R help - Mar 2007 - setting LD_LIBRARY_PATH

Dear R-help,

I am trying to use a package (not from CRAN) which includes two shared
library (.so) files. The maintainer suggests inserting two lines
in /usr/bin/R,

LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:path-to-package/lib
export LD_LIBRARY_PATH

This works, but I felt more comfortable putting the first line
in .Renviron or $R_HOME/etc/Renviron.site. However this doesn't seem to
work, and I cannot see why it doesn't.

School of Biological Sciences, University of Edinburgh

On Mon, 2007-03-26 at 13:53 +0100, ian white wrote:
> Dear R-help,
> 
> I am trying to use a package (not from CRAN) which includes two shared
> library (.so) files. The maintainer suggests inserting two lines
> in /usr/bin/R,
> 
> LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:path-to-package/lib
> export LD_LIBRARY_PATH
> 
> This works, but I felt more comfortable putting the first line
> in .Renviron or $R_HOME/etc/Renviron.site. However this doesn't seem to
> work, and I cannot see why it doesn't.
Your best bet is to add the paths to the lib files in /etc/ld.so.conf
and then run /sbin/ldconfig to update the environment. Both of these
would be done as root (ie. su or sudo).

That way, you don't have to worry about editing application specific
files every time they get overwritten during an update.

HTH,

Marc Schwartz

On Mon, 26 Mar 2007, ian white wrote:
> Dear R-help,
>
> I am trying to use a package (not from CRAN) which includes two shared
> library (.so) files. The maintainer suggests inserting two lines
> in /usr/bin/R,
>
> LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:path-to-package/lib
> export LD_LIBRARY_PATH
(Not a very good idea, not least because there is another copy at 
R_HOME/bin/R.  Better to modify R_HOME/etc/ldpaths, which deals with 
setting LD_LIBRARY_PATH.)
> This works, but I felt more comfortable putting the first line
> in .Renviron or $R_HOME/etc/Renviron.site. However this doesn't seem to
> work, and I cannot see why it doesn't.
Those files are read by the process.  You don't state your OS, but many 
OSes make sure that the paths for dlopen are cached before the process has 
a chance to change LD_LIBRARY_PATH, for security-related reasons.  Most
OSes are silent about this, but Solaris says

      If other objects were link-edited with pathname  when  path-
      name  was  built,  that is, the pathname has dependencies on
      other objects, those objects will automatically be loaded by
      dlopen(). The directory search path used to find both  path-
      name and the other needed objects may be affected by setting
      the  environment variable LD_LIBRARY_PATH, which is analyzed
      once at process startup, and from a runpath  setting  within
      the object from which the call to dlopen() originated.

As dlopen came from SunOS, it seems the behaviour has been copied by most 
implementations of dlopen.  (AFAICS it is not touched on by POSIX.)

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595