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

[Robert Gentleman]

Hi Mark,
   Yes, there does seem to be something wrong with GOstats right now - 
some of the code base has been moved around.

   Unfortunately I do not have a windows computer to try and build a new 
version. If you have the right set of build tools then I recommend 
building GOstats off of the subversion archive and seeing if that fixes 
the issue.  It did for me today, but my error message was different. 
What happens if you just do
library("GOstats")
before doing anything else? Does it load then?

   Now the really bad news, most of the folks from here are enroute to 
New Zealand for the DSC and will be pretty much out of contact for at 
least a week (and more like two) so answers, help, fixes to the build 
process etc are going to be slow, and intermittent, over that time period.

  best wishes
    Robert




Mark W Kimpel wrote:
> 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"

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org