EBImage installs but won't load on Mac OS 10.6.4
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W. A. Green ▴ 40
@w-a-green-4296
Last seen 7.2 years ago
Probably this is a question for Gregoire Pau, but I know there have been others who had trouble installing EBImage on Snow Leopard....Haven't found a fix for my problem on BioC or R-sig-mac lists, though. On: platform x86_64-apple-darwin9.8.0 arch x86_64 os darwin9.8.0 system x86_64, darwin9.8.0 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) The source installation seems to run fine (see output below), but > library(EBImage) gives: Error in library(EBImage) : there is no package called 'EBImage' The only error in the install process seems to be: Xlib: extension "RANDR" missing on display ":0.0". which doesn't seems to prevent gtk-demo from opening an X window and running fine. bash-3.2$ gtk-demo Xlib: extension "RANDR" missing on display ":0.0". bash-3.2$ convert -version Version: ImageMagick 6.5.8-4 2009-12-15 Q16 http://www.imagemagick.org Copyright: Copyright (C) 1999-2009 ImageMagick Studio LLC Features: bash-3.2$ pkg-config gtk+-2.0 --libs -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lintl -liconv bash-3.2$ Magick-config --libs -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lgomp -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread -lltdl I've also tried local source installs from the mac gui in both R and R64 and install.packages() from within R....Nothing seems to work. Any guidance would be much appreciated, Walton Here's the install output: bash-3.2$ sudo R CMD INSTALL EBImage_3.5.5.tar.gz * installing to library ???/Library/Frameworks/R.framework/Resources/library??? * installing *source* package ???EBImage??? ... checking for Magick-config... yes * found ImageMagick version 6.6.3 Q16 * found ImageMagick includes in -I/opt/local/include/ImageMagick checking for pkg-config... yes * compiling with GTK+ support ----------------------------------------------------- configure: creating ./config.status config.status: creating src/Makevars ** libs *** arch - x86_64 gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c EBImage.c -o EBImage.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c conversions.c -o conversions.o conversions.c: In function ???magick2SEXP???: conversions.c:148: warning: ???DispatchImage??? is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:265) conversions.c:153: warning: ???DispatchImage??? is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:265) conversions.c:155: warning: ???DispatchImage??? is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:265) conversions.c:157: warning: ???DispatchImage??? is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:265) conversions.c:162: warning: ???DispatchImage??? is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:265) gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c display.c -o display.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c distmap.c -o distmap.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c drawable.c -o drawable.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c features_haralick.c -o features_haralick.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c features_hull.c -o features_hull.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c features_moments.c -o features_moments.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c features_zernike.c -o features_zernike.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c filters_magick.c -o filters_magick.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c floodFill.cpp -o floodFill.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c io.c -o io.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c morphology.c -o morphology.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c normalize.c -o normalize.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c objects.c -o objects.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c ocontour.c -o ocontour.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c propagate.cpp -o propagate.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c thresh.c -o thresh.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c tile.c -o tile.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c tools.c -o tools.o gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c translate.c -o translate.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick -fPIC -g -O2 -c watershed.cpp -o watershed.o g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o EBImage.so EBImage.o conversions.o display.o distmap.o drawable.o features_haralick.o features_hull.o features_moments.o features_zernike.o filters_magick.o floodFill.o io.o morphology.o normalize.o objects.o ocontour.o propagate.o thresh.o tile.o tools.o translate.o watershed.o -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lintl -liconv -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread -lltdl -L/opt/local/lib -lMagickWand -lMagickCore -llcms -ltiff -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread -lltdl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Xlib: extension "RANDR" missing on display ":0.0". * DONE (EBImage) ## .signature # Walton A. Green # E-mail: $ echo wagreenXbricol.net | tr 'X' '@' # URL: <http: www.bricol.net=""> # Phone: (203) 640-8122 #################### 60 characters wide ####################
GUI PROcess convert EBImage GUI PROcess convert EBImage • 809 views
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Entering edit mode
Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.2 years ago
Hello Walton, EBImage works fine on Mac systems. It seems that you're facing a problem caused by the concurrent installation of different versions of R and/or of different architecture (32-bit and 64-bit), unrelated to EBImage. From your R CMD INSTALL output, it appears that you installed the 64-bit version of EBImage, see: "installing to /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64" What is your version of R, when started from the command line ? Did you try to start R and load EBImage from the command line ? Did it work ? Did you try to start R64.app and load EBImage ? The warning message 'Xlib: extension "RANDR" missing on display ":0.0"' is caused by the MacPort version of GTK+. I don't know why it pops up but it seems harmless. Hope this helps, Greg --- Gregoire Pau EMBL Research officer http://www.embl.de/~gpau/ On 14/10/2010 07:50, W. A. Green wrote: > > Probably this is a question for Gregoire Pau, but I know there have been > others who had trouble installing EBImage on Snow Leopard....Haven't > found a fix for my problem on BioC or R-sig-mac lists, though. > > On: > > platform x86_64-apple-darwin9.8.0 > arch x86_64 > os darwin9.8.0 > system x86_64, darwin9.8.0 > status > major 2 > minor 11.1 > year 2010 > month 05 > day 31 > svn rev 52157 > language R > version.string R version 2.11.1 (2010-05-31) > > The source installation seems to run fine (see output below), but > >> library(EBImage) > > gives: > > Error in library(EBImage) : there is no package called 'EBImage' > > The only error in the install process seems to be: > > Xlib: extension "RANDR" missing on display ":0.0". > > which doesn't seems to prevent gtk-demo from opening an X window and > running fine. > > bash-3.2$ gtk-demo > Xlib: extension "RANDR" missing on display ":0.0". > bash-3.2$ convert -version > Version: ImageMagick 6.5.8-4 2009-12-15 Q16 http://www.imagemagick.org > Copyright: Copyright (C) 1999-2009 ImageMagick Studio LLC > Features: > > bash-3.2$ pkg-config gtk+-2.0 --libs > -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 > -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite > -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 > -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig > -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 > -lglib-2.0 -lintl -liconv > bash-3.2$ Magick-config --libs > -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg > -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM > -lICE -lX11 -lXt -lbz2 -lz -lm -lgomp -lclparser -Wl,-framework,OpenCL > -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm > -lpthread -lltdl > > I've also tried local source installs from the mac gui in both R and R64 > and install.packages() from within R....Nothing seems to work. > > Any guidance would be much appreciated, > > Walton > > Here's the install output: > > bash-3.2$ sudo R CMD INSTALL EBImage_3.5.5.tar.gz > * installing to library > ???/Library/Frameworks/R.framework/Resources/library??? > * installing *source* package ???EBImage??? ... > checking for Magick-config... yes > * found ImageMagick version 6.6.3 Q16 > * found ImageMagick includes in -I/opt/local/include/ImageMagick > checking for pkg-config... yes > * compiling with GTK+ support > ----------------------------------------------------- > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > *** arch - x86_64 > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c EBImage.c -o EBImage.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c conversions.c -o conversions.o > conversions.c: In function ???magick2SEXP???: > conversions.c:148: warning: ???DispatchImage??? is deprecated (declared > at /opt/local/include/ImageMagick/magick/deprecate.h:265) > conversions.c:153: warning: ???DispatchImage??? is deprecated (declared > at /opt/local/include/ImageMagick/magick/deprecate.h:265) > conversions.c:155: warning: ???DispatchImage??? is deprecated (declared > at /opt/local/include/ImageMagick/magick/deprecate.h:265) > conversions.c:157: warning: ???DispatchImage??? is deprecated (declared > at /opt/local/include/ImageMagick/magick/deprecate.h:265) > conversions.c:162: warning: ???DispatchImage??? is deprecated (declared > at /opt/local/include/ImageMagick/magick/deprecate.h:265) > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c display.c -o display.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c distmap.c -o distmap.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c drawable.c -o drawable.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c features_haralick.c -o features_haralick.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c features_hull.c -o features_hull.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c features_moments.c -o features_moments.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c features_zernike.c -o features_zernike.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c filters_magick.c -o filters_magick.o > g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp > -I/opt/local/include/ImageMagick -fPIC -g -O2 -c floodFill.cpp -o > floodFill.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c io.c -o io.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c morphology.c -o morphology.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c normalize.c -o normalize.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c objects.c -o objects.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c ocontour.c -o ocontour.o > g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp > -I/opt/local/include/ImageMagick -fPIC -g -O2 -c propagate.cpp -o > propagate.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c thresh.c -o thresh.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c tile.c -o tile.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c tools.c -o tools.o > gcc -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT > -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include > -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo > -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ > -I/opt/local/include -I/opt/local/include/glib-2.0 > -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 > -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall > -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick > -fPIC -g -O2 -c translate.c -o translate.o > g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/x86_64 > -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp > -I/opt/local/include/ImageMagick -fPIC -g -O2 -c watershed.cpp -o > watershed.o > g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined > dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib > -o EBImage.so EBImage.o conversions.o display.o distmap.o drawable.o > features_haralick.o features_hull.o features_moments.o features_zernike.o > filters_magick.o floodFill.o io.o morphology.o normalize.o objects.o > ocontour.o propagate.o thresh.o tile.o tools.o translate.o watershed.o > -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 > -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage > -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 -lpng12 > -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat > -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lintl > -liconv -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib > -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg > -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM > -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser -Wl,-framework,OpenCL > -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm > -lpthread -lltdl -L/opt/local/lib -lMagickWand -lMagickCore -llcms -ltiff > -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz > -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser > -Wl,-framework,OpenCL > -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm > -lpthread -lltdl -F/Library/Frameworks/R.framework/.. -framework R > -Wl,-framework -Wl,CoreFoundation > installing to > /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64 > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > Xlib: extension "RANDR" missing on display ":0.0". > > * DONE (EBImage) > > ## .signature > # Walton A. Green > # E-mail: $ echo wagreenXbricol.net | tr 'X' '@' > # URL: <http: www.bricol.net=""> > # Phone: (203) 640-8122 > #################### 60 characters wide #################### > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Walton, you are using MacPorts, right? Possibly you unintentionally installed another R as a dependency through MacPorts. I had the same effect. That MacPorts R will be $ which R /opt/local/bin/R and will become your default R on the console (if you just type 'R') then, but the packages you install through the GUI don't go there, the package installs are distinct. The cran Mac R is normally in /usr/bin/R try to find our where the package is installed. Hope that helps Michael Am Oct 15, 2010 um 3:10 PM schrieb Gregoire Pau: > Hello Walton, > > EBImage works fine on Mac systems. It seems that you're facing a problem caused by the concurrent installation of different versions of R and/or of different architecture (32-bit and 64-bit), unrelated to EBImage. > > From your R CMD INSTALL output, it appears that you installed the 64-bit version of EBImage, see: > "installing to /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64" > > What is your version of R, when started from the command line ? Did you try to start R and load EBImage from the command line ? Did it work ? Did you try to start R64.app and load EBImage ? > > The warning message 'Xlib: extension "RANDR" missing on display ":0.0"' is caused by the MacPort version of GTK+. I don't know why it pops up but it seems harmless. > > Hope this helps, > > Greg > --- > Gregoire Pau > EMBL Research officer > http://www.embl.de/~gpau/ > > On 14/10/2010 07:50, W. A. Green wrote: >> >> Probably this is a question for Gregoire Pau, but I know there have been >> others who had trouble installing EBImage on Snow Leopard....Haven't >> found a fix for my problem on BioC or R-sig-mac lists, though. >> >> On: >> >> platform x86_64-apple-darwin9.8.0 >> arch x86_64 >> os darwin9.8.0 >> system x86_64, darwin9.8.0 >> status >> major 2 >> minor 11.1 >> year 2010 >> month 05 >> day 31 >> svn rev 52157 >> language R >> version.string R version 2.11.1 (2010-05-31) >> >> The source installation seems to run fine (see output below), but >> >>> library(EBImage) >> >> gives: >> >> Error in library(EBImage) : there is no package called 'EBImage' >> >> The only error in the install process seems to be: >> >> Xlib: extension "RANDR" missing on display ":0.0". >> >> which doesn't seems to prevent gtk-demo from opening an X window and >> running fine. >> >> bash-3.2$ gtk-demo >> Xlib: extension "RANDR" missing on display ":0.0". >> bash-3.2$ convert -version >> Version: ImageMagick 6.5.8-4 2009-12-15 Q16 http://www.imagemagick.org >> Copyright: Copyright (C) 1999-2009 ImageMagick Studio LLC >> Features: >> >> bash-3.2$ pkg-config gtk+-2.0 --libs >> -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 >> -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite >> -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 >> -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig >> -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 >> -lglib-2.0 -lintl -liconv >> bash-3.2$ Magick-config --libs >> -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg >> -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM >> -lICE -lX11 -lXt -lbz2 -lz -lm -lgomp -lclparser -Wl,-framework,OpenCL >> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >> -lpthread -lltdl >> >> I've also tried local source installs from the mac gui in both R and R64 >> and install.packages() from within R....Nothing seems to work. >> >> Any guidance would be much appreciated, >> >> Walton >> >> Here's the install output: >> >> bash-3.2$ sudo R CMD INSTALL EBImage_3.5.5.tar.gz >> * installing to library >> ???/Library/Frameworks/R.framework/Resources/library??? >> * installing *source* package ???EBImage??? ... >> checking for Magick-config... yes >> * found ImageMagick version 6.6.3 Q16 >> * found ImageMagick includes in -I/opt/local/include/ImageMagick >> checking for pkg-config... yes >> * compiling with GTK+ support >> ----------------------------------------------------- >> configure: creating ./config.status >> config.status: creating src/Makevars >> ** libs >> *** arch - x86_64 >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c EBImage.c -o EBImage.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c conversions.c -o conversions.o >> conversions.c: In function ???magick2SEXP???: >> conversions.c:148: warning: ???DispatchImage??? is deprecated (declared >> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >> conversions.c:153: warning: ???DispatchImage??? is deprecated (declared >> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >> conversions.c:155: warning: ???DispatchImage??? is deprecated (declared >> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >> conversions.c:157: warning: ???DispatchImage??? is deprecated (declared >> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >> conversions.c:162: warning: ???DispatchImage??? is deprecated (declared >> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c display.c -o display.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c distmap.c -o distmap.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c drawable.c -o drawable.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c features_haralick.c -o features_haralick.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c features_hull.c -o features_hull.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c features_moments.c -o features_moments.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c features_zernike.c -o features_zernike.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c filters_magick.c -o filters_magick.o >> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp >> -I/opt/local/include/ImageMagick -fPIC -g -O2 -c floodFill.cpp -o >> floodFill.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c io.c -o io.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c morphology.c -o morphology.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c normalize.c -o normalize.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c objects.c -o objects.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c ocontour.c -o ocontour.o >> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp >> -I/opt/local/include/ImageMagick -fPIC -g -O2 -c propagate.cpp -o >> propagate.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c thresh.c -o thresh.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c tile.c -o tile.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c tools.c -o tools.o >> gcc -arch x86_64 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >> -I/opt/local/include -I/opt/local/include/glib-2.0 >> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >> -fPIC -g -O2 -c translate.c -o translate.o >> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >> -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp >> -I/opt/local/include/ImageMagick -fPIC -g -O2 -c watershed.cpp -o >> watershed.o >> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined >> dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib >> -o EBImage.so EBImage.o conversions.o display.o distmap.o drawable.o >> features_haralick.o features_hull.o features_moments.o features_zernike.o >> filters_magick.o floodFill.o io.o morphology.o normalize.o objects.o >> ocontour.o propagate.o thresh.o tile.o tools.o translate.o watershed.o >> -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 >> -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage >> -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 -lpng12 >> -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat >> -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lintl >> -liconv -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib >> -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg >> -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM >> -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser -Wl,-framework,OpenCL >> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >> -lpthread -lltdl -L/opt/local/lib -lMagickWand -lMagickCore -llcms -ltiff >> -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz >> -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser >> -Wl,-framework,OpenCL >> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >> -lpthread -lltdl -F/Library/Frameworks/R.framework/.. -framework R >> -Wl,-framework -Wl,CoreFoundation >> installing to >> /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64 >> ** R >> ** inst >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices ... >> ** testing if installed package can be loaded >> Xlib: extension "RANDR" missing on display ":0.0". >> >> * DONE (EBImage) >> >> ## .signature >> # Walton A. Green >> # E-mail: $ echo wagreenXbricol.net | tr 'X' '@' >> # URL: <http: www.bricol.net=""> >> # Phone: (203) 640-8122 >> #################### 60 characters wide #################### >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Greg and Michael, Thanks; I thought it might be something like invoking the wrong version of R, but I tried it every way I could think of and was unable to fix it, including installing and loading from: R.app R64.app R invoked from Terminal window R invoked from X11 window with the .app GUIs I tried both the package installer and install.packages(); at the commandline I tried both R CMD INSTALL and install.packages(). (In all cases as a source install by the superuser.) R from commandline (usr/bin/R) is: > version _ platform x86_64-apple-darwin9.8.0 arch x86_64 os darwin9.8.0 system x86_64, darwin9.8.0 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) and /opt/local/bin/R doesn't seem to exist (as I've never installed R from macports). I did have an old fink version, which I don't think was the problem as it was farther down in my PATH. Also I just removed it and tried R CMD INSTALL from a terminal window again, whih seemed to go fine, but gave same error on loading: Error in library(EBImage) : there is no package called 'EBImage' weirdly, install.packages(repos = NULL, '/Users/wag/Desktop/EBImage_3.5.5.tar.gz') gives a different load-time error: Error in library(EBImage) : 'EBImage' is not a valid installed package (both the .app versions give this error as well as: > install.packages(repos = NULL, '/Users/wag/Desktop/EBImage_3.5.5.tar.gz') Error: cannot remove prior installation of package 'EBImage' I had EBImage running fine on my old (OS 10.4) machine, but have been trying to get it running on this new computer for a couple weeks now....Any other ideas? A 'clean' install? Surely just trashing R.app and R64.app isn't clean enough; from where would I have to remove R.frameworks? > remove.packages('EBImage') Warning in remove.packages("EBImage") : argument 'lib' is missing: using /Library/Frameworks/R.framework/Resources/library Doesn't help either; still get the 'cannot remove prior installation' error.... Walton ## .signature # Walton A. Green # E-mail: $ echo wagreenXbricol.net | tr 'X' '@' # URL: <http: www.bricol.net=""> # Phone: (203) 640-8122 #################### 60 characters wide #################### On Fri, 15 Oct 2010, Michael Dondrup wrote: > Hi Walton, > > you are using MacPorts, right? Possibly you unintentionally installed another R as a dependency through MacPorts. I had the same effect. That MacPorts R will be > $ which R > /opt/local/bin/R > and will become your default R on the console (if you just type 'R') then, but the packages you install through the GUI don't go there, the package installs are distinct. The cran Mac R is > normally in /usr/bin/R > try to find our where the package is installed. > > Hope that helps > Michael > > Am Oct 15, 2010 um 3:10 PM schrieb Gregoire Pau: > >> Hello Walton, >> >> EBImage works fine on Mac systems. It seems that you're facing a problem caused by the concurrent installation of different versions of R and/or of different architecture (32-bit and 64-bit), unrelated to EBImage. >> >> From your R CMD INSTALL output, it appears that you installed the 64-bit version of EBImage, see: >> "installing to /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64" >> >> What is your version of R, when started from the command line ? Did you try to start R and load EBImage from the command line ? Did it work ? Did you try to start R64.app and load EBImage ? >> >> The warning message 'Xlib: extension "RANDR" missing on display ":0.0"' is caused by the MacPort version of GTK+. I don't know why it pops up but it seems harmless. >> >> Hope this helps, >> >> Greg >> --- >> Gregoire Pau >> EMBL Research officer >> http://www.embl.de/~gpau/ >> >> On 14/10/2010 07:50, W. A. Green wrote: >>> >>> Probably this is a question for Gregoire Pau, but I know there have been >>> others who had trouble installing EBImage on Snow Leopard....Haven't >>> found a fix for my problem on BioC or R-sig-mac lists, though. >>> >>> On: >>> >>> platform x86_64-apple-darwin9.8.0 >>> arch x86_64 >>> os darwin9.8.0 >>> system x86_64, darwin9.8.0 >>> status >>> major 2 >>> minor 11.1 >>> year 2010 >>> month 05 >>> day 31 >>> svn rev 52157 >>> language R >>> version.string R version 2.11.1 (2010-05-31) >>> >>> The source installation seems to run fine (see output below), but >>> >>>> library(EBImage) >>> >>> gives: >>> >>> Error in library(EBImage) : there is no package called 'EBImage' >>> >>> The only error in the install process seems to be: >>> >>> Xlib: extension "RANDR" missing on display ":0.0". >>> >>> which doesn't seems to prevent gtk-demo from opening an X window and >>> running fine. >>> >>> bash-3.2$ gtk-demo >>> Xlib: extension "RANDR" missing on display ":0.0". >>> bash-3.2$ convert -version >>> Version: ImageMagick 6.5.8-4 2009-12-15 Q16 http://www.imagemagick.org >>> Copyright: Copyright (C) 1999-2009 ImageMagick Studio LLC >>> Features: >>> >>> bash-3.2$ pkg-config gtk+-2.0 --libs >>> -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 >>> -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite >>> -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 >>> -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig >>> -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 >>> -lglib-2.0 -lintl -liconv >>> bash-3.2$ Magick-config --libs >>> -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg >>> -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM >>> -lICE -lX11 -lXt -lbz2 -lz -lm -lgomp -lclparser -Wl,-framework,OpenCL >>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>> -lpthread -lltdl >>> >>> I've also tried local source installs from the mac gui in both R and R64 >>> and install.packages() from within R....Nothing seems to work. >>> >>> Any guidance would be much appreciated, >>> >>> Walton >>> >>> Here's the install output: >>> >>> bash-3.2$ sudo R CMD INSTALL EBImage_3.5.5.tar.gz >>> * installing to library >>> ???/Library/Frameworks/R.framework/Resources/library??? >>> * installing *source* package ???EBImage??? ... >>> checking for Magick-config... yes >>> * found ImageMagick version 6.6.3 Q16 >>> * found ImageMagick includes in -I/opt/local/include/ImageMagick >>> checking for pkg-config... yes >>> * compiling with GTK+ support >>> ----------------------------------------------------- >>> configure: creating ./config.status >>> config.status: creating src/Makevars >>> ** libs >>> *** arch - x86_64 >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c EBImage.c -o EBImage.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c conversions.c -o conversions.o >>> conversions.c: In function ???magick2SEXP???: >>> conversions.c:148: warning: ???DispatchImage??? is deprecated (declared >>> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >>> conversions.c:153: warning: ???DispatchImage??? is deprecated (declared >>> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >>> conversions.c:155: warning: ???DispatchImage??? is deprecated (declared >>> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >>> conversions.c:157: warning: ???DispatchImage??? is deprecated (declared >>> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >>> conversions.c:162: warning: ???DispatchImage??? is deprecated (declared >>> at /opt/local/include/ImageMagick/magick/deprecate.h:265) >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c display.c -o display.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c distmap.c -o distmap.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c drawable.c -o drawable.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c features_haralick.c -o features_haralick.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c features_hull.c -o features_hull.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c features_moments.c -o features_moments.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c features_zernike.c -o features_zernike.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c filters_magick.c -o filters_magick.o >>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp >>> -I/opt/local/include/ImageMagick -fPIC -g -O2 -c floodFill.cpp -o >>> floodFill.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c io.c -o io.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c morphology.c -o morphology.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c normalize.c -o normalize.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c objects.c -o objects.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c ocontour.c -o ocontour.o >>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp >>> -I/opt/local/include/ImageMagick -fPIC -g -O2 -c propagate.cpp -o >>> propagate.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c thresh.c -o thresh.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c tile.c -o tile.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c tools.c -o tools.o >>> gcc -arch x86_64 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT >>> -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include >>> -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo >>> -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ >>> -I/opt/local/include -I/opt/local/include/glib-2.0 >>> -I/opt/local/lib/glib-2.0/include -I/opt/local/include/pixman-1 >>> -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -Wall >>> -I/opt/local/include/ImageMagick -fopenmp -I/opt/local/include/ImageMagick >>> -fPIC -g -O2 -c translate.c -o translate.o >>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/x86_64 >>> -I/usr/local/include -Wall -I/opt/local/include/ImageMagick -fopenmp >>> -I/opt/local/include/ImageMagick -fPIC -g -O2 -c watershed.cpp -o >>> watershed.o >>> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined >>> dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib >>> -o EBImage.so EBImage.o conversions.o display.o distmap.o drawable.o >>> features_haralick.o features_hull.o features_moments.o features_zernike.o >>> filters_magick.o floodFill.o io.o morphology.o normalize.o objects.o >>> ocontour.o propagate.o thresh.o tile.o tools.o translate.o watershed.o >>> -L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 >>> -lpangocairo-1.0 -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage >>> -lpangoft2-1.0 -lgio-2.0 -lXext -lXfixes -lcairo -lpixman-1 -lpng12 >>> -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat >>> -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lintl >>> -liconv -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib >>> -L/opt/local/lib -lMagickCore -llcms -ltiff -lfreetype -ljpeg >>> -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz -liconv -lXext -lSM >>> -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser -Wl,-framework,OpenCL >>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>> -lpthread -lltdl -L/opt/local/lib -lMagickWand -lMagickCore -llcms -ltiff >>> -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lexpat -lfreetype -lz >>> -liconv -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lclparser >>> -Wl,-framework,OpenCL >>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>> -lpthread -lltdl -F/Library/Frameworks/R.framework/.. -framework R >>> -Wl,-framework -Wl,CoreFoundation >>> installing to >>> /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64 >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> ** help >>> *** installing help indices >>> ** building package indices ... >>> ** testing if installed package can be loaded >>> Xlib: extension "RANDR" missing on display ":0.0". >>> >>> * DONE (EBImage) >>> >>> ## .signature >>> # Walton A. Green >>> # E-mail: $ echo wagreenXbricol.net | tr 'X' '@' >>> # URL: <http: www.bricol.net=""> >>> # Phone: (203) 640-8122 >>> #################### 60 characters wide #################### >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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