[BioC] Problem with saveXML on mac

[hdvi at well.ox.ac.uk]

Hi Duncan and others,

I have a problem with saveXML. I'm trying to to this:

> saveXML(toGXL(test), file="test.gxl")

where 'test' is an object of class graphNEL. This works fine on a linux
and PC, but not on mac, which is my standard machine for running R
(sessionInfo below).

> saveXML(toGXL(test), file="test.gxl")
Error in NextMethod("saveXML", object = doc$value()) :
	no method to invoke
> methods(saveXML)
[1] saveXML.XMLInternalDOM*      saveXML.XMLInternalDocument*
saveXML.XMLNode*             saveXML.XMLOutputStream*
   Non-visible functions are asterisked

Any ideas?

Thanks
\Heidi

## MAC ##
> sessionInfo()
R version 2.4.1 (2006-12-18)
i386-apple-darwin8.8.1

locale:
en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
geneplotter     GOstats    Category  genefilter    survival        KEGG   
    RBGL    annotate     Biobase
   "1.12.0"     "2.0.4"     "2.0.3"    "1.12.0"      "2.30"    "1.14.1"   
"1.10.0"    "1.12.1"    "1.12.2"
         GO       graph         XML
   "1.14.1"    "1.12.1"     "1.6-0"

## LINUX ##
> sessionInfo()
R version 2.5.0 alpha (2007-03-30 r40957)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
          XML       GOstats      Category AnnotationDbi       RSQLite
      "1.6-2"      "2.1.13"      "2.1.28"      "0.0.56"       "0.5-3"
          DBI        Matrix       lattice    genefilter      survival
      "0.2-1"   "0.9975-11"      "0.15-1"     "1.13.12"        "2.31"
         KEGG          RBGL      annotate       Biobase            GO
    "1.15.13"      "1.11.4"      "1.13.8"     "1.13.44"     "1.15.13"
        graph
     "1.13.9"

## PC##

Don't have the sessionInfo here, but it's back with R2.0

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Heidi Dvinge

European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
Mail: heidi at ebi.ac.uk
Phone: +44 (0) 1223 492 550
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