how to make jni.h be found?

Question

In Ubuntu 12.04, I have jdk7 from sun/oracle installed. When locate jni.h, it prints multiple locations

/usr/lib/jvm/java-6-openjdk-amd64/inclu         


        

Answer 1

For me it was a simple matter of being sure to include the JDK installation (I'd only had the JRE). My R CMD javareconf output was looking like:

Java interpreter : /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
Java version     : 1.8.0_191
Java home path   : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java compiler    : not present
Java headers gen.:
Java archive tool:

trying to compile and link a JNI program
detected JNI cpp flags    :
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java library path:
JNI cpp flags    :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.

And indeed there was no include file in my $JAVA_HOME. Very simple remedy:

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

(note that this is specifically intended to install the openJDK and not the one from Oracle)

Afterwards all is well:

Java interpreter : /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
Java version     : 1.8.0_191
Java home path   : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java compiler    : /usr/lib/jvm/java-8-openjdk-amd64/jre/../bin/javac
Java headers gen.: /usr/lib/jvm/java-8-openjdk-amd64/jre/../bin/javah
Java archive tool: /usr/lib/jvm/java-8-openjdk-amd64/jre/../bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include/linux     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

Answer 2

I usually define my JAVA_HOME variable like so:

export JAVA_HOME=/usr/lib/jvm/java/

Therein are the necessary include files. I sometimes add the below to my .barshrc when I compile a lot of things that need it.

Answer 3

In case you are on Ubuntu:

#X means 6,7,8...
apt install openjdk-X-jdk

Answer 4

None of the posted solutions worked for me.

I had to vi into my Makefile and edit the path so that the path to the include folder and the OS subsystem (in my case, -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux) was correct. This allowed me to run make and make install without issues.

Answer 5

I don't know if this applies in this case, but sometimes the file got deleted for unknown reasons, copying it again into the respective folder should resolve the problem.