[BioC] EBImage install problems

[Oleg Sklyar]

Hi Crispin,

installing imagemagick from source you obviously executed the 
./configure script first, did you path the --prefix argument? If yes, 
you need to set your LD_LIBRARY_PATH and maybe LIBDIR variable to point 
to the directory included in your --prefix added /lib. E.g. by default, 
the prefix is /usr and thus the libraries are installed into /usr/lib

Search for libmagick.so on your file system and include the path to it 
into your LD_LIBRARY_PATH, on my system (default installation) it is:

* /usr/lib: ls libmagic.so.1
libmagic.so.1      libmagic.so.1.0.0

Now the libmagick9-dev is the binary package that you would install on a 
system like Ubuntu or Debian installing from repositories. On RedHat it 
is different, but in any case you do not need it if you install 
imagemagick from source.

Best,
Oleg



Wolfgang Huber wrote:
> 
> Hi Crispin,
> 
> - The libmagick9-dev package contains header files (e.g. filename.h) for 
> the libmagick9 library. AfaIk it does not contain executable code. It is 
> necessary for compiling other programs that want to use functions or 
> other symbols from libmagick9. From your description, it appears as if 
> the header files are present, and found by R CMD INSTALL, on your system.
> 
> - However, it seems that the loader does not find certain shared library 
> files. Did you set LD_LIBRARY_PATH to include the location of where you 
> installed the libmagick9 object files?
> 
>  Best wishes
>     Wolfgang
> 
> 
> Crispin Miller wrote:
>> Hi,
>> We're trying to install EBImage (2.5.0) on a 64 bit RedHat (EL4) machine
>> against R 2.8.0, in a development version of Bioconductor.
>>
>> To do this, we've installed ImageMagick 6.4.1 from source... EBImage 
>> appears
>> to install OK and compile without errors or warnings. However when we 
>> load
>> the library we get:
>>
>>
>>  > library(EBImage)
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared library
>> ...
>>
>> It's looking for EBImage.so, which is present - i.e.
>>    R/library/EBImage/libs/EBImage.so  exists.
>>
>>
>> Looking into things a bit further, we can't locate the library
>> libmagick9-dev, mentioned in the installation instructions. As we 
>> understand
>> it, this should be created if ImageMagick is installed from source. Is 
>> this
>> correct? - and can any one suggest what we need to do to make sure it's
>> built?
>> Any help much appreciated,
>>
>> Crispin
> 
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-- 
Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466