[BioC] Problems with SVGAnnotation package

[Martin Morgan]

On 04/29/2013 06:58 PM, Dan Tenenbaum wrote:
> Hi Kevin,
>
>
>
> On Mon, Apr 29, 2013 at 2:10 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
>> Hi,
>>
>> I'm having trouble using the SVGAnnotation package with R 3.0.0. In
>> particular, I'm unable to run any of the examples available at
>> http://www.omegahat.org/SVGAnnotation/tests/examples.html ; these all
>> worked AFAIK with R prior to 3.0.0. Here's some example output from trying
>> to run the first example on the page:
>>
>>> ?SVGAnnotation
>>> svg("pairs_link.svg", 14, 10)
>>> pairs(mtcars[,1:3], cex = 2)
>>> dev.off()
>> RStudioGD
>>          2
>>>
>>> doc = xmlParse("pairs_link.svg")
>>> linkPlots(doc)
>> Error in tmp[i] : invalid subscript type 'list'
>>> saveXML(doc, "pairs_link.svg")
>> [1] "pairs_link.svg"
>>
>> Note the error occuring with 'linkPlots(doc)'. Tracebacks suggest the error
>> occurs in 'getPlotRegionNodes'; however, I am not familiar enough with the
>> package to debug further.
>>
>>> sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] SVGAnnotation_0.93-1 XML_3.95-0.2

The example above 'worked for me' with XML 3.96-1.1, which is available in 
source but binary from CRAN; it could be that

   biocLite("XML", type="source")

does the trick (or perhaps causes more headaches...; probably it requires a 
'devel' version of libxml installed, and I don't know how that works on Mac...)

Martin

>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.0.0
>>
>> Any insight would be helpful.
>>
>
> I recommend contacting
> packageDescription("SVGAnnotation")$Maintainer
> as this is not a Bioconductor package (it's not a CRAN package either).
> Dan
>
>
>> Thanks,
>> -Kevin
>>
>>          [[alternative HTML version deleted]]
>>
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