[BioC] Problems with SVGAnnotation package

[Dan Tenenbaum]

On Mon, Apr 29, 2013 at 7:40 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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...)
>

I have no trouble installing xml 3.96-1.1 from source on a Mountain
Lion system, but I have the same error as Kevin, unfortunately.

Dan


> 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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793