Skip to content

Cannot install rJava on Ubuntu 16.04 #200

@GanjinZero

Description

@GanjinZero

When install rJava by

install.packages('rJava')

It shows:
...
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.

I have tried

R CMD javareconf

It shows:
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.8.0_03-Ubuntu
Java home path : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/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
x86_64-conda_cos6-linux-gnu-cc -I"/home/veritas/anaconda3/envs/r/lib/R/include" -DNDEBUG -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include/linux -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/veritas/anaconda3/envs/r/include -Wl,-rpath-link,/home/veritas/anaconda3/envs/r/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/veritas/anaconda3/envs/r/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c conftest.c -o conftest.o
x86_64-conda_cos6-linux-gnu-cc -shared -L/home/veritas/anaconda3/envs/r/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/home/veritas/anaconda3/envs/r/lib -L/home/veritas/anaconda3/envs/r/lib -Wl,-rpath-link,/home/veritas/anaconda3/envs/r/lib -o conftest.so conftest.o -L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm -L/home/veritas/anaconda3/envs/r/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 /home/veritas/anaconda3/envs/r/lib/R
Done.

So how can I fix my problem? This R is installed by Anaconda3.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions