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

[Dan Tenenbaum]

On Fri, Aug 17, 2012 at 2:22 AM, Olin Silander <olinsilander at gmail.com> wrote:
> 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 EBImage installation vignette, warns against installing the Mac
binary package, and in fact there isn't one on Bioconductor.

The recommended way to install it is:
source("http://bioconductor.org/biocLite.R")
biocLite("EBImage", type="source")

Let us know if that works for you.
Dan


>
> 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
>
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