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RGL
7 messages · Duncan Murdoch, David Winsemius, Guillaume Meurice +2 more
On 12-07-26 7:46 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.
I don't know the solution, but if you don't get one from someone else, you might have more luck on the R-sig-mac list. Duncan Murdoch
Below you will find : - installation from binaries - installation from sources - sessionInfo() 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 [[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.
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 [[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.
David Winsemius, MD West Hartford, CT
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On Jul 27, 2012, at 03:48 , David Winsemius wrote:
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.
[snip]
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.
Yes. The new CRAN binaries work for me too (and are in the non-X11 version if run from the R app). For source compiles, I think you need to follow the hint about libraries for dependencies at the bottom of http://cran.r-project.org/bin/macosx/. I believe we have seen the R_decompress1 error before, though. If you can reproduce it, it might be worth digging deeper --- over on R-sig-Mac.
Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
On 27/07/2012 09:14, peter dalgaard wrote:
On Jul 27, 2012, at 03:48 , David Winsemius wrote:
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.
[snip]
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.
Yes. The new CRAN binaries work for me too (and are in the non-X11 version if run from the R app). For source compiles, I think you need to follow the hint about libraries for dependencies at the bottom of http://cran.r-project.org/bin/macosx/. I believe we have seen the R_decompress1 error before, though. If you can reproduce it, it might be worth digging deeper --- over on R-sig-Mac.
It almost always indicates a corrupted lazyload database. One way to corrupt it is to update the package whilst it is in use (which corrupts it for the running session, at least).
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On Jul 27, 2012, at 11:05 , Prof Brian Ripley wrote:
On 27/07/2012 09:14, peter dalgaard wrote:
I believe we have seen the R_decompress1 error before, though. If you can reproduce it, it might be worth digging deeper --- over on R-sig-Mac.
It almost always indicates a corrupted lazyload database. One way to corrupt it is to update the package whilst it is in use (which corrupts it for the running session, at least).
Or, as I just found out, upgrading and then installing from a running copy of the previous version... (Yes, it is hot in .dk today, why do you ask?) -pd
Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com