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