R CMD javareconf not finding jni.h
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
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