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john herbert

2011-May-23 13:43 UTC

[R] RGL package installation problem on Centos

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]]

Duncan Murdoch

2011-May-23 18:37 UTC

head link

[R] RGL package installation problem on Centos

On 11-05-23 9:43 AM, john herbert 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;
The error sounds like one reported back in November on Ubuntu.  As in 
that case, I don't know what the cause is, but the debugging advice I 
gave then might help you to determine it.  Here's a copy of a recent 
message on the topic.

Duncan Murdoch
> FYI, I have downloaded the latest version of rgl from CRAN and successfully
installed and used it on my 64-bit Ubuntu (10.10) build of R-2.13.0.  I
don't know what has changed (exactly) for it to work now versus when we
communicated six-months ago, but thanks for maintaining such an excellent
resource for the R community.
>
>
> cheers...
>
> Brandon
> On 23 November 2010 18:31, Duncan Murdoch <murdoch.duncan at
gmail.com> wrote:
>
>     On 23/11/2010 1:02 PM, Brandon Whitcher wrote:
>
>         Apologies for emailing you directly, but I wanted to ask for your
help as
>         quickly as possible.  I have R 2.12.0 installed on my Ubuntu 64-bit
10.04
>         laptop.  I have installed rgl (from CRAN) and it does
compile/install.
>         However, when it is loaded into R, I get a segmentation fault (end
of
>         message).  The configuration doesn't throw up anything obvious
to me... but
>         I'm not such an expert.  Any suggestions would be great.
>
>
>     I'd try building and running it in 32 bit mode.   I don't have
a 64 bit Ubuntu machine to run on.  I have run it on 32 bit Ubuntu (on a Mac
laptop).
>
>     You could also try installing it in 64 bit mode without the automatic
test load (use --no-test-load on the INSTALL command line), and see if it
segfaults in a regular situation; my guess is that it will.  But in this case
you can run it under a debugger, and maybe get some more information about
what's going wrong.
>
>     Duncan Murdoch
>
>
>
>         * installing *source* package 'rgl' ...
>         checking for gcc... gcc -m64 -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 -m64 -std=gnu99 accepts -g... yes
>         checking for gcc -m64 -std=gnu99 option to accept ISO C89... none
needed
>         checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
>         checking for gcc... (cached) gcc -m64 -std=gnu99
>         checking whether we are using the GNU C compiler... (cached) yes
>         checking whether gcc -m64 -std=gnu99 accepts -g... (cached) yes
>         checking for gcc -m64 -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
>
>         cheers...
>
>         Brandon
>
>
>         ** testing if installed package can be loaded
>
>          *** caught segfault ***
>         address 0x4, cause 'memory not mapped'
>
>         Traceback:
>          1: .Call(rgl_init, initValue)
>          2: rgl.init(initValue)
>          3: fun(...)
>          4: doTryCatch(return(expr), name, parentenv, handler)
>          5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>          6: tryCatchList(expr, classes, parentenv, handlers)
>          7: tryCatch(fun(...), error = identity)
>          8: runHook(".onLoad", package, env, package.lib,
package)
>          9: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
>         keep.source)
>         10: doTryCatch(return(expr), name, parentenv, handler)
>         11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>         12: tryCatchList(expr, classes, parentenv, handlers)
>         13: tryCatch(expr, error = function(e) {    call<-
conditionCall(e)    if
>         (!is.null(call)) {        if (identical(call[[1L]],
>         quote(doTryCatch)))             call<- sys.call(-4L)       
dcall<-
>         deparse(call)[1L]        prefix<- paste("Error in",
dcall, ": ")
>         LONG<- 75L        msg<- conditionMessage(e)        sm<-
strsplit(msg,
>         "\n")[[1L]]        w<- 14L + nchar(dcall, type =
"w") + nchar(sm[1L], type
>         = "w")        if (is.na(w))             w<- 14L +
nchar(dcall, type = "b")
>         + nchar(sm[1L],                 type = "b")        if
(w>  LONG)
>         prefix<- paste(prefix, "\n  ", sep = "")   
}    else prefix<- "Error :
>         "    msg<- paste(prefix, conditionMessage(e),
"\n", sep = "")
>         .Internal(seterrmessage(msg[1L]))    if (!silent&&
>         identical(getOption("show.error.messages"),        
TRUE)) {        cat(msg,
>         file = stderr())        .Internal(printDeferredWarnings())    }
>         invisible(structure(msg, class = "try-error"))})
>         14: try({    ns<- loadNamespace(package, c(which.lib.loc,
lib.loc),
>         keep.source = keep.source)    dataPath<-
file.path(which.lib.loc, package,
>         "data")    env<- attachNamespace(ns, pos = pos,
dataPath >         dataPath,         deps)})
>         15: library(pkg_name, lib.loc = lib, character.only = TRUE,
logical.return >         TRUE)
>         16: withCallingHandlers(expr, packageStartupMessage = function(c)
>         invokeRestart("muffleMessage"))
>         17: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
>         character.only = TRUE, logical.return = TRUE))
>         18: doTryCatch(return(expr), name, parentenv, handler)
>         19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>         20: tryCatchList(expr, classes, parentenv, handlers)
>         21: tryCatch(expr, error = function(e) {    call<-
conditionCall(e)    if
>         (!is.null(call)) {        if (identical(call[[1L]],
>         quote(doTryCatch)))             call<- sys.call(-4L)       
dcall<-
>         deparse(call)[1L]        prefix<- paste("Error in",
dcall, ": ")
>         LONG<- 75L        msg<- conditionMessage(e)        sm<-
strsplit(msg,
>         "\n")[[1L]]        w<- 14L + nchar(dcall, type =
"w") + nchar(sm[1L], type
>         = "w")        if (is.na(w))             w<- 14L +
nchar(dcall, type = "b")
>         + nchar(sm[1L],                 type = "b")        if
(w>  LONG)
>         prefix<- paste(prefix, "\n  ", sep = "")   
}    else prefix<- "Error :
>         "    msg<- paste(prefix, conditionMessage(e),
"\n", sep = "")
>         .Internal(seterrmessage(msg[1L]))    if (!silent&&
>         identical(getOption("show.error.messages"),        
TRUE)) {        cat(msg,
>         file = stderr())        .Internal(printDeferredWarnings())    }
>         invisible(structure(msg, class = "try-error"))})
>         22: try(suppressPackageStartupMessages(library(pkg_name, lib.loc =
lib,
>         character.only = TRUE, logical.return = TRUE)))
>         23: do_install_source(pkg_name, instdir, pkg, desc)
>         24: do_install(pkg)
>         25: tools:::.install_packages()
>         aborting ...
>         Segmentation fault
>
>         The downloaded packages are in
>             '/tmp/RtmpFC4Uwq/downloaded_packages'
>         Warning message:
>         In install.packages("rgl") :
>           installation of package 'rgl' had non-zero exit status
>
>
>
Continuing with John's post...
>
> 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
>
> 	[[alternative HTML version deleted]]
>
>
>
>
> ______________________________________________
> 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.

Mike Marchywka

2011-May-23 19:38 UTC

head link

[R] RGL package installation problem on Centos

----------------------------------------
Date: Mon, 23 May 2011 14:43:59 +0100
From: arraystruggles at gmail.com
To: r-help at r-project.org
Subject: [R] RGL package installation problem on Centos


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'

I just did install of R from source built with various
options to support Rapache and tried to load rgl.
First it complained no display so I went back
to bash and did "export DISPLAY=:0" and it seemed
to load ok. Do you have X running and a display set?
Not sure what happens if you have R without X11 support
for example. 

I probably installed with dep=TRUE and only cygwin I do recall
some issues with missing dependencies.? Try setting dependencies to
true and see if that helps.











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

        [[alternative HTML version deleted]]


______________________________________________
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.

john herbert

2011-May-25 10:08 UTC

head link

[R] RGL package installation problem on Centos

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
 *** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
 1: .C(rgl_spheres, success = as.integer(FALSE), idata,
as.numeric(vertex),     as.numeric(radius), NAOK = TRUE)
 2: rgl.spheres(x = c(0.506515614656334, -0.610549216480097,
1.08552683577513, 0.189935807154803, 1.3670636776769, 1.0181689602839,
-1.51133180077403, 1.41127485066926, 0.199668469858345, -1.22523054947931),
y = c(-0.323499291411831, -1.00507951141751, -0.901821819799205,
1.41189828512003, -0.131573335707317, -0.308459525548042, 1.50221794165404,
-0.154047787639801, 0.44717002689869, -0.93671163236924), z c(0.836709660070246,
-0.251235618242673, -2.02289120416259,
0.499914144749108, -0.458094619767492, 1.48047512280956, 0.80987242929676,
-1.17963322744287, 0.81492625128413, 0.475181724036684), radius
c(0.174093995941803, 0.75503840832971, 0.562892300076783, 0.541058518458158,
0.724675815086812, 0.828356854617596, 0.423405217472464, 0.540400178171694,
0.0765824350528419, 0.55016236170195), color = c("#FF0000FF",
"#FF9900FF",
"#CCFF00FF", "#33FF00FF", "#00FF66FF",
"#00FFFFFF", "#0066FFFF",
"#3300FFFF", "#CC00FFFF", "#FF0099FF"), alpha = 1,
lit = TRUE, ambient "#000000", specular = "#FFFFFF",
emission = "#000000",     shininess = 50,
smooth = TRUE, front = "filled", back = "filled",     size =
3, lwd = 1, fog
= FALSE, point_antialias = FALSE,     line_antialias = FALSE, texture NULL,
textype = "rgb",     texmipmap = FALSE, texminfilter =
"linear",
texmagfilter = "linear",     texenvmap = FALSE)
 3: do.call("rgl.spheres", c(list(x = x, y = y, z = z, radius =
radius),
.fixMaterialArgs(..., Params = save)))
 4: spheres3d(rnorm(10), rnorm(10), rnorm(10), radius = runif(10),     color
= rainbow(10))
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

Does this error message make anything clearer?





On Mon, May 23, 2011 at 2:43 PM, john herbert
<arraystruggles@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 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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