[R] R INSTALL: problem related to LD_LIBRARY_PATH

[Agustin Lobo]

A solution to the problem has been including 
/lib in the first place in the definition of LD_LIBRARY_PATH
in the R script, but, as BRD says, this might not be
the correct order.

Therefore, I've located the libpthread.so.0 files and...
I do not have a duplicate, I have a triplicate!

> locate libpthread.so.0
/lib/libpthread.so.0
/usr/local/lib/libpthread.so.0
/usr/local/openev/Linux/lib/libpthread.so.0

the newest is in /usr/local/lib, but probably is an older
version that was installed by who knows what software.

Is there any way I could check the versions of these libpthread.so.0
files? 

By now, what I've done has been to rename 
/usr/local/lib/libpthread.so.0 
to
/usr/local/lib/libpthread.so.0_maybeolder

and, now, even without including /lib in LD_LIBRARY_PATH,
R INSTALL works fine.

Thanks for your help!

Dr. Agustin Lobo
Instituto de Ciencias de la Tierra (CSIC)
Lluis Sole Sabaris s/n
08028 Barcelona SPAIN
tel 34 93409 5410
fax 34 93411 0012
alobo at ija.csic.es


On Thu, 18 Jul 2002, Prof Brian D Ripley wrote:

> On 18 Jul 2002, Peter Dalgaard BSA wrote:
> 
> > 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)?
> 
> The next check I would do would be `ldd tar' both with LD_LIBRARY_PATH set
> and unset.  That should tell you what is being found in different places.
> I agree with Peter: /usr/local/lib looks to contain incompatible versions,
> probably older ones.  You may want to set LDFLAGS when building R to
> exclude /usr/local/lib if you can't clean up the incompatibilities.
> 
> It is intentional that /usr/local/lib precedes /usr/lib, and AFAIK the
> standard places (/usr/lib, /lib if different) are searched after those in
> LD_LIBRARY_PATH.  Some Unixes have /usr/local/lib in the standard places,
> but these days most do not.
> 
> -- 
> 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 272860 (secr)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
> 

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