Re: [R] RGL package installation problem on Centos

From: john herbert <arraystruggles_at_gmail.com>
Date: Wed, 25 May 2011 11:08:00 +0100

Hi.
Thank you for your help. From your suggestions, I tried the following;

R CMD INSTALL --no-test-load rgl_0.92.798.tar.gz

This seemed to load and install (starting R and issuing library(rgl) did not flag any problems
But running the sphere example from rgl, it causes big problems :-)

# R
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.   Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
> library(rgl)
> open3d()

[1] 1
> spheres3d(rnorm(10), rnorm(10), rnorm(10), radius=runif(10),
color=rainbow(10))
X Error of failed request: GLXUnsupportedPrivateRequest   Major opcode of failed request: 143 (GLX)   Minor opcode of failed request: 16 (X_GLXVendorPrivate)   Serial number of failed request: 75
  Current serial number in output stream: 80

Does this error message make anything clearer?

On Mon, May 23, 2011 at 2:43 PM, john herbert <arraystruggles_at_gmail.com>wrote:

> Dear R users,
> I have installed the latest version of R from source on Centos (using
> configure and make install).
> This seemed to work fine, with no Errors reported and R at the command line
> starts R.

>

> However, if I try and installed the package rgl using;
> install.packages("rgl")
> I get the following error;
>

> installing to /usr/local/lib64/R/library/rgl/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
> aborting ...
> sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R'
> --no-save --slave < /tmp/RtmpkvIjOb/file6d97876
> ERROR: loading failed
> * removing ‚/usr/local/lib64/R/library/rgl‚
> The downloaded packages are in
> ‚/tmp/Rtmp5OaGuQ/downloaded_packages‚
> Updating HTML index of packages in '.Library'
> Making packages.html ... done
> Warning message:
> In install.packages("rgl") :
> installation of package 'rgl' had non-zero exit status
> I read that Open GL header files have to be present and are in
> /usr/include/GL.
> I also read about different graphics cards causing problems but I don't
> know how to find this info out.
>

> Any help appreciated and full error message included below.
>

> Thanks,
>

> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>

> #################### full error ######################
> > install.packages("rgl")
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> trying URL '
http://cran.ma.imperial.ac.uk/src/contrib/rgl_0.92.798.tar.gz'
> Content type 'application/x-gzip' length 1677772 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
> * installing *source* package ‚rgl‚ ...
> checking for gcc... gcc -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for gcc... (cached) gcc -std=gnu99
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc -std=gnu99 accepts -g... (cached) yes
> checking for gcc -std=gnu99 option to accept ISO C89... (cached) none
> needed
> checking for libpng-config... yes
> configure: using libpng-config
> configure: using libpng dynamic linkage
> checking for X... libraries , headers
> checking GL/gl.h usability... yes
> checking GL/gl.h presence... yes
> checking for GL/gl.h... yes
> checking GL/glu.h usability... yes
> checking GL/glu.h presence... yes
> checking for GL/glu.h... yes
> checking for glEnd in -lGL... yes
> checking for gluProject in -lGLU... yes
> checking for freetype-config... yes
> configure: using Freetype and FTGL
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Background.cpp -o
> Background.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Color.cpp -o Color.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Disposable.cpp -o
> Disposable.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Light.cpp -o Light.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c LineSet.cpp -o LineSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c LineStripSet.cpp -o
> LineStripSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Material.cpp -o Material.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c PointSet.cpp -o PointSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c PrimitiveSet.cpp -o
> PrimitiveSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c QuadSet.cpp -o QuadSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c RenderContext.cpp -o
> RenderContext.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Shape.cpp -o Shape.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereMesh.cpp -o
> SphereMesh.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c SphereSet.cpp -o SphereSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c SpriteSet.cpp -o SpriteSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c String.cpp -o String.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Surface.cpp -o Surface.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c TextSet.cpp -o TextSet.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Texture.cpp -o Texture.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c Viewpoint.cpp -o Viewpoint.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c api.cpp -o api.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c assert.cpp -o assert.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c callbacks.cpp -o callbacks.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c device.cpp -o device.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c devicemanager.cpp -o
> devicemanager.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c fps.cpp -o fps.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c ftgl.cpp -o ftgl.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c geom.cpp -o geom.o
> gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_PNG_H
> -I/usr/include/libpng12 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2
> -Iext -I/usr/local/include -fpic -g -O2 -c gl2ps.c -o gl2ps.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c glErrors.cpp -o glErrors.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c glgui.cpp -o glgui.o
> glgui.cpp: In constructor ‚GLFTFont::GLFTFont(const char*, int, double,
> const char*)‚:
> glgui.cpp:118: warning: converting to ‚unsigned int‚ from ‚double‚
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c gui.cpp -o gui.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c init.cpp -o init.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c osxgui.cpp -o osxgui.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c osxlib.cpp -o osxlib.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c par3d.cpp -o par3d.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c pixmap.cpp -o pixmap.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c render.cpp -o render.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c rglmath.cpp -o rglmath.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c rglview.cpp -o rglview.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c scene.cpp -o scene.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c select.cpp -o select.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c win32gui.cpp -o win32gui.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c win32lib.cpp -o win32lib.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c x11gui.cpp -o x11gui.o
> g++ -I/usr/local/lib64/R/include -DHAVE_PNG_H -I/usr/include/libpng12
> -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext
> -I/usr/local/include -g -O2 -fpic -g -O2 -c x11lib.cpp -o x11lib.o
> g++ -shared -L/usr/local/lib64 -o rgl.so BBoxDeco.o Background.o Color.o
> Disposable.o Light.o LineSet.o LineStripSet.o Material.o PointSet.o
> PrimitiveSet.o QuadSet.o RenderContext.o Shape.o SphereMesh.o SphereSet.o
> SpriteSet.o String.o Surface.o TextSet.o Texture.o Viewpoint.o api.o
> assert.o callbacks.o device.o devicemanager.o fps.o ftgl.o geom.o gl2ps.o
> glErrors.o glgui.o gui.o init.o osxgui.o osxlib.o par3d.o pixmap.o render.o
> rglmath.o rglview.o scene.o select.o win32gui.o win32lib.o x11gui.o x11lib.o
> -lGLU -lGL -L/usr/lib64 -lpng12 -lX11 -lfreetype
> installing to /usr/local/lib64/R/library/rgl/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
> aborting ...
> sh: line 1: 23732 Segmentation fault '/usr/local/lib64/R/bin/R'
> --no-save --slave < /tmp/RtmpkvIjOb/file6d97876
> ERROR: loading failed
> * removing ‚/usr/local/lib64/R/library/rgl‚
> The downloaded packages are in
> ‚/tmp/Rtmp5OaGuQ/downloaded_packages‚
> Updating HTML index of packages in '.Library'
> Making packages.html ... done
> Warning message:
> In install.packages("rgl") :
> installation of package 'rgl' had non-zero exit status
>

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