Re: [R] RGL

Thu, 26 Jul 2012 18:50:32 -0700 


On Jul 26, 2012, at 4:46 AM, Guillaume Meurice wrote:


Dear all,
I was willing to use the library "rgl" to plot some 3D graphics, but unfortunately, I wan't able to instal the library. The error message is below.
I would be very grateful if you could give me any clues about how I can solve this. 


Below you will find :
- installation from binaries
- installation from sources
- sessionInfo()
The error messages in the"sources" install dialog suggests a problem with your system installation of freetype. I was running rgl v0.92.861 on Leopard without problems. I just tried installing the current version offered to the GUI installer, v0.92.880, restarting and got an error on attempting to load while in version 2.14.2,
After updating R to the current version I am able to install rgl_0.92.892 from binary using the GUI Package Installer and then load and run code in either R64 or 32-bit R. 

>  sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     grDevices utils     datasets  graphics  methods   base

other attached packages:
[1] rgl_0.92.892   lattice_0.20-6

loaded via a namespace (and not attached):
[1] grid_2.15.1  tools_2.15.1
You have a fairly full system. I wonder if you should restart and try with a few less packages? 

And as Duncan suggested, you _should_ be posting on the R-SIG-Mac list.

--
David.

Bests,
--
Guillaume Meurice - PhD
Plateforme de Bioinformatique

Here is the installation from binaries :
=======================

install.packages("rgl")

trying URL 
'http://mirror.ibcp.fr/pub/CRAN/bin/macosx/leopard/contrib/2.15/rgl_0.92.892.tgz'
Content type 'application/x-gzip' length 7774197 bytes (7.4 Mb)
opened URL
==================================================
downloaded 7.4 Mb


The downloaded binary packages are in
/var/folders/20/20puJrE0FrWErlnMP5nP6E+++TI/-Tmp-//RtmplpCNL5/ downloaded_packages 
library(rgl)

Error in get(Info[i, 1], envir = env) :
 internal error -3 in R_decompress1
Error: package/namespace load failed for ‘rgl’
=======================




Here is the installation from sources :
=======================

install.packages("rgl", type="source")

trying URL 'http://mirror.ibcp.fr/pub/CRAN/src/contrib/rgl_0.92.892.tar.gz'
Content type 'application/x-gzip' length 1713881 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

=================================================
Setting G.Meurice environment for useful day work

### Sourcing some useful stuff
- ugf.exp.utils.IO.R
- cqFea4CGH.R
- cqFea4GE.R
- cqFea4miRNA.R
- cqFea4CH3.R

Loading required package: snow
Loading required package: utils
### Defining Global Variables
- dir.arraydesign       : directory to agilent array design
- dir.svn                       : directory to local svn repository


### Hooooooooommmmmmmmm
It's interesting that SAS Institute feels that non-peer-reviewed software with hidden implementations of analytic methods that cannot be reproduced by others 
should be trusted when building aircraft engines.
-- Frank Harrell (in response to the statement of the SAS director of technology product marketing: "We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.") 
     R-help (January 2009)




Now it's time to work
=================================================
* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... checking whether we are cross compiling... no 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -arch x86_64 - std=gnu99 -E 
checking for gcc... (cached) gcc -arch x86_64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... (cached) none needed 
checking for libpng-config... no
checking libpng... checking for grep that handles long lines and - e... /usr/bin/grep 
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking png.h usability... no
checking png.h presence... no
checking for png.h... no
checking for png_read_update_info in -lpng... no
configure: libpng header and lib found
configure: using libpng dynamic linkage
checking for X... libraries /usr/X11/lib, headers
checking for glEnd in -lGL... yes
checking for gluProject in -lGLU... yes
checking for freetype-config... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c BBoxDeco.cpp -o BBoxDeco.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Background.cpp -o Background.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Color.cpp -o Color.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Disposable.cpp -o Disposable.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Light.cpp -o Light.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c LineSet.cpp -o LineSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c LineStripSet.cpp -o LineStripSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Material.cpp -o Material.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c PlaneSet.cpp -o PlaneSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c PointSet.cpp -o PointSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c PrimitiveSet.cpp -o PrimitiveSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c QuadSet.cpp -o QuadSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c RenderContext.cpp -o RenderContext.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Shape.cpp -o Shape.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c SphereMesh.cpp -o SphereMesh.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c SphereSet.cpp -o SphereSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c SpriteSet.cpp -o SpriteSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c String.cpp -o String.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Surface.cpp -o Surface.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c TextSet.cpp -o TextSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Texture.cpp -o Texture.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c Viewpoint.cpp -o Viewpoint.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c api.cpp -o api.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c assert.cpp -o assert.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c callbacks.cpp -o callbacks.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c device.cpp -o device.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c devicemanager.cpp -o devicemanager.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c fps.cpp -o fps.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c ftgl.cpp -o ftgl.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c geom.cpp -o geom.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/ Resources/include -I/Library/Frameworks/R.framework/Resources/ include/x86_64 -DNDEBUG -I/System/Library/Frameworks/ OpenGL.framework/Headers -DHAVE_PNG_H -DDarwin -DNO_GL_PREFIX -I/ usr/X11R6/include -Iext -I/usr/local/include -fPIC -g -O2 -c gl2ps.c -o gl2ps.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c glErrors.cpp -o glErrors.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c glgui.cpp -o glgui.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c gui.cpp -o gui.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c init.cpp -o init.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c par3d.cpp -o par3d.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c pixmap.cpp -o pixmap.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c render.cpp -o render.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c rglmath.cpp -o rglmath.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c rglview.cpp -o rglview.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c scene.cpp -o scene.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c select.cpp -o select.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c win32gui.cpp -o win32gui.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c win32lib.cpp -o win32lib.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c x11gui.cpp -o x11gui.o x11gui.cpp: In constructor ‘gui::X11GUIFactory::X11GUIFactory(const char*)’: x11gui.cpp:468: warning: deprecated conversion from string constant to ‘char*’ g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H - DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/ include -g -O2 -fPIC -g -O2 -c x11lib.cpp -o x11lib.o g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names - undefined dynamic_lookup -single_module -multiply_defined suppress - L/usr/local/lib -o rgl.so ABCLineSet.o BBoxDeco.o Background.o Color.o Disposable.o Light.o LineSet.o LineStripSet.o Material.o PlaneSet.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 par3d.o pixmap.o render.o rglmath.o rglview.o scene.o select.o win32gui.o win32lib.o x11gui.o x11lib.o -lGLU -lGL - framework OpenGL -dylib_file /System/Library/Frameworks/ OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/ Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib -lpng - L/usr/X11/lib -lX11 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation 
mkdir Temp
mv x11*.o Temp
mkdir -p AGL
mv AGL/* .
MAKINGAGL=TRUE /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o aglrgl.so *.cpp *.c \ 
                osx/*.mm osx/*.cpp
mv: rename AGL/* to ./*: No such file or directory
make: [aglrgl.so] Error 1 (ignored)
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - DHAVE_PNG_H -DRGL_USE_COCOA -Iext -I/usr/local/include -g -O2 - fPIC -g -O2 -c x11gui.cpp -o x11gui.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - DHAVE_PNG_H -DRGL_USE_COCOA -Iext -I/usr/local/include -g -O2 - fPIC -g -O2 -c x11lib.cpp -o x11lib.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG - DHAVE_PNG_H -DRGL_USE_COCOA -Iext -I/usr/local/include -fPIC -c osx/osxgui.mm -o osx/osxgui.o osx/osxgui.mm:9:2: error: #error Cocoa backend reguires FreeType font reneder 
make[1]: *** [osx/osxgui.o] Error 1
make: *** [aglrgl.so] Error 1
ERROR: compilation failed for package ‘rgl’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/ library/rgl’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.15/ Resources/library/rgl’ 

The downloaded source packages are in
‘/private/var/folders/20/20puJrE0FrWErlnMP5nP6E+++TI/-Tmp-/ RtmplpCNL5/downloaded_packages’ 
Warning message:
In install.packages("rgl", type = "source") :
 installation of package ‘rgl’ had non-zero exit status
=======================




sessionInfo()

R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines stats graphics grDevices datasets utils methods base 

other attached packages:
[1] plotrix_3.4-2 RColorBrewer_1.0-5 mclust_3.4.11 multicore_0.1-7 LVSmiRNA_1.6.0 [6] vsn_3.24.0 affy_1.34.0 MASS_7.3-19 quantreg_4.81 SparseM_0.96 [11] Biobase_2.16.0 BiocGenerics_0.2.0 pvclust_1.2-2 arrayQualityMetrics_3.12.0 impute_1.30.0 [16] marray_1.34.0 limma_3.12.1 fortunes_1.5-0 snowfall_1.84 snow_0.3-9 

loaded via a namespace (and not attached):
[1] affyio_1.24.0 affyPLM_1.32.0 annotate_1.34.1 AnnotationDbi_1.18.1 beadarray_2.6.0 BeadDataPackR_1.8.0 [7] BiocInstaller_1.4.7 Biostrings_2.24.1 Cairo_1.5-1 cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [13] genefilter_1.38.0 grid_2.15.1 Hmisc_3.9-3 hwriter_1.3 IRanges_1.14.4 KernSmooth_2.23-8 [19] lattice_0.20-6 latticeExtra_0.6-19 plyr_1.7.1 preprocessCore_1.18.0 reshape2_1.2.1 RSQLite_0.11.1 [25] setRNG_2011.11-2 stats4_2.15.1 stringr_0.6 survival_2.36-14 SVGAnnotation_0.93-1 tools_2.15.1 
[31] XML_3.9-4             xtable_1.7-0          zlibbioc_1.2.0


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David Winsemius, MD
West Hartford, CT

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