[R] Problem in library.dynam problems on Linux

[Peter Dalgaard]

"Sinnwell, Jason P." <Sinnwell.Jason at mayo.edu> writes:

> 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 at 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
> ** data
> ** demo
> ** inst
> ** preparing package for lazy loading
> 
> ** help
>  >>> Building/Updating help pages for package 'haplo.stats'
>      Formats: text html latex example 
> ** building package indices ...
> * DONE (haplo.stats)
> 
> ## 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

Hmmmm.. Does "mount -l" show something interesting on the filesystem
containing the .so file? (e.g., option noexec).

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907