libjvm.so: cannot open shared object file: No such file or directory

问题

Trying to install the rJava package on R, on my 14.10 ubuntu, using this code

if (!require(rJava)) install.packages('rJava')

got few errors related to java including jni problems, after reinstalling the jdk, and tried to run the same code again, got that error

Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/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 ‘/usr/local/lib/R/site-library/rJava’
Warning in install.packages :
  installation of package ‘rJava’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpfFjrp0/downloaded_packages’
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rJava’

looked for solutions, to find just about everyone suggesting (for x64) to execute those commands

export LD_LIBRARY_PATH=/usr/lib/jvm/java-8-oracle/lib/amd64:/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server
sudo R CMD javareconf

but that didn't work, is there anything else I can do? I will provide any needed details

回答1:

I was getting the same error when I was trying to load rJava in RStudio. The following solution worked for me

1) sudo rstudio-server stop
2) export LD_LIBRARY_PATH=/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/jre/lib/amd64/default
3) sudo rstudio-server start

After performing the above steps, I was able to run the following successfuly in RStudio

> library("DBI")
> library("rJava")
> library("RJDBC")

回答2:

To solve this,

Run

sudo R CMD javareconf
Add the following to to /etc/environment. This will then be set every time your machine restarts.

LD_LIBRARY_PATH=/usr/lib/jvm/default-java/jre/lib/amd64/server/

(change to your path)
Run the following:

source /etc/environment
rstudio server restart

回答3:

in case none of the above works, try this and thank me later (generic answer) :)

R CMD javareconf -e
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$JAVA_LD_LIBRARY_PATH

回答4:

I solved a similar issue by running the following command every time I want to open RStudio. Go to the folder which contains the rstudio executable, open up the terminal and type:

LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/jre/lib/server: open -a rstudio

Of course you have to change the path according to your Java version.
If the previous solution does not work, try reading this article: http://allanino.me/blog/programming/installing-some-r-packages/.
If this solution does not work too, the last chance you have is to install rJava compiling it from the source code.

回答5:

If someone is coming here now, Please try the approach below:

Steps:

Find your R location. It will be stored in rsession-ld-library-path in rserver.conf file. Or just by doing which R. The location usually is /usr/lib64/R/lib or /usr/lib64/microsoft-r/3.3/lib64/R/lib
Find the libjvm.so file which is usually in the usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server path depending on which jre you're using. Check in $JAVA_HOME environment.
Create a symlink using ln -s sudo ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib64/microsoft-r/3.3/lib64/R/lib/libjvm.so
Restart R server

回答6:

Check if $JAVA_HOME points to the correct location by

echo $JAVA_HOME

I am using openjdk, however $JAVA_HOME was pointing to some non-existing oracle-java folder.

After fixing $JAVA_HOME run

sudo R CMD javareconf

Check the output. Java headers gen. should point to /usr/bin/javah. For example:

djhurio@Skyforger ~ $ sudo R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version     : 11.0.1
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/lib/jvm/default-java/bin/jar

After this I can install and load rJava package.