rApache not reading ldpaths

[jeroen]

Running Ubuntu 16.04 with r-cran-java. Loading rJavain the console works fine, but when loading it inside rApache on the same machine gives:

 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/lib/R/site-library/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory

I think /usr/bin/R sources /usr/lib/R/etc/ldpaths which sets LD_LIBRARY_PATH to the path where libjvm.so lives (i.e. ${JAVA_HOME}/jre/lib/amd64/server) before starting the repl.

What would be the most natural way to do this accomplish the same thing in rapache? The problem is that ldpaths is a shell script which sets an environment variable, so calling this via system() does not work because that sets the LD_LIBRARY_PATH only in the system() subprocess.

[s-u]

Ideally, you should use R CMD to setup the environment, so if let's say if you are running

sh startme.sh

then for Java to work you'd run

R CMD sh startme.sh

instead. Alternatively, whatever you're starting can use R CMD sh -c set to get all the necessary R environment variables.

[jeroen]

We should probably do this before our call to Rf_initEmbeddedR at https://github.com/jeffreyhorner/rapache/blob/master/mod_R.c#L973-L1010

[jeffreyhorner]

What's happening is that the linux service script(unity, init, system, etc.) ought to be amended to update the LD_LIBRARY_PATH (And other side effects of R CMD sh) prior to starting the server. Typically, the service script runs in a minimal environment.

I've known about this issue for a long time, but I'm not sure the best way to fix it.

[jeffreyhorner]

Here's a version of the init script that ultimately get's placed into /etc/init.d/apache2 on ubuntu:

http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/vivid/apache2/vivid/view/head:/debian/apache2.2-common.apache2.init

It references a file that's typically located at /etc/apache2/envvars

Maybe we need an additional config tool that outputs the side effects of R CMD sh and update that!

[jeroen]

Modifying global apache configs is difficult to setup and sound dangerous, especially if people are running other (non-R) websites on the same apache box.

Can we just output the variables we need to a file and run base::readRenviron() to source them? Or is there more to it than setting environment variables?

[jeffreyhorner]

You'll see in the /etc/init.d/apache2 script that the environment has to be set up at the invocation of apachectl. The facility for setting up that enviroment seems to be defined by the content of /etc/apache2/envvars, which would affect all the sites including non-R sites.

[jeffreyhorner]

Something like this would populate the R environment to /etc/apache2/envvars:

#!/bin/bash
# save this to /tmp/exportenv.sh
for i in `env`; do
   echo export $i
done

Then run

/usr/bin/env -i R CMD sh /tmp/exportenv.sh >> /etc/apache2/envvars

But this doesn't solve it completely as there are some env vars that contain spaces like:

LN_S=ln -s

So that shows up as two lines in the /etc/apache2/envvars like this:

export LN_S=ln
export -s

And then there are other strange env vars like:

export _=/usr/bin/env

[jeroen]

I really don't like hardcoding that stuff in /etc/apache2/envvars. It becomes a mess when you upgrade R and then need to re-do this stuff. I guess I need to hack a runtime solution.

[jeroen]

What I don't understand is what R CMD sh does beyond the things in /usr/lib/R/etc/ldpaths ?

[alexvpickering]

Just confirming that I was able to solve the same issue by adding export LD_LIBRARY_PATH=/usr/lib/jvm/default-java/jre/lib/amd64/server (directory with libjvm.so - can differ) to /etc/apache2/envvars.

Another issue arose however from the same rJava-dependent function call (mailR::send.mail) which works fine as user www-data from the terminal. No response is received and the apache2 logs show:

[Sat Jan 20 08:03:11.177569 2018] [:error] [pid 3967:tid 140146487838464] [client 192.168.1.67:41784] rApache Notice! *** stack smashing detected ***: /usr/sbin/apache2 terminated [Sat Jan 20 08:03:11.932544 2018] [core:notice] [pid 24498:tid 140146758621056] AH00051: child pid 3967 exit signal Aborted (6), possible coredump in /etc/apache2

[jeroen]

@alexvpickering I have never seen this stack smashing detected error. If you can reproduce it you can open a separate issue.