error: unable to load installed packages just now

Question

When I tried to run the R console in Eclipse, I got this error:

....Please make sure that R package 'rj' (1.1 or compatible) is installed...

So I tried to install it in the R console like this:

install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")

and got this error:

 ** testing if installed package can be loaded
 Error : .onLoad failed in loadNamespace() for 'rj.gd', details:
 call: dyn.load(file, DLLpath = DLLpath, ...)
 error: unable to load shared object '/home/alex/R/x86_64-pc-linux-gnu-library/2.15/rj.gd/libs/rj.gd.so':
 libjvm.so: cannot open shared object file: No such file or directory
 Error: loading failed
 Execution halted
 ERROR: loading failed

and I found that when installing rJava using: install.packages("rJava") gets a similar error:

** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/alex/R/x86_64-pc-linux-gnu-library/2.15/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

When I run sudo R CMD javareconf,I got this output:

Java interpreter : /usr/bin/java
Java version     : 1.7.0
Java home path   : /usr/lib/jvm/java-7-oracle/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
NOTE: Your JVM has a bogus java.library.path system property!
Trying a heuristic via sun.boot.library.path to find jvm library...
Java library path: $(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/lib/amd64/server
JNI linker flags : -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/lib/amd64/server -ljvm
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux

Updating Java configuration in /etc/R
Done.

by the way,my configuration is:

Ubuntu 11.10 64bit
Eclipse 3.7
Oracle-1.7-jdk
R version 2.15.1 

Cockney

Answer 1

I found the solution:

export LD_LIBRARY_PATH=/usr/lib/jvm/java-7-oracle/lib/amd64:/usr/lib/jvm/java-7-oracle/jre/lib/amd64/server

then

sudo R CMD javareconf

Note: The path (java-7-oracle) needs to be updated based on your Java installation.

Cockney

Answer 2

For Linux(Ubuntu) users: If you have oracle-java (7/8) installed. It'll be at this location /usr/lib/jvm and sudo access is required.

Create the file /etc/ld.so.conf.d/java.conf with the following entries:

/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server

(Replace java-8-oracle with java-7-oracle depending on your java version)

Then:

sudo ldconfig

Restart RStudio and then install the rJava package.

OR

Also an alternative method is to export LD_LIBRARY_PATH with the value of Java library path obtained from the command R CMD javareconf -e and run install.packages

Teresetereshkova

Great work! Could you please explain what have you done? It is not clear for me (but I'm very happy because it worked!). Thank you very much! – Lacuna

ldconfig is a command which will configure dynamic linker run-time bindings. It creates and updates the necessary links and cache for use by the run-time linker. – Teresetereshkova

for some reason running ldconfig told me my /usr/lib/libjvm.so was 'empty'. I fixed this by sudo ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so (you should use your own java version) – Hilaryhilbert

@ThomasLuechtefeld : Yeah thats true. You have to modify it as mentioned in the answer "depending on your java version". Thanks for mentioning command in comment. – Teresetereshkova

Worked great for me! Thx! – Magnesia

Answer 3

I got similar issue and was able to resolve it by running

R CMD javareconf -e

Output of the R CMD javareconf -e

Java interpreter : /export/apps/jdk/JDK-1_6_0_27/jre/bin/java
Java version     : 1.6.0_27
Java home path   : /export/apps/jdk/JDK-1_6_0_27
Java compiler    : /export/apps/jdk/JDK-1_6_0_27/bin/javac
Java headers gen.: /export/apps/jdk/JDK-1_6_0_27/bin/javah
Java archive tool: /export/apps/jdk/JDK-1_6_0_27/bin/jar
Java library path: /export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64/server:/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64:/export/apps/jdk/JDK-1_6_0_27/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64/server -L/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64 -L/export/apps/jdk/JDK-1_6_0_27/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I/export/apps/jdk/JDK-1_6_0_27/include -I/export/apps/jdk/JDK-1_6_0_27/include/linux

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

After setting LD_LIBRARY_PATH to the same value as JAVA_LD_LIBRARY_PATH as shown in the output above. I was able to install rj.

export LD_LIBRARY_PATH=/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64/server:/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64:/export/apps/jdk/JDK-1_6_0_27/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib

Run R and then install rj by

install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")

Jezreel

If you using RStudio, you may also have to restart it by service rstudio-server restart – Malawi

Just type export in the command line. After following what @Jezreel has mentioned, you may see that LD_LIBRARY_PATH has got updated – Cotoneaster

Answer 4

I did the following and it worked for me:

export LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
sudo R CMD javareconf

I had to restart R then as well.

Plaudit

I wasted a lot of time, until I found your answer, the key was to run the second command as root. – Spec

Answer 5

Years later, I ended up on this question after searching for an error reported by R after I had unsuccessfully installed a package on that required shifting to Oracle's Java.

All I had to do to fix it was:

$ sudo R CMD javareconf

Pyrogenic

I spoke too soon. The problem arose again and running javareconf again didn't fix it this time. Moreover, running sudo R to install.packages("rJava") didn't fix it either. – Pyrogenic

+1 this command seemed to fix some env parameters but still stuck in trying to install rJava, any ideas for this here? – Complice

Can someone explain in some detail what does R CMD javareconf do? – Sherrilsherrill

Answer 6

or just set the library in R?

I just ran this command in R:

Sys.setenv(JAVA_HOME='/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server')

(replace "/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server" with your Java library path which can be found running "sudo R CMD javareconf")

Might not be the most elegant solution - but it worked for me!

Mcadoo

Answer 7

I did not had the jdk installed which I could fix with sudo apt-get install jdk-* After that i could run the sudo R CMD javareconf which always drew an error message before. Everything was set correctly and no manual tweeks where required, and after that package installation ran smootly in R (restart required).

Dora

Answer 8

When facing missing limjvm.so errors make sure that the correct ldpaths is picked up from the standard configuration in /etc/R versus the one in /usr/lib/R/etc.

Copulation

Answer 9

This fixes the LD_LIBRARY_PATH problem for me (Linux, Debian 7.1.0, tc-shell, R version 3.0.2):

Add this line to .cshrc:

setenv LD_LIBRARY_PATH $JAVA_HOME/jre/lib/amd64:$JAVA_HOME/jre/lib/amd64/server

Adding this command to ~/.login was not enough; the environment variable LD_LIBRARY_PATH was still not known in new xterms: echo $LD_LIBRARY_PATH : LD_LIBRARY_PATH: Undefined variable. (Why??)

Curiously, when starting R as superuser, there was no problem with finding libjvm.so .

Polydipsia

Answer 10

I fixed this by just running R with sudo, and then running install.packages('rJava`).

Silber

Answer 11

None of the above worked for me, the only solution that installed rJava on Linux Ubuntu without any problems was to pass RScript command after installation of the base R:

$ sudo Rscript -e 'install.packages("rJava", repos = "http://cran.r-project.org/")'

Anole