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 â/usr/local/lib64/R/library/rglâ
The downloaded packages are in
â/tmp/Rtmp5OaGuQ/downloaded_packagesâ
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 ârglâ ...
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 âGLFTFont::GLFTFont(const char*, int, double,
const char*)â:
glgui.cpp:118: warning: converting to âunsigned intâ from âdoubleâ
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 â/usr/local/lib64/R/library/rglâ
The downloaded packages are in
â/tmp/Rtmp5OaGuQ/downloaded_packagesâ
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
[[alternative HTML version deleted]]
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