HenrikBengtsson
commented
2 years ago The help suggests this can be done by setting JAVA_HOME before configuring;
$ R CMD javareconf --help
Usage: R CMD javareconf [options]
Detect current Java setup and update the corresponding configuration in R.
Options:
-h, --help print this help message and exit
-v, --version print version info and exit
-n, --dry-run perform Java detection, but don't touch any
configuration files
-e <prog> same as -n but exports all detected variables
and runs <prog>. If -e is the last argument
or <prog> is '' then a shell is used instead
xxx=yyy evaluate the corresponding expression
(e.g. JAVA_HOME=/usr/lib/java)
Environment variables that can be used to influence the detection:
JAVA path to a Java interpreter executable
By default first 'java' command found on the PATH
is taken (unless JAVA_HOME is also specified).
JAVA_HOME home of the Java environment. If not specified,
it will be detected automatically from the Java
interpreter.
JAVAC path to a Java compiler
JAVAH path to a Java header/stub generator
JAR path to a Java archive tool
Values specified when R was configured will be used unless overridden.
The following variables should be used with extreme caution. They
must all match, so use only if you have a very special setup that
javareconf cannot detect automatically:
JAVA_LD_LIBRARY_PATH library path necessary at run-time
JAVA_CPPFLAGS C preprocessor flags necessary to compile JNI programs
JAVA_LIBS libraries (as linker flags) necessary to compile
JNI programs
Report bugs at <https://bugs.R-project.org>.A quick test confirms that this seems to work:
$ JAVA_HOME=/usr/lib/jvm/java-openjdk/jre R CMD javareconf
Java interpreter : /usr/lib/jvm/java-openjdk/jre/bin/java
Java version : 1.8.0_312
Java home path : /usr/lib/jvm/java-openjdk/jre
Java compiler : /usr/lib/jvm/java-openjdk/jre/../bin/javac
Java headers gen.: /usr/lib/jvm/java-openjdk/jre/../bin/javah
Java archive tool: /usr/lib/jvm/java-openjdk/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 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/usr/lib/jvm/java-openjdk/jre/../include -I/usr/lib/jvm/java-openjdk/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c conftest.c -o conftest.o
gcc -shared -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib/jvm/java-openjdk/jre/lib/amd64/server -ljvm -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-openjdk/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 /software/c4/cbi/software/R-4.1.2-gcc8/lib64/R
Done.
Issue
We run
R CMD javareconfwhenever we install R. However, this will only be valid as long as Java is not updated, i.e. the path to Java is not updated.For example, when R 4.1.1 was installed, we had:
but when R 4.1.2, we had:
Solutions
R CMD javareconffor all installed versions once in a whileJAVA_HOMEto point to a slightly more stable version, e.g. instead of/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.312.b07-1.el7_9.x86_64/jrehave it set to/usr/lib/jvm/java-1.8.0-openjdk/jre, which is a symbolic link to the former.