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

[Dan Tenenbaum]

On Fri, Aug 17, 2012 at 9:41 AM, Olin Silander <olinsilander at gmail.com> wrote:
> Magick-config seems to be in my PATH:
>
> osilander$ which Magick-config
> /opt/local/bin/Magick-config
>
> as does opt/local/bin:
>
> osilander$ echo $PATH
> /opt/local/bin:/opt/local/sbin:/usr/local/bin//bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:
>
> my sessionInfo (all of it) - I do have consistent locale issues but I have
> ignored these mostly, maybe that is the problem:


OK, forgetting about sessionInfo() and biocLite() for the moment, it
seems like you get farther when you use R CMD INSTALL.
But it seems like 'make' decided there was nothing to do, so maybe
there were remnants of  a previous incomplete build. So I suggest
using either
R CMD INSTALL --preclean
or running
R CMD INSTALL against a tarball, not a directory.
Dan


>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.7
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>
> And the messages when I start R:
>
> During startup - Warning messages:
> 1: Setting LC_CTYPE failed, using "C"
> 2: Setting LC_COLLATE failed, using "C"
> 3: Setting LC_TIME failed, using "C"
> 4: Setting LC_MESSAGES failed, using "C"
> 5: Setting LC_PAPER failed, using "C"
> [R.app GUI 1.52 (6188) i386-apple-darwin9.8.0]
>
> WARNING: You're using a non-UTF8 locale, therefore only ASCII characters
> will work.
> Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system
> preferences accordingly.
> [History restored from /Users/osilander/.Rhistory]
>
>> source("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.4.7, ?biocLite for help
>> 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/RtmpKkCErx/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
>
>
> On Aug 17, 2012, at 6:31 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
> 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
>
>
>
>
> ----------------------------------------
> Olin Silander
> Computational and Systems Biology
> Biozentrum, University of Basel
> Klingelbergstr. 50/70
> CH-4056 Basel
> Switzerland
> 061 267 1621
> olinsilander at gmail.com
>
>
>