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

Fri Aug 17 18:31:48 CEST 2012

On Fri, Aug 17, 2012 at 9:21 AM, Olin Silander <olinsilander at gmail.com> wrote:
> Thanks for the suggestion. Unfortunately this doesn't seem to work either - I get the same error that I did previously:

Is Magick-config in your PATH?

I also wonder if this could be a locale issue. Can you send your sessionInfo()?

I am able to install EBImage from source using biocLite(). Maybe
because /opt/local/bin is in my path?
Dan

>
> biocLite("EBImage", type="source")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.7.
> Installing package(s) 'EBImage'
> 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/RtmpEwsd5x/downloaded_packages'
> Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> Warning message:
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package 'EBImage' had non-zero exit status
>
>
> This seems very strange,  as when I try to install from terminal, the ImageMagick check seems fine (as does the suggested check in the vignette):
>
> 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
>
> Cheers,
> Olin
>
>
> On Aug 17, 2012, at 6:15 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>> 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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>
> ----------------------------------------
> Olin Silander
> Computational and Systems Biology
> Biozentrum, University of Basel
> Klingelbergstr. 50/70
> CH-4056 Basel
> Switzerland
> 061 267 1621
> olinsilander at gmail.com
>
>
>