Problem with rJava on Rstudio in Anaconda on Cent OS7

p.urban · June 23, 2022, 1:42pm

Hello,
I have rstudio in jupyter (both R and Jupyter are from anaconda). Unfortunatelly I have problem with rJava package. When I try to load the package I have following error:

Loading required package: rJava
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for ‘rJava’, details:
call: dyn.load(file, DLLpath = DLLpath, …)
error: nie można załadować współdzielonego obiektu ‘/opt/anaconda3/envs/R_kernel/lib/R/library/rJava/libs/rJava.so’:
libjvm.so: nie można otworzyć pliku obiektu dzielonego: Nie ma takiego pliku ani katalogu

I try
sudo R CMD javareconf JAVA_HOME=/opt/anaconda3/envs/R_kernel/lib

but still it doesn’t help.
I check also

Sys.getenv(“JAVA_HOME”) which give me ‘/opt/anaconda3/envs/R_kernel’
Sys.getenv(“LD_LIBRARY_PATH”) or Sys.getenv(“LIBRARY_PATH”) give me empty result (only ").

What can I do also to have rJava working properly ?

sweller · June 23, 2022, 3:01pm

Do you have a JAVA JDK installed? This is required in order for the rJava package to work.
I suggest looking at this discussion for further information:

github.com/rstudio/rstudio

rJava fails to load

opened 04:46PM - 22 Feb 18 UTC

closed 10:19PM - 12 Mar 18 UTC

kevinushey

bug

### System details RStudio Edition : Desktop RStudio Version : v1.2.…331 OS Version : macOS 10.13.3 R Version : 3.4.3 ### Steps to reproduce the problem ```r library(rJava) ``` ### Describe the problem in detail ``` > library(rJava) 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 '/Users/kevin/Library/R/3.4/library/rJava/libs/rJava.so': dlopen(/Users/kevin/Library/R/3.4/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib Referenced from: /Users/kevin/Library/R/3.4/library/rJava/libs/rJava.so Reason: image not found ``` ### Describe the behavior you expected We should be able to load `rJava`. ### Notes It looks like, in v1.2, we're setting the wrong environment variable: ``` > Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH") [1] "/Library/Frameworks/R.framework/Resources/lib:/Users/kevin/lib:/usr/local/lib:/usr/lib::" > Sys.getenv("DYLD_LIBRARY_PATH") [1] "/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/server" ```

p.urban · June 28, 2022, 7:07am

Dear sweller,
Yes I have installed JAVA JDK:

My version:
openjdk version “11.0.15” 2022-04-19 LTS
OpenJDK Runtime Environment 18.9 (build 11.0.15+9-LTS)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.15+9-LTS, mixed mode, sharing)

I also read “rJava fails to load” nad try solutions from there, but unfortunatelly, still it isn’t working.

sweller · June 28, 2022, 3:43pm

Can you run the command:
‘R CMD javareconf’

and paste the output below?

Thanks.