[BioC] Problems installing EBImage - Symbol not found: _gdk_display

[Olin Silander]

I am having problems installing EBImage. I am running R 2.15.1 on OSX Mountain Lion and have X11 open using with Xquartz 2.7.2

The output when I try to install EBImage:

osilander$ R CMD INSTALL EBImage
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘EBImage’ ...
checking for Magick-config... yes
* found ImageMagick version 6.7.8 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 - i386
make: Nothing to be done for `all'.
installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘EBImage-installation.Rnw’ 
   ‘EBImage-introduction.Rnw’ 
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage/libs/i386/EBImage.so':
  dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage/libs/i386/EBImage.so, 6): Symbol not found: _gdk_display
  Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage/libs/i386/EBImage.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage/libs/i386/EBImage.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage’

I also tried installing from within the R GUI, and get the following errors:

biocLite("EBImage")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.7.
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
Installing package(s) 'EBImage'
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
Warning message:
package 'EBImage' is not available (for R version 2.15.1)

Finally, I tried using the R Package Installer, and get a different error:

trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/EBImage_3.12.0.tar.gz'
Content type 'application/x-gzip' length 4738660 bytes (4.5 Mb)
opened URL
==================================================
downloaded 4.5 Mb

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_PAPER failed, using "C" 
* installing *source* package 'EBImage' ...
checking for Magick-config... no
configure: error: "ImageMagick or ImageMagick includes not found!"
ERROR: configuration failed for package 'EBImage'
* removing '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/EBImage'

The downloaded source packages are in
	'/private/var/folders/xq/60l5wb_91c71yn4y2lz8f4_w0000gq/T/RtmpT9XfJ2/downloaded_packages'


I also tried using 'chooseBioCmirror()' to change my mirror to Seattle.

The checks for gtk and ImageMagick seem okay except for a single warning:

pz-mlm06020-02:Downloads osilander$ gtk-demo
(process:1307): Gtk-WARNING **: Locale not supported by C library.
	Using the fallback 'C' locale.


osilander$ pkg-config gtk+-2.0 --libs

-L/opt/local/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lpangocairo-1.0 -lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lgdk_pixbuf-2.0 -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm -lfreetype -lfontconfig -lgobject-2.0 -lglib-2.0 -lintl


osilander$ convert -version

Version: ImageMagick 6.7.8-3 2012-08-15 Q16 http://www.imagemagick.org
Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC
Features:  OpenCL


osilander$ Magick-config --libs

-L/opt/local/lib -lMagickCore

Thanks in advance,
Olin

----------------------------------------
Olin Silander
Computational and Systems Biology
Biozentrum, University of Basel
Klingelbergstr. 50/70
CH-4056 Basel
Switzerland
061 267 1621
olinsilander at gmail.com