[BioC] error while loading the genefilter package [R 2.8.1. on Mac OSX 10.5.6]

[Patrick Aboyoun]

Massimo,
The problem is in the version of the genefilter Mac OS X 10.5 (Leopard) 
binary package you are using. I just downloaded genefilter version 1.22 
for BioC 2.3 from bioconductor.org and don't see the dynamic linking to 
libgfortran that is suggested by your error message:

sandbox$ otool -L genefilter/libs/i386/genefilter.so
genefilter/libs/i386/genefilter.so:
    genefilter.so (compatibility version 0.0.0, current version 0.0.0)
    
/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libR.dylib 
(compatibility version 2.8.0, current version 2.8.0)
    
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 
(compatibility version 150.0.0, current version 476.15.0)
    /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current 
version 7.4.0)
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current 
version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 111.1.1)

Try to reinstall genefilter using biocLite("genefilter") and let me know 
if the problem persists. Perhaps it is with a different library. Include 
your sessionInfo() in your response so I can help troubleshoot any 
problems that arise.


Patrick


Massimo Pinto wrote:
> Greetings BioC list readers,
>
> on a Mac OSX 10.5.6 with R 2.8.1 I have successfully installed a series of
> packages by typing the following code on the R Console.
>
>   
>>     source("http://bioconductor.org/biocLite.R")
>>     biocLite()
>>     
>
> [...]
>
> however, this is what I am getting when I try to load genefilter, which is
> required by the package Agi4x44PreProcess
>
>   
>> library(genefilter)
>>     
> 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)'.
>
> Loading required package: survival
> Loading required package: splines
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so':
>   dlopen(/Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so,
> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>   Referenced from:
> /Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so
>   Reason: image not found
> Error: package/namespace load failed for 'genefilter'
>
> There is no /Library/Frameworks/ directory on my disk. Looks like I have got
> a messy installation. Does this look familiar to any of you?
> Yours,
> Massimo
>
>