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

[James W. MacDonald]

Hi Simon,

Simon Urbanek wrote:
> 
> 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.

The recipe for failure is directed towards BioC packages, which tend to 
have complicated dependencies. A significant proportion of the questions 
on the BioC listserv are due to people downloading things directly and 
installing and then wondering why they don't work (because they have the 
wrong version, are missing dependencies, etc).

The affy package is a perfect example. It relies on affyio and 
preprocessCore, so if any one package is out of sync you can get weird 
errors that would have been avoided by using biocLite().

> 
> 
>> 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 ...

Good call. I somehow translated .tgz to .tar.gz when I read the original 
post. My bad.

Best,

Jim


> 
> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
> 

-- 
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