9

After upgrading from Ubuntu 16 to 18.4, I am not able to install the rJava package in R.

I read other posts like this, but I didn't solve my issue. if I run install.packages("rJava") on R, Results is this:

Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/salvatore/R/x86_64-pc-linux-gnu-library/3.5/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/salvatore/R/x86_64-pc-linux-gnu-library/3.5/rJava’

when I run sudo R CMD javareconf:

Java interpreter : /usr/lib/jvm/java-8-oracle/jre/bin/java
Java version     : 1.8.0_181
Java home path   : /usr/lib/jvm/java-8-oracle
Java compiler    : /usr/lib/jvm/java-8-oracle/bin/javac
Java headers gen.: /usr/lib/jvm/java-8-oracle/bin/javah
Java archive tool: /usr/lib/jvm/java-8-oracle/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)/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/java-8-oracle/include -I/usr/lib/jvm/java-8-oracle/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-oNcpyf/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-8-oracle
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

Any help would be welcome.

Salvo Comunque
  • 105

4 Answers4

6

On my clean installation of Ubuntu 18.04 LTS I did the following

sudo apt-get install r-base-dev default-jdk

(so I have R 3.4 from official repository).

Then in R or in RStudio 1.1.456 session:

install.packages('rJava')

and it ended with

* DONE (rJava)

Note: I'm using default OpenJDK 11 from Bionic repository -

$ update-java-alternatives -l
java-1.11.0-openjdk-amd64      1101      /usr/lib/jvm/java-1.11.0-openjdk-amd64
N0rbert
  • 103,263
6

In my case, I also had to use: sudo R CMD javareconf, to make it work.

ThunderBird
  • 1,963
  • 13
  • 22
  • 31
Niels
  • 76
2

Running Ubuntu 18.04 64-bit, R 3.60, and RStudio 1.2.1335.

In my case, I had to do the following:

  1. (Temporarily) disable Oracle Java 8 by renaming jdk.csh and jdk.sh to jdk.csh.old and jdk.sh.old (in etc/profile.d).

  2. Install java-11-openjdk.

  3. Add JAVA_HOME="/usr/lib/jvm/java-11-openjdk" to /etc/environment.

  4. Run "sudo update-alternatives --config java" and select "/usr/lib/jvm/java-11-openjdk-amd64.bin/java".

  5. Run "sudo R CMD javareconf".

  6. Logout/login.

  7. Open RStudio and install rJava.

rJava then installed with no errors.

Hypersphere
  • 129
  • 4
0

For me, I create a bash file using some of code of the previous answers. This is the bash file:

# 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

export JAVA_HOME=/opt/apps/jdk
export JAVA_LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/amd64/server
export JAVA_CPPFLAGS="-I$JAVA_HOME/include -I$JAVA_HOME/include/linux "
export JAVA_LIBS="-L$JAVA_HOME/jre/lib/amd64/server -ljvm" 

env|grep JAVA

R CMD javareconf
Luis Garreta
  • 1