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ebimage problems

3 messages · kraman, Martin Morgan, Gregoire Pau

kraman
# 
Hello, I've been having some trouble working with the aroma package and have
realized that it's my ebimage is at the root of the problem. The package
builds but during testing it fails because of an undefined symbol as seen
below:

 

installing to /usr/local/lib64/R/library/EBImage/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

** building package indices ...

** testing if installed package can be loaded

Error in dyn.load(file, DLLpath = DLLpath, ...) :

  unable to load shared library
'/usr/local/lib64/R/library/EBImage/libs/EBImage.so':

  /usr/local/lib64/R/library/EBImage/libs/EBImage.so: undefined symbol:
MagickCoreTerminus

ERROR: loading failed

* removing ?/usr/local/lib64/R/library/EBImage?

 

The downloaded packages are in

        ?/tmp/RtmpE4xaFL/downloaded_packages?

Updating HTML index of packages in '.Library'

Warning message:

In install.packages(pkgs = pkgs, repos = repos, ...) :

  installation of package 'EBImage' had non-zero exit status



Any suggestions/ feedback would be greatly appreciated! 
Thanks
-K
Martin Morgan
#
On 12/15/2010 06:39 AM, kraman wrote:
Hi K --

This is a Bioconductor package so asking on that list is appropriate

  http://bioconductor.org/help/mailing-list/

(as is cc'ing the package maintainer,
packageDescription('EBImage')$Maintainer).

I'd guess that the ImageMagick library is not installed correctly on
your system, with the solution being to use your system software package
manager to install it correctly. In particular the path to
libImageMagickCore is probably not discovered by ldconfig or defined in
LD_LIBRARY_PATH.

With a little more detail for diagnosing this, I did
U MagickCoreTerminus

to verify that the symbol is defined in EBImage.so, and then
libMagickCore.so.3 => /usr/lib64/libMagickCore.so.3 (0x00007ff05a3b0000)
	libMagickWand.so.3 => /usr/lib64/libMagickWand.so.3 (0x00007ff05858b000

to be told where my system finds the appropriate library (guessing at
the library name for grep). Likely the command above for you indicates
'not found'. To find the location of the library I did
/usr/lib64/libMagickCore.so
/usr/lib64/libMagickCore.so.3
/usr/lib64/libMagickCore.so.3.0.0

perhaps your libMagickCore is found in a non-standard location? And then

  LD_LIBRARY_PATH=/usr/lib64/ R -e "library(EBImage)"

verifies that the issue is resolved by helping your system find the
correct libraries.

Martin

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Gregoire Pau
    

    

      
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Dear Kraman,

MagickCoreTerminus() has been present in ImageMagick for quite a long 
time. It seems likely that you're using a very old version of 
ImageMagick. Please install a newer one.

Which versions of ImageMagick, R and EBImage are using ?

Best regards,

Greg
---
Gregoire Pau
EMBL Research officer
http://www.embl.de/~gpau/

        
On 15/12/2010 15:39, kraman wrote: