Re: [R] rgl build warnings and loading error on Linux

From: Charles C. Berry <cberry_at_tajo.ucsd.edu>
Date: Wed, 09 Apr 2008 12:05:21 -0700

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))

then

 	grep glNormal3f tmp.debug.*

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

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:

http://www.linux.org/docs/ldp/howto/Program-Library-HOWTO/shared-libraries.html

---

Have you tried opengl-update?


HTH,

Chuck



>
> Thank you in advance,
> Liviu
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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 ______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Received on Wed 09 Apr 2008 - 19:09:15 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 09 Apr 2008 - 19:30:27 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive