EBImage installs but won't load on Mac OS 10.6.4
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Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.1 years ago
Hi Walton, EBImage works fine on 64-bit machines. Permissions cannot explain why R64.app hangs. Did you check if the 64-bit versions of GTK and ImageMagick have been correctly installed ? How did you install them ? What is the result of 'otool -L' on the EBImage.so object ? Cheers, Greg --- Gregoire Pau EMBL Research officer http://www.embl.de/~gpau/ On 30/11/2010 18:25, W. A. Green wrote: > > Finally, after a lot of brainstorming, (mostly) fixed Turned out to be a > permissions issue: because I installed EBImage as root, group and other > execute permissions were not set. > > Tried: > > chmod -R a+rx /Library/Frameworks/R.framework/Resources/library/EBImage > chmod -R g+w /Library/Frameworks/R.framework/Resources/library/EBImage > > and now no problem loading from R invoked in an X11 or Terminal window, > though R64.app still hangs on: > > library(EBImage) > > Do I still have some permissions wrong? > > drwxrwxr-x 14 root admin 476B Nov 30 11:29 . > drwxrwxr-x 54 root admin 1.8K Nov 30 11:30 .. > -rw-rw-r-- 1 root admin 823B Nov 30 11:29 DESCRIPTION > -rw-rw-r-- 1 root admin 1.9K Nov 30 11:29 INDEX > -rw-rw-r-- 1 root admin 24K Nov 30 11:29 LICENSE > drwxrwxr-x 8 root admin 272B Nov 30 11:29 Meta > -rw-rw-r-- 1 root admin 1.4K Nov 30 11:29 NAMESPACE > drwxrwxr-x 5 root admin 170B Nov 30 11:29 R > drwxrwxr-x 10 root admin 340B Nov 30 11:29 doc > drwxrwxr-x 7 root admin 238B Nov 30 11:29 help > drwxrwxr-x 3 root admin 102B Nov 30 11:29 html > drwxrwxr-x 7 root admin 238B Nov 30 11:29 images > drwxrwxr-x 3 root admin 102B Nov 30 11:29 libs > drwxrwxr-x 4 root admin 136B Nov 30 11:29 scripts > > Thanks for the help, > > 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 >> >>
GO GUI PROcess convert EBImage GO GUI PROcess convert EBImage • 757 views
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W. A. Green ▴ 40
@w-a-green-4296
Last seen 7.1 years ago
Finally, after a lot of brainstorming, (mostly) fixed Turned out to be a permissions issue: because I installed EBImage as root, group and other execute permissions were not set. Tried: chmod -R a+rx /Library/Frameworks/R.framework/Resources/library/EBImage chmod -R g+w /Library/Frameworks/R.framework/Resources/library/EBImage and now no problem loading from R invoked in an X11 or Terminal window, though R64.app still hangs on: library(EBImage) Do I still have some permissions wrong? drwxrwxr-x 14 root admin 476B Nov 30 11:29 . drwxrwxr-x 54 root admin 1.8K Nov 30 11:30 .. -rw-rw-r-- 1 root admin 823B Nov 30 11:29 DESCRIPTION -rw-rw-r-- 1 root admin 1.9K Nov 30 11:29 INDEX -rw-rw-r-- 1 root admin 24K Nov 30 11:29 LICENSE drwxrwxr-x 8 root admin 272B Nov 30 11:29 Meta -rw-rw-r-- 1 root admin 1.4K Nov 30 11:29 NAMESPACE drwxrwxr-x 5 root admin 170B Nov 30 11:29 R drwxrwxr-x 10 root admin 340B Nov 30 11:29 doc drwxrwxr-x 7 root admin 238B Nov 30 11:29 help drwxrwxr-x 3 root admin 102B Nov 30 11:29 html drwxrwxr-x 7 root admin 238B Nov 30 11:29 images drwxrwxr-x 3 root admin 102B Nov 30 11:29 libs drwxrwxr-x 4 root admin 136B Nov 30 11:29 scripts Thanks for the help, 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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