[R] R INSTALL: problem related to LD_LIBRARY_PATH

[Peter Dalgaard BSA]

Agustin Lobo <alobo at paleo.ija.csic.es> writes:

> Well, I've found that the line in INSTALL
> that gives the problem is
> gzip -dc "${1}" | (cd "${tmpdir}" && tar -xf -)
> ("tar: /usr/local/lib/libpthread.so.0: version `GLIBC_2.2' not found
> (required by /lib/librt.so.1)")
> 
> If I run that command from the shell, i.e.,
> 
> gzip -dc KernSmooth_2.22-7.tar.gz | (cd /tmp/R.INSTALL.2186 && tar -xf -)
> 
> it runs ok.
> 
> I've compared my environment setings within R INSTALL and outside R
> INSTALL and found that a major difference is that 
> in my shell I do not have LD_LIBRARY_PATH set to anything, while R
> sets LD_LIBRARY_PATH to:
> 
> LD_LIBRARY_PATH=/usr/local/lib/R/bin:/usr/local/lib:/usr/local/lib:/usr/local/lib:
> /usr/lib/gcc-lib/i486-suse-linux/2.95.3:/usr/i486-suse-linux/lib:/usr/X11/lib:/usr/lib:/usr/lib:
> /usr/X11R6/lib:/usr/lib:/usr/lib:/usr/lib
> 
> If I include 
> unset LD_LIBRARY_PATH 
> 
> in INSTALL, R INSTALL works.
> 
> Therefore, it's clear that I have a problem with the LD_LIBRARY_PATH env.
> var. that is set by R.
> 
> Does anyone know what can be wrong with my R LD_LIBRARY_PATH ?

This is really Kurt's domain, but the absence of /lib in the path
looks suspicious. You could try inserting it manually (and get rid of
the duplicates). Also, are you sure you want to pick up libpthread
from /usr/local (could this be an old version)?

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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