-get install openjdk-8-jdk