Re: [R] Error with rgl loading in BATCH mode

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue, 11 Dec 2007 10:24:25 +0000 (GMT)

I don't think this is anything to do with BATCH mode: the machine you are running R BATCH on does not have GLU installed. rgl *will* load on a system without an X server running.

KernSmooth does *not* require the rgl *package*, so you are (twice) blaming an innocent party. You have doctored the output to give a false impression, and should be blaming some other package that loads all of KernSmooth, mvtnorm and rgl (perhaps package ks).

On Tue, 11 Dec 2007, Umberto Amato wrote:

> Dear all,
> I'm trying to run a script that requires KernSmooth in BATCH mode but I get
> an error while loading rgl library that is needed by KernSmooth. Actually I
> have to run several batch files through a queue of a cluster, so I wouldn't
> need graphics at all.
> I installed the latest releases of R (2.6.1) and rgl on my CentOS 4.2 Linux
> (clone of Red Hat EL) endowed with Rocks 4.2.1 suite for clusters.
> If I run the R script from a ssh session on my PC equipped with X Server (I
> use Xming), everithing goes smoothly, rgl package is loaded correctly and
> the script runs smoothly. However when run in batch mode (that is through a
> submission to the cluster batch queue, where X Server evidently is not
> available) I have the following error when loading rgl:

You truncated the output here without indication to give a misleading context.

> Loading required package: KernSmooth
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Loading required package: mvtnorm
> Loading required package: rgl
> Error in dyn.load(file, ...) :
> unable to load shared library '/opt/R-2.6.1/library/rgl/libs/rgl.so':
> libGLU.so.1: cannot open shared object file: No such file or directory
> Error : .onLoad failed in 'loadNamespace' for 'rgl'
> Error: package 'rgl' could not be loaded
> Execution halted
>
> I am issuing the follwing R bach command:
> R CMD BATCH --vanilla --slave KS_S1.R
>
> This kind of error appeared 3 years ago on this same list in a different
> contest: no final solution was given, but apparently newer versions of rgl
> fixed the problem. Does anyone have a clue about how to manage this problem
> for BATCH mode? Alternatively, since rgl shouldn't be needed at all becasue
> running in BATCH mode, does someone know how to prevent KernSmooth loading
> rgl?
>
> Thanks so much
>
> Umberto Amato
> Istituto per le Applicazioni del Calcolo 'Mauro Picone' CNR
> Sede di Napoli
> Via Pietro Castellino 111
> I-80131 Napoli, Italy
>
> Tel. +39 0816132377
> Fax +39 0816132597
> E-mail: u.amato_at_iac.cnr.it
>
> ______________________________________________
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>

-- 
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 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Tue 11 Dec 2007 - 10:32:19 GMT

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