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Install rJava on RHEL6: even with identical Java path I get: error: One or more JNI types differ from the corresponding native type

I am working on a Linux server RHEL6 and I installed anaconda. I have the following setup

 conda-env version : 4.3.13
 conda-build version : 2.1.4
 python version : 2.7.13.final.0
 rpy2 : 2.8.5

I installed rpy2 to use R in python. But with the version of R installed with conda I have issue to installed "rJava". 

checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package 'rJava'

With my standalone version of R installed on the same machine I don't have issue, so I know I have the correct version installed.

For my 2 different setup with the same R version (standalone R with R with conda), I have the same Java version 

 java -version
openjdk version "1.8.0_121"
OpenJDK Runtime Environment (build 1.8.0_121-b13)
OpenJDK 64-Bit Server VM (build 25.121-b13, mixed mode)

For both setup, the following variables doesn't exit 

R_JAVA_LD_LIBRARY_PATH
JAVA_HOME

defined. The PATH are very similar for standalone:

PATH=/opt/ccda/anaconda2/bin:/opt/opennlp/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

while for R installed with conda I have:

PATH=/opt/ccda/anaconda2/envs/py27CCA/bin:/opt/ccda/anaconda2/bin:/opt/ccda/anaconda2/bin:/opt/opennlp/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

Here the info during the compilation. For the standalone R version:

interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm

While for the R version installed with conda:

interpreter : '/usr/lib/jvm/java/jre/bin/java'
archiver    : '/usr/lib/jvm/java/jre/../bin/jar'
compiler    : '/usr/lib/jvm/java/jre/../bin/javac'
header prep.: '/usr/lib/jvm/java/jre/../bin/javah'
cpp flags   : '-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm'

I tried to get the same path using:

export JAVA_HOME=/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java
export R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
export JAVA_CPPFLAGS="-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux"

by the way:

/usr/bin/java -> /etc/alternatives/java
/etc/alternatives/java -> /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java

but after rerunning:

 R CMD javareconf

and recompiling I get the same error while the path seems the same now:

interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm'

so I don't understand what this means "One or more JNI types differ" and what I should in path and flag to have it working.

R CMD javareconf
Java interpreter : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java
Java version     : 1.8.0_121
Java home path   : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64
Java compiler    : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/../bin/javac
Java headers gen.: /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/../bin/javah
Java archive tool: /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/../bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    : -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux
detected JNI linker flags : -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/opt/ccda/anaconda2/envs/py27CCA/lib/R/include -DNDEBUG -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux -I/opt/ccda/anaconda2/envs/py27CCA/include    -fpic  -I/opt/ccda/anaconda2/envs/py27CCA/include  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/opt/ccda/anaconda2/envs/py27CCA/lib/R/lib -L/opt/ccda/anaconda2/envs/py27CCA/lib -lgfortran -o conftest.so conftest.o -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm -L/opt/ccda/anaconda2/envs/py27CCA/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64
Java library path: /usr/lib/jvm/java/jre/lib/amd64/server
JNI cpp flags    : -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux
JNI linker flags : -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm
Updating Java configuration in /opt/ccda/anaconda2/envs/py27CCA/lib/R
Done.

I am out of idea since I don't really understand the meaning of the error messages. I tried all the suggestion from the various thread related to similar issues.

Edit: using export 

LD_LIBRARY_PATH=$JAVA_HOME/lib/amd64:$JAVA_HOME/lib/amd64/server

solve part of the problem (in such case JAVA_HOME is not needed anymore) but i there is too other issue:

  • -m64 flags is not used in this case (while it is used with the standalone R version)

  • /usr/bin/ld: cannot find -liconv

but the library exist:

/opt/ccda/anaconda2/envs/py27CCA/lib/libiconv.so
/opt/ccda/anaconda2/envs/py27CCA/lib/libiconv.so.2
/opt/ccda/anaconda2/envs/py27CCA/lib/libiconv.so.2.5.1
/opt/ccda/anaconda2/envs/py27CCA/lib/preloadable_libiconv.so

but may be not in the path used so I need to fix this now.

Solution

  • Make sure to reconfigure your R environment with explicit settings pointing to JDK.

    Make sure that JAVA_HOME points to JDK

    export JAVA_HOME=your_JDK_installation

    Then, reconfigure R and pass all the locations explicitly

    sudo R CMD javareconf \
JAVA_HOME=${JAVA_HOME} \
JAVA=${JAVA_HOME/bin/java \
JAVAC=${JAVA_HOME}/bin/javac \
JAVAH=${JAVA_HOME}/bin/javah \
JAR=${JAVA_HOME}/bin/jar \
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/server \
JAVA_CPPFLAGS="-I${JAVA_HOME}/include -I${JAVA_HOME}/include/linux"

    Then, try to configure rJava outside R

    curl https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz -o rJava_0.9-8.tar.gz
tar zxf rJava_0.9-8.tar.gz
cd rJava
./configure

    if it works, you should be able to install it from sources inside R

    install.packages("rJava", type="source")