rJava not loading in rstudio server

Question

I am using rstudio on ubuntu 12.4 server with r 3.1.1. Installed rJava successfully. But not able to load the rjava library. I am using "rstudio" as a user.

Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/rstudio/R/x86_64-pc-linux-gnu-library/3.1/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
Error: package ‘rJava’ could not be loaded

But I could see the file in the mentioned loacation.

Also when I did in Rstudio...

>Sys.getenv("LD_LIBRARY_PATH")

[1] "/usr/lib/R/lib:/lib:/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@:@JAVA_LD@"

When I did sudo R CMD javareconf I get following

Java interpreter : /usr/bin/java
Java version     : 1.6.0_32
Java home path   : /usr/lib/jvm/java-6-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 progam
detected JNI cpp flags    :
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
compilation terminated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /usr/lib/jvm/java-6-openjdk-amd64/jre
Java library path:
JNI cpp flags    :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.

Can anyone please help to resolve the issue.

Thanks, Amit

cory · Accepted Answer · 2014-09-15 19:28:48Z

2

Try sudo apt-get install r-cran-rjava

answered Sep 15, 2014 at 19:28

cory

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Dutta Over a year ago

Thanks for your reply... I already did that ... it is not helping

Dutta · Accepted Answer · 2014-09-15 19:55:30Z

2

Also you guys should install sudo apt-get install r-cran-rjava and then

R CMD javareconf (as root)

and you are good to go I think...

answered Sep 15, 2014 at 19:55

Dutta

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Hack-R Over a year ago

This was not a solution for me. Success with those commands seems to work for R in the terminal but not RStudio Server.

pengchy · Accepted Answer · 2014-09-15 23:47:13Z

1

install rJava with unroot user

here is my successfully installed experience:

download the latest jdk and uncompressed, then:

export JAVA_HOME=/public/software/jdk1.8.0_11/
export PATH=$PATH:$JAVA_HOME/bin
export CLASSPATH=.:/public/software/jdk1.8.0_11/lib/
~/soft/bin/R CMD INSTALL ~/soft/R/R_package_archive/rJava_0.9-6.tar.gz

done!

answered Sep 15, 2014 at 23:47

pengchy

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Enrique Pérez Herrero · Accepted Answer · 2016-11-03 19:47:12Z

1

This worked for me:

Reinstall rJava package

install.packages("rJava")

answered Nov 3, 2016 at 19:47

Enrique Pérez Herrero

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zeehio · Accepted Answer · 2018-09-17 13:04:45Z

0

I was going crazy because I could make rJava work on a terminal, but not on rstudio-server. In the end this worked for me:

sudo systemctl restart rstudio-server
sudo rstudio-server kill-all

It does kill all rstudio server sessions though.

answered Sep 17, 2018 at 13:04

zeehio

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