[R] ebimage problems

[Martin Morgan]

On 12/15/2010 06:39 AM, kraman wrote:
> 
> 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

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

> cd ~/R/x86_64-unknown-linux-gnu-library/2.13/EBImage/libs
> R CMD nm EBImage.so |grep MagickCoreTerminus
                 U MagickCoreTerminus

to verify that the symbol is defined in EBImage.so, and then

> R CMD ldd EBImage.so |grep Magick
	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

> locate libMagickCore
/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


> 
> * removing â/usr/local/lib64/R/library/EBImageâ
> 
>  
> 
> The downloaded packages are in
> 
>         â/tmp/RtmpE4xaFL/downloaded_packagesâ
> 
> 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


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