[BioC] affy won't load

[Kasper Daniel Hansen]

The warning you get does not really matter. I assume you are  
installing the binary version of R on a "standard" system, not  
something like iNquery.

I am at a bit of a loss here. My version of affy does not link against  
that library, but I am on ppc. Could you try to do the following from  
Terminal
# otool -L affy.so
(where you have navigated to the folder where affy.so is, see your  
output). Have you installed the developer tools? And the stuff you get  
when you click "customize" during the R installation? Still, that  
should not be necessary. And could you please check (in R) what the  
pkgType option is set to?

Kasper

On Jun 15, 2008, at 5:56 PM, jason smith wrote:

> Hi Kasper,
>
> I downloaded and installed the latest Mac binary (R 2.7.0.dmg) from  
> CRAN. Then I ran biocLite() followed by library(affy). I have pasted  
> part of my previous msg below.
>
> I have installed R 2.7.0 GUI 1.24
> (5102) on an intel MacBook running OS 10.5.3. R seems to be working  
> and when I use biocLite to install packages I get a
> warning. Then when I try to load the packages everything seems to  
> work except affy (and some related)
> packages. Here is what I get:
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()
> Running biocinstall version 2.2.9 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> Will install the following packages:
> [1] "affy"         "affydata"     "affyPLM"      "annaffy"       
> "annotate"     "Biobase"      "Biostrings"   "DynDoc"       "gcrma"
> [10] "genefilter"   "geneplotter"  "hgu95av2.db"  "limma"         
> "marray"       "matchprobes"  "multtest"     "ROC"          "vsn"
> [19] "xtable"       "affyQCReport"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies  
> = dependencies,  :
>  argument 'lib' is missing: using '/Users/sjorges2002/Library/R/2.7/ 
> library'
>
> And later when I try to load affy:
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library '/Users/sjorges2002/Library/R/2.7/ 
> library/affy/libs/i386/affy.so':
>  dlopen(/Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/ 
> affy.so, 6): Library not
> loaded: /usr/local/lib/libintl.3.dylib
>  Referenced from: /Users/sjorges2002/Library/R/2.7/library/affy/libs/ 
> i386/affy.so
>  Reason: image not found
> Error in library(affy) : .First.lib failed for 'affy'
>
> Thanks,
> Jason
>
>
>
>