[R-SIG-Mac] installation of affy under Mac OS X 10.5.6 (Leopard)

[Simon Urbanek]

On Apr 21, 2009, at 10:48 , James W. MacDonald wrote:

> And downloading the tarball and installing is a recipe for failure.

Why? People that don't have direct internet connection do that on a  
regular basis. You only have to make sure you don't unpack the content  
involuntarily.


> If you want to install source packages, just use the correct  
> arguments.
>
> biocLite("affy", type = "source")
>
> will get you the correct affy version plus all required dependencies.
>

I don't think Massimo was talking about source packages. That would  
require much more - you'll need Xcode tools etc. and you wouldn't see  
the error he was having since you'd be compiling it yourself. Note  
that on Mac binary packages are also tar balls and R knows what to do  
with them ...

Cheers,
Simon

PS: Normally you don't need development tools for binary packages - as  
I was pointing out there is something wrong with the binary Massimo  
was using.


>
>
> Kjell Konis wrote:
>> It looks like you don't have all the development tools installed.   
>> The missing library /usr/local/lib/libgfortran.2.dylib is part of  
>> the Fortran compiler which is included with the full R installer.
>> Kjell
>> On 21 avr. 09, at 15:10, Massimo Pinto wrote:
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>> '/Library/Frameworks/R.framework/Resources/library/preprocessCore/ 
>>> libs/i386/preprocessCore.so':
>>> dlopen(/Library/Frameworks/R.framework/Resources/library/ 
>>> preprocessCore/libs/i386/preprocessCore.so,
>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>> Referenced from:
>>> /Library/Frameworks/R.framework/Resources/library/preprocessCore/ 
>>> libs/i386/preprocessCore.so
>>> Reason: image not found
>>> Error: package/namespace load failed for 'affy'
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>
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