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

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

Answer 2

Had the same issue. Fixed by specifying the path to the Java folder. Briefly, after installing Java you may get a line like this.

update-alternatives: using /usr/lib/jvm/java-9-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode

I specified that path as JAVA_HOME argument when calling javareconf, as follows.

sudo R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-9-openjdk-amd64/bin/jar

Hope this is useful

Answer 3

I solved the problem by editing the java-config file

sudo nano /usr/lib/R/etc/javaconf

set the correct JAVA_HOME in this row:
: ${JAVA_HOME=/usr/local/java/jdk-9.0.1}

Answer 4

I already had Java 11 on ubuntu 18.04 but had to install jdk-11.0.1 following this guide: https://websiteforstudents.com/how-to-install-oracle-java-jdk-11-on-ubuntu-18-04-16-04-18-10/

I then changed JAVA_HOME in javaconf, just like @Spanska Forteva

sudo nano /usr/lib/R/etc/javaconfIn javaconf 

I found that the path to an old version of java was still specified.

## Versions from settings when configure was run
: ${JAVA_HOME=/usr/lib/jvm/default-java}
: ${JAVA_CPPFLAGS=~autodetect~}
: ${JAVA_LD_LIBRARY_PATH=~autodetect~}
: ${JAVA_LIBS=~autodetect~}

I changed the path to JAVA_HOME to my newly installed jdk:

: ${JAVA_HOME=/usr/lib/jvm/jdk-11.0.1}

Then ran the CMD with the path to jni.h specified:

sudo R CMD javareconf /usr/lib/jvm/jdk-11.0.1/include/jni.h

The last bit might not be needed, it should be able to look in that folder anyway, but that is what I did.

Answer 5

Had the same problem and could finally fix it. After a lot of searching, this worked for me (I basically followed the guide here: https://www3.ntu.edu.sg/home/ehchua/programming/howto/JDK_Howto.html ):

• downloading and unpacking the JDK (jdk1.8.0_201) to /usr/java/
• downloading and unpacking the JRE (jre1.8.0_201) to /usr/java/ (not sure if I needed this step but I did it in previous attempts to solve this problem)
• Informing Ubuntu of the new java using appropriate versions

For this I ran:

$ sudo update-alternatives --install "/usr/bin/java" "java" "/usr/java/jdk1.8.0_201/bin/java" 1

$ sudo update-alternatives --install "/usr/bin/javac" "javac" "/usr/java/jdk1.8.0_201/bin/javac" 1

$ sudo update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/java/jdk1.8.0_201/bin/javaws" 1

followed by

$ sudo update-alternatives --set java /usr/java/jdk1.8.0_201/bin/java

$ sudo update-alternatives --set javac /usr/java/jdk1.8.0_201/bin/javac

$ sudo update-alternatives --set javaws /usr/java/jdk1.8.0_201/bin/javaws

Then I could finally see my java in the alternatives in

sudo update-alternatives --config java

where I selected the newly installed java. Then I ran

 sudo R CMD javareconf JAVA_HOME=/usr/java/jdk1.8.0_201/bin/

in which I specified again my java jdk path explicitely. After this finished successfully I was able to install rJava in Rstudio which I needed to install glmulti.

Answer 6

In my case, I had to run

R CMD javareconf

as su , just sudo didn't work.

Answer 7

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.