[BioC] problem with GOstats, developmental version?

[Jenny Drnevich]

Hi Seth and everyone,

First, we will all miss you Seth! Good luck in your new career.  But 
while you're still with Bioconductor, hopefully you can help me with 
a problem I'm having with GOstats in R-devel 2.6.  I'm copying and 
pasting directly from the vignette GOstatsHyperG.pdf, Aug 23, 2007, 
and everything's fine until this point:

 >hgOver <- hyperGTest(params)
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function "edges", for 
signature "graphNEL"

(sessionInfo below)

I don't have this problem when following the vignette from June 8, 
2007 using R 2.5, which seems to be identical in terms of code (that 
sessionInfo below as well).  Am I missing something, or is there a 
problem somewhere in the developmental version or in a dependent 
package?  Let me know if you need more info...

Thanks,
Jenny


 > sessionInfo()
R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
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   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] hgu95av2.db_1.17.3     ALL_1.4.3              Rgraphviz_1.15.5
  [4] ath1121501_1.17.0      affyQCReport_1.15.3    geneplotter_1.15.7
  [7] lattice_0.16-3         RColorBrewer_1.0-1     simpleaffy_2.11.22
[10] made4_1.11.1           scatterplot3d_0.3-24   ade4_1.4-3
[13] affyPLM_1.13.6         affydata_1.11.3        affycoretools_1.9.4
[16] annaffy_1.9.1          KEGG_1.17.0            GO_1.17.0
[19] xtable_1.5-1           gcrma_2.9.1            matchprobes_1.9.10
[22] biomaRt_1.11.4         RCurl_0.8-1            XML_1.9-0
[25] GOstats_2.3.15         Category_2.3.28        genefilter_1.15.11
[28] survival_2.32          RBGL_1.13.6            annotate_1.15.6
[31] GO.db_1.17.1           AnnotationDbi_0.1.9    RSQLite_0.6-0
[34] DBI_0.2-3              graph_1.15.14          limma_2.11.10
[37] affy_1.15.7            preprocessCore_0.99.12 affyio_1.5.8
[40] Biobase_1.15.29

loaded via a namespace (and not attached):
[1] cluster_1.11.7     grid_2.6.0         KernSmooth_2.22-21



 > sessionInfo()
R version 2.5.0 (2007-04-23)
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"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
           ALL     Rgraphviz      hgu95av2  affyQCReport   geneplotter
       "1.4.3"      "1.14.1"      "1.16.0"      "1.14.0"      "1.14.0"
  RColorBrewer    simpleaffy         made4 scatterplot3d          ade4
       "0.2-3"     "2.10.31"      "1.10.0"      "0.3-24"       "1.4-3"
       affyPLM      affydata affycoretools       annaffy        xtable
      "1.12.0"      "1.11.2"       "1.8.0"       "1.8.1"       "1.4-6"
         gcrma   matchprobes       biomaRt         RCurl           XML
       "2.8.1"       "1.8.1"      "1.10.0"       "0.8-0"       "1.7-1"
       GOstats      Category        Matrix       lattice    genefilter
       "2.2.6"       "2.2.3"   "0.99875-2"      "0.15-8"      "1.14.1"
      survival          KEGG          RBGL      annotate            GO
        "2.31"      "1.16.0"      "1.12.0"      "1.14.1"      "1.16.0"
         graph         limma          affy        affyio       Biobase
      "1.14.2"      "2.10.5"      "1.14.1"       "1.4.0"      "1.14.0"
       RWinEdt
       "1.7-5"
 >


Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu