[R] Problem in library.dynam problems on Linux

From: Sinnwell, Jason P. <Sinnwell.Jason_at_mayo.edu>
Date: Fri 25 Aug 2006 - 07:21:11 EST

We have R 2.2.1 installed on a Linux cluster that seems to have problems loading either of our shared object libraries for packages. This seems to be happening on both local and global versions of packages that we install. However, we have only noticed this problem in the past 3 months on this R installation, whereas some users had success before then. It could be that something on our system changed, but I am not an admin so I wouldn't know where to look. Can anyone help with this problem?

## A LOCAL INSTALLATION OF HAPLO.STATS APPEARS SUCCESSFUL [sinnwell@dnode0 rpack]$ R CMD INSTALL -l /home/sinnwell/rdir/tmplib haplo.stats * Installing *source* package 'haplo.stats' ...
** libs

make: `haplo.stats.so' is up to date.
** R

## TRY AND LOAD THE LOCALLY INSTALLED LIBRARY, YET THE SYSTEM COMMAND SHOWS THE .so FILE IS THERE

R> library(haplo.stats, lib.loc="/home/sinnwell/rdir/tmplib/") Error in dyn.load(x, as.logical(local), as.logical(now)) :

        unable to load shared library '/home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so':   /home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so: cannot open shared object file: No such file or directory Error in library(haplo.stats, lib.loc = "/home/sinnwell/rdir/tmplib/") :

        .First.lib failed for 'haplo.stats' R> system('ls -al /home/sinnwell/rdir/tmplib/haplo.stats/libs') total 88

drwxr-xr-x   2 sinnwell sinnwell  4096 Aug 24 15:14 .
drwxr-xr-x  13 sinnwell sinnwell  4096 Aug 24 15:14 ..
-rwxr-xr-x   1 sinnwell sinnwell 61566 Aug 24 15:14 haplo.stats.so
R> version
         _                
platform i686-pc-linux-gnu
arch     i686             
os       linux-gnu        
system   i686, linux-gnu  
status                    
major    2                
minor    2.1              
year     2005             
month    12               
day      20               
svn rev  36812            

language R

Also, the .First.lib for haplo.stats looks like this:

.First.lib <- function(lib, pkg) {

   library.dynam("haplo.stats", pkg, lib) }

Thanks for you suggestions,
Jason Sinnwell


 Jason Sinnwell             
 Mayo Clinic, Rochester     
 Division of Biostatistics  
 ph:  507.284.3270          

 fax: 507.284.9542

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