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 include jni h  usr lib jvm jdk1 7 0 07 include jni h       In the header file generated by JDK  there is include  lt jni h gt   and currently it complains   fatal error  jni h  No such file or directory    In my Makefile  there is no specification of locations where jni h is  And I am asking if possible to configure certain system parameter to make path of jni h  say   usr lib jvm jdk1 7 0 07 include jni h  to be known when being compiled

User · Answer

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.

User · Answer

Above answers give you a hardcoded path solution   This is bad on so many levels  java version change  OS change  etc    Cleaner solution is to add   JAVA HOME     shell dirname    readlink -f    which java   sed  s jre bin       near the top of your makefile  then add   -I  JAVA HOME  include   To your include flags   I am posting this because I ran into the same problem and spent too much time googling for wrong answers  I am building an app on multiple platforms so the build environment needs to be transportable

User · Answer

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

User · Answer

Installing the OpenJDK Development Kit  JDK  should fix your problem   sudo apt-get install openjdk-X-jdk   This should make you able to compile without problems

User · Answer

You have to tell your compiler where is the include directory  Something like this   gcc -I usr lib jvm jdk1 7 0 07 include   But it depends on your makefile

User · Answer

Use the following code   make -I usr lib jvm jdk  include   where jdk  is the directory name of your jdk installation  e g  jdk1 7 0    And there wouldn t be a system-wide solution since the directory name would be different with different builds of JDK downloaded and installed  If you desire an automated solution  please include all commands in a single script and run the said script in Terminal

User · Answer

It needs both jni h and jni md h files  Try this  gcc -I usr lib jvm jdk1 7 0 07 include     -I usr lib jvm jdk1 7 0 07 include linux filename c   This will include both the broad JNI files and the ones necessary for linux

User · Answer

Setting JAVA INCLUDE DIR to where jni h is located should solve your problem  setting CPPFLAGS did not work for me   Assuming it is  usr lib64 java include   export JAVA INCLUDE DIR  usr lib64 java include

User · Answer

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

User · Answer

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

User · Answer

In case you are on Ubuntu    X means 6 7 8    apt install openjdk-X-jdk

[java] how to make jni.h be found?

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