[BioC] Problem with saveXML on mac

[Duncan Temple Lang]

Hi Heidi

 This is one is reasonably easy, I hope.
You need version 1.6-1 or higher on your Mac.
You have it on your Linux machine, but not on your Mac.
That may be because you are getting a binary version
from a repository and that is not up to date
with the releases from the Omegahat site.
If you have the compilers installed on your Mac,
the R command

  install.packages("XML", repos = "http://www.omegahat.org/R",
                      type = "source")

will get the latest version (1.6-3) and build it.

  D.

hdvi at well.ox.ac.uk wrote:
> 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
> 
> ------------<<>>------------
> 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
> ------------<<>>------------
>