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s-u avatar s-u commented on August 28, 2024

Please see https://github.com/s-u/rJava - scroll down to the Troubleshooting section for Linux. config.log is next to configure in your build directory. If you don't have write permission to the R installation, you can use -e to start a shell with the configured variables set as environment variables.

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jessijessi avatar jessijessi commented on August 28, 2024

Thank you for the suggestions, I have launched "R CMD javareconf -e" and I found this error:

Java interpreter : /usr/bin/java
Java version     : 1.8.0_282
Java home path   : /share/apps/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/openjdk-11.0.2-fu22jzad3otvgxftqlynpxiqt4emtqiq
Java compiler    : /share/apps/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/openjdk-11.0.2-fu22jzad3otvgxftqlynpxiqt4emtqiq/bin/javac
Java headers gen.:
Java archive tool: /share/apps/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/openjdk-11.0.2-fu22jzad3otvgxftqlynpxiqt4emtqiq/bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    :
detected JNI linker flags :
using C compiler: ‘gcc (GCC) 10.2.0’
gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG   -I///share/apps/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/openjdk-11.0.2-fu22jzad3otvgxftqlynpxiqt4emtqiq/include    -fpic  -g -O2  -c conftest.c -o conftest.o
In file included from conftest.c:1:
///share/apps/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/openjdk-11.0.2-fu22jzad3otvgxftqlynpxiqt4emtqiq/include/jni.h:45:10: fatal error: jni_md.h: No such file or directory
   45 | #include "jni_md.h"
      |          ^~~~~~~~~~
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:191: conftest.o] Error 1
Unable to compile a JNI program

The following Java variables have been exported:
JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
Running: /bin/bash

Do you know how can I solve the issue?

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