Making rApache load rJava

June 13, 2012

(This article was first published on Odd Hypothesis, and kindly contributed to R-bloggers)

Here at work I’ve been in the business of developing webapps using R as the backend computational framework.  The list of parts to get this running is pretty lightweight, just:

I’m not going to cover how to set these things up here, there is pretty good documentation around the web and on rApache’s site.  Instead, I’m going to talk about a hair pulling setback I encountered early on.


R scripts run behind rApache cannot load rJava without throwing an HTTP 500 error


Specifically, if you look at the error_log file you see something like the following:

Loading required package: rJava
Error : .onLoad failed in loadNamespace() for ‘rJava’, details:
  call: dyn.load(file, DLLpath = DLLpath, …)
  error: unable to load shared object ‘/usr/local/lib64/R/library/rJava/libs/’: cannot open shared object file: No such file or directory
Error: package ‘rJava’ could not be loaded

Running the same R script from

  • a user login session … no problem.
  • behind PHP (via a system() call) … no problem.

Suffice it to say, this had me really really stumped.  Stumped enough to give up temporarily and settle with calling R code that needed rJava via a PHP-to-shell intermediary.  Of course, that got confusing and unscalable quite quickly, forcing me to find a real solution.

So I started digging and found one unanswered post on the rApache Google Group relating to this problem dating back to 2010 (it’s answered now, with my solution as detailed below).  Not helpful.

More digging produced this post, which pointed me in the direction of the LD_LIBRARY_PATH variable, which apparently you shouldn’t mess with directly unless you want a lot of R pain.

Using the following one line test script:

cat(Sys.getenv()[‘LD_LIBRARY_PATH’], ‘\n’)

I quickly determined that rApache was NOT setting this variable, or anything else defined in


before creating an instance of R.

From the folks that work on RStudio, R needs this variable set before starting R for rJava to initialize correctly – i.e. be able to find

So how do you do this in an Apache process?  I know that using a SetEnv directive in httpd.conf is a dead end.  Thankfully, folks at the Ubuntu forums found a way.


Here’s my modification of the Ubuntu forum solution.

Step 1:
Add a file to:




with just a single line:


which happens to be the direct parent path to on my server.

Step 2:
As root, run:


Step 3:
Restart Apache


After all this rigamarole it appears that I can load packages that depend on rJava from within rApache – i.e.  lines like


no longer complain and I’m not getting any more HTTP 500 errors as a result, which makes me happy for the moment.  How long this happiness lasts depends.  R scripts within rApache still don’t see an LD_LIBRARY_PATH variable, but at least the parent Apache process knows where to find

To leave a comment for the author, please follow the link and comment on their blog: Odd Hypothesis. offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.


Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)