[BioC] Problem with saveXML on mac

[hdvi at well.ox.ac.uk]

Hi Duncan,

I ran the XML as you specified below, and got version 1.6-2, instead of
1.6-0 which is the CRAN version. When trying the run saveXML the error
message persists though.

I think it might be a problem with my R installation (R version 2.4.1
(2006-12-18) built from binary), since the function seems to work on
another mac (built from source). Also, it worked on a PC, which has an XML
version older than the 1.6-0. Haven't had any other problems with R on
this mac though.

Cheers
\Heidi

>
> 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
>> ------------<<>>------------
>>
>