[Bioc-devel] GOstats won't load with BioC 2.0

[Mark W Kimpel]

I can't get GOstats to load in BioC 2.0. New and old versions load with 
BioC 1.9, but neither will load with BioC1.9.

Possibly a coincidence, but tonight I just installed the latest Biobase 
version.

Attached is error, some debugging info, and sessionInfo()  Thanks, Mark

Enter a frame number, or 0 to exit

1: limma.contrast.output.func(affy.object.preprocessed, fit2, rslt, 
contrast.num = 1, pheno.trait = "Treatment", anal.pref, ap.cutoff = 0.5, 
IQR.cutoff = 25, named.gene.filte
2: GO.anal.func(t.tab.annot.obj, initialPValue, FDR_Threshold, 
maxIterations, plateauIterations, pValueDecrementer, testDirection, 
sig.gene.threshold, total.gene.min, total.g
3: require(GOstats)
4: library(package, lib.loc = lib.loc, character.only = TRUE, logical = 
TRUE, warn.conflicts = warn.conflicts, keep.source = keep.source, 
version = version)
5: try({
6: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = 
keep.source)

Selection: 0
Loading required package: rat2302
[1] 1


 > sessionInfo()
R version 2.5.0 Under development (unstable) (2007-01-31 r40628)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "stats"     "graphics"  "grDevices" "datasets"  "utils" 
     "tools"     "methods"   "base"

other attached packages:
         rat2302        Category            KEGG            RBGL 
annotate              GO           graph xlsReadWritePro          qvalue 
      rat2302cdf      genefilter
        "1.15.0"        "2.1.14"        "1.15.1"        "1.11.4" 
"1.13.6"        "1.15.1"        "1.13.6"         "1.0.6"         "1.9.0" 
        "1.15.0"        "1.13.8"
        survival           limma            affy          affyio 
  Biobase
          "2.31"         "2.9.9"       "1.13.14"         "1.3.3" 
"1.13.36"
-- 
Mark W. Kimpel MD
Neuroinformatics
Department of Psychiatry
Indiana University School of Medicine