[BioC] Problems installing EBImage - Symbol not found: _gdk_display
Olin Silander
olinsilander at gmail.com
Mon Aug 20 09:36:15 CEST 2012
I tried:
R CMD INSTALL --preclean EBImage
R CMD INSTALL --preclean EBImage_4.0.1.tar.gz
R CMD INSTALL EBImage_4.0.1.tar.gz
but all failed again with the same error:
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 did see some warnings for ImageMagick which I did not see previously or which were not there previously:
conversions.c: In function ‘magick2SEXP’:
conversions.c:135: warning: ‘DispatchImage’ is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:280)
conversions.c:137: warning: ‘DispatchImage’ is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:280)
conversions.c:139: warning: ‘DispatchImage’ is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:280)
conversions.c:144: warning: ‘DispatchImage’ is deprecated (declared at /opt/local/include/ImageMagick/magick/deprecate.h:280)
tile.c: In function ‘untile’:
tile.c:130: warning: unused variable ‘id’
and a long series (about 25) of warnings along the following lines:
ld: warning: ld: warning: ld: warning: ld: warning: ignoring file /opt/local/lib/libpangocairo-1.0.dylib, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 6 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): /opt/local/lib/libpangocairo-1.0.dylibignoring file /opt/local/lib/libgtk-x11-2.0.dylib, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 6 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386):
-Olin
On Aug 17, 2012, at 9:16 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
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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
>>
>>
>>
----------------------------------------
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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