[R] rgl build warnings and loading error on Linux

Charles C. Berry cberry at tajo.ucsd.edu
Wed Apr 9 21:05:21 CEST 2008

On Wed, 9 Apr 2008, Liviu Andronic wrote:

> Dear R users,
> This is a follow-up of a recent discussion on building rgl on Gentoo
> Linux. Please read bellow.
> On Tue, Mar 18, 2008 at 7:24 PM, Charles C. Berry <cberry at tajo.ucsd.edu> wrote:
>>  Below substitute 'nvidia-drivers' or whatever you use for
>> <your-video-drivers>
>>         emerge -D mesa <your-video-drivers>
>>         revdep-rebuild -X
>>         R
>>         install.packages("rgl")
> I have entirely updated my system using "emerge -tva -DNu world", also
> meaning that I switched to R version 2.6.2. I have rebuilt all
> packages broken by this update using "revdep-rebuild -i -tva -X". Just
> to make sure, afterwards I have also "emerge -tva mesa
> xf86-video-i810". My mesa USE flags look like this:
> localhost liviu # eix mesa
> media-libs/mesa
>     Installed versions:  7.0.2(15:23:17 09/04/08)(video_cards_i810
> -debug -doc -kernel_FreeBSD -motif -nptl -pic [..])
> Building and loading rgl has only switched the error message:
>> dyn.load("/usr/lib/R/library/rgl/libs/rgl.so")
> Error in dyn.load("/usr/lib/R/library/rgl/libs/rgl.so") :
>  unable to load shared library '/usr/lib/R/library/rgl/libs/rgl.so':
>  /usr/lib/R/library/rgl/libs/rgl.so: undefined symbol: glNormal3f
> Previously it was: "undefined symbol: glTexCoordPointer".
> Does this look like an rgl or a Gentoo Linux issue? Would any of the
> disabled mesa USE flags be worth enabling?

A couple of guesses here.


Does 'glxgears' work or give you a similar error message??

Obviously, if it breaks, your system is the issue.


You can get some sense of what is going on by setting

 	export LD_DEBUG_OUTPUT=tmp.debug
 	export LD_DEBUG=all

running something - like glxgears or R (invoking library(rgl))


 	grep glNormal3f tmp.debug.*

For one of my gentoo systems running an ati video card, I get this after 

cberry at coyote ~ $ grep glNormal3f tmp.debug.*
       6846:     symbol=glNormal3f;  lookup in file=glxgears [0]
       6846:     symbol=glNormal3f;  lookup in file=/usr/lib/libglut.so.3 [0]
       6846:     symbol=glNormal3f;  lookup in file=/usr/lib/libGLU.so.1 [0]
       6846:     symbol=glNormal3f;  lookup in file=//usr/lib64/opengl/ati/lib/libGL.so.1 [0]
       6864:      binding file glxgears [0] to 
//usr/lib64/opengl/ati/lib/libGL.so.1 [0]: 
normal symbol `glNormal3f'

and after R <return> library(rgl) I get many more lines, but again 
ending with this long (wrapped) line"

 	6857:  binding file /home/cberry/lib.loc/rgl/libs/rgl.so [0] to
 	//usr/lib64/opengl/ati/lib/libGL.so.1 [0]: normal symbol `glNormal3f'

Maybe this helps:



Have you tried opengl-update?



> Thank you in advance,
> Liviu
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

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