[BioC] RamiGO package function getAmigoTree broken

Dan Tenenbaum dtenenba at fhcrc.org
Sat Apr 5 01:48:10 CEST 2014


Hello Asta,

----- Original Message -----
> From: "Asta Laiho" <asta.laiho at btk.fi>
> To: bioconductor at r-project.org
> Sent: Wednesday, April 2, 2014 1:37:14 AM
> Subject: [BioC] RamiGO package function getAmigoTree broken
> 
> Hi,
> 
> I have routinely used the RamiGO package (that I really like!) for
> plotting go graphs but now something seems to have gone broken for
> the getAmigoTree function:
> 

The release versionof Ramigo has been fixed. Version 1.8.1 will be available late tomorrow (Saturday) morning (Seattle time).

You can install it with:

source("http://bioconductor.org/biocLite.R")
biocLite("RamiGO")

Dan


> goIDs <- c("GO:0051130","GO:0019912","GO:0005783")
> color <- c("lightblue","red","yellow")
> pp <- getAmigoTree(goIDs=goIDs,color=color,
> +                    filename="example")
> Error during wrapup: unable to open <!DOCTYPE HTML PUBLIC
> "-//IETF//DTD HTML 2.0//EN">
> <html><head>
> <title>301 Moved Permanently</title>
> </head><body>
> <h1>Moved Permanently</h1>
> <p>The document has moved <a
> href="http://amigo.geneontology.org/visualize">here</a>.</p>
> </body></html>
> 
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] C/UTF-8/C/C/C/C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] RamiGO_1.8.0 gsubfn_0.6-5 proto_0.3-10
> 
> loaded via a namespace (and not attached):
>  [1] BiocGenerics_0.8.0 RCurl_1.95-4.1     RCytoscape_1.12.0
>   XML_3.95-0.2
>  [5] XMLRPC_0.3-0       graph_1.40.1       igraph_0.7.0
>        parallel_3.0.2
>  [9] png_0.1-7          stats4_3.0.2       tcltk_3.0.2
>         tools_3.0.2
> 
> I hope it�s possible to fix the package!
> 
> Best wishes,
> Asta Laiho
> 	[[alternative HTML version deleted]]
> 
> 
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