[BioC] affy won't load

jason smith sjorges2002 at yahoo.com
Sun Jun 15 03:22:55 CEST 2008


Hi, 

First I'd like to thank everyone for bioconductor- it has been very useful. I have installed R 2.7.0 GUI 1.24 (5102) on an intel Mac running OS 10.5.3. R seems to be working and when I use biocLite to load 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'

What can I do to fix this?

Thanks,
Jason



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