[ESS] ESS and LD_LIBRARY_PATH

[Marc Schwartz]

On Wed, 2006-10-18 at 15:14 -0500, Erik Iverson wrote:
> Hello -
> 
> Apologies if this is something simple; I've tried everything I can think 
> of!  I am on RHLE 4, R version 2.3.1, ESS 5.3.0.
> 
> I have downloaded an R package called Cairo (not on CRAN).  The package
> Cairo needs to have the Cairo library (www.cairographics.org) installed
> to function.  Because I'm doing this at work, and do not have root 
> access, I have installed the Cairo graphics library in ~/lib, as is my 
> standard practice (I'm *not* talking about the R package Cairo here, I'm 
> talking about the Cairo graphics library).  I then have LD_LIBRARY_PATH 
> set to ~/lib in my .cshrc file.  I then installed the R Cairo package 
> with R CMD INSTALL.
> 
> Now, from my shell in KDE, I can start R and load the Cairo package.
>  > library(Cairo)
>  >
> This is great!
> 
> However, I try from ESS 5.3.0 under XEmacs, also using R version 2.3.1
>  > library(Cairo)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> 	unable to load shared library '/u/iverson/R.tools/lib/Cairo/libs/Cairo.so':
>    libcairo.so.2: cannot open shared object file: No such file or directory
> Error in library(Cairo) : .First.lib failed for 'Cairo'
> 
> It can't find libcairo.so.2, which is in ~/lib.
> 
> I can't figure out why when starting R from my shell, I can load Cairo, 
> but not when using R under ESS.
> 
> I check the LD_LIBRARY_PATH environment variable from the R session 
> started in my shell:
>  > Sys.getenv("LD_LIBRARY_PATH")
> LD_LIBRARY_PATH
> "/s/pkg/linux/R/2.2.1/lib/R/lib: ... :/u/iverson/lib"
> I omit some paths here, but note it has ~/lib.
> 
> I now check LD_LIBRARY_PATH from the R session in ESS:
>  > Sys.getenv("LD_LIBRARY_PATH")
>  
> 
>                                                 LD_LIBRARY_PATH
> "/s/pkg/linux/R/2.2.1/lib/R/lib: ..."
> This returned the same string as above, *except* for ~/lib!
> I thought, no problem, I'll just append ~/lib to LD_LIBRARY_PATH using 
> Sys.putenv() in R under ESS.
> 
> It looked like it appended ~/lib correctly according to Sys.getenv(), 
> but library(Cairo) still wouldn't work, same error as above to my 
> surprise.  Setting LD_LIBRARY_PATH in my .Renviron file didn't change 
> the error message either.
> 
> Any thoughts on this?  I was able to get the Cairo package loaded in an 
> R session started from my Xemacs shell also, so my naive guess is that 
> this isn't an Xemacs issue.
> 
> Thanks for any help or suggestions anyone can offer, I've tried all I 
> can think of!
> Erik Iverson

Erik,

This behavior sounds similar to what I experienced earlier in the year
on FC4 when using the RODBC package with the Oracle ODBC Linux Driver:

http://tolstoy.newcastle.edu.au/R/devel/06/03/4447.html

All had worked well up until some change, which I have yet to identify.
I can only presume that there was some system update that altered the
behavior of the user environment. Tracking through the various login
shell scripts, I could not identify differences in the login shell
versus the interactive shell relative to environment settings.

That behavioral change resulted in LD_LIBRARY_PATH being "stepped on" as
you seem to be experiencing.

After several go rounds with possible solutions, I finally did the
following:

1. As root (ie. su), edit /etc/ld.so.conf and add the path to the file.
For example, in my case, it now contains:

$ cat /etc/ld.so.conf
include ld.so.conf.d/*.conf
/usr/lib/oracle/10.2.0.1/client/lib


2. Then, also as root, run:

/sbin/ldconfig

That will update the LD_LIBRARY_PATH with the change(s) you make in the
file.


Once you do that, you should be good to go.

Note that setting LD_LIBRARY_PATH in this fashion, it will not show up
in the bash shell:

$ $LD_LIBRARY_PATH
$ 

Nor within R:

> Sys.getenv("LD_LIBRARY_PATH")

LD_LIBRARY_PATH
"/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre/lib/i386"


However, it does work.  :-)

HTH,

Marc Schwartz