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

[Simon Urbanek]

Massimo,

On Apr 21, 2009, at 9:10 AM, Massimo Pinto wrote:

> Greetings all
> last week I attempted to install the genefilter package using
> BiocLite(genefilter) from the R prompt. Despite having a Mac OS X  
> 10.5.6.
> (Tiger), for some reason which I don't understand in full, BioC 2.3  
> believes
> I am running on Mac OS X 10.4 (Leopard)
>
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>

This shows you what kind of R you are running (i.e. where was the R  
compiled), not what your OS is. You are running the Tiger release of  
R, which is ok since it is designed for Mac OS X 10.4 (Tiger) and  
later which includes your 10.5.


> therefore, when I run biocLite, general Mac binaries are installed  
> and this results in execution errors.
>

The "therefore" is wrong here ;).


> Much thanks to the help found on this list, I have downloaded the  
> tarball for OSX 10.5 binaries and installed manually. It worked just  
> fine.
>
> Today I have encountered a similar problem with the package affy.  
> Accordingly, I have downloaded the OS X 10.5 binaries and installed  
> manually:
>
>> install.packages("/Users/massimopinto/Desktop/affy_1.20.2.tgz",  
>> repos=NULL, dependencies=TRUE)
>
> however, when I load the library:
>
>> library(affy)
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> 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'
>

The problem above doesn't come from affy, but from the preprocessCore  
package (see the error). The binary for preprocessCore you use is not  
quite correct. It uses local Fortran libraries on the machine that  
built it where it should be using the Fortran library inside R. If  
this is a binary from the BioC repository, please notify the  
maintainers, otherwise re-install the binary of preprocessCore from  
BioC. Note the the correct mailing list for such questions is BioC.

A work-around (that fixes the symptom, not the problem) is to install  
the full R (you seem to have only the mini version installed) which  
includes a local Fortran compiler - or you can install the Fortran  
manually from
http://cran.r-project.org/bin/macosx/tools/

Cheers,
Simon




> ===the package does not get loaded as a library cannot be found.  
> Similarly,
> I run into problems if I install as follows:
>
>> install.packages("affy", repos="
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/ 
> ",
> contriburl="
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/ 
> ",
> dependencies=TRUE)
> trying URL '
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8//affy_1.20.2.tgz
> '
> Content type 'application/x-gzip' length 1452708 bytes (1.4 Mb)
> [...]
>
> Could it be that the binaries at
> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/are
> in fact compiled for Tiger?
>
> Massimo
> -- 
>
> Massimo Pinto
> Post Doctoral Research Fellow
> Enrico Fermi Centre and Italian Public Health Research Institute  
> (ISS), Rome
> http://claimid.com/massimopinto
>
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>
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