Entering edit mode
@suzystiegelmeyersyngentacom-5940
Last seen 9.1 years ago
United States
Hi everyone,
I'm having some trouble with the RamiGO package. I'm getting an error
when executing getAmigoTree. Can anyone recommend a workaround?
Maybe the server is having a bad day but it is hard to tell. Here is
a log of what is happening:
> ids=c("GO:0009058","GO:0015995")
> pngamigo=getAmigoTree(goIDs=ids,color="pink",filename="test_bp.png",
picType="png",saveResult=T)
Error in readPNG(aa) :
unable to open
<html><head>
<title>301 Moved Permanently</title>
</head><body>
Moved Permanently
The document has moved here.
</body></html> Looking in the code it has the default server as webserver <- http://amigo.geneontology.org/cgi-bin/amigo/visualize. I tried a new webserver according to the "moved permanently message" above, but no luck. > pngamigo=getAmigoTree(goIDs=ids,color="pink",filename="grmzm2g323024 _bp.png",picType="png",webserver="http://amigo.geneontology.org/visual ize",saveResult=T) Error: Internal Server Error So, any ideas? Happy Friday BTW. Thanks, Suzy > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 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 car_2.0-19 loaded via a namespace (and not attached): [1] BiocGenerics_0.8.0 graph_1.40.1 igraph_0.7.0 MASS_7.3-30 nnet_7.3-7 [6] parallel_3.0.3 png_0.1-7 RCurl_1.95-4.1 RCytoscape_1.12.0 stats4_3.0.3 [11] tcltk_3.0.3 tools_3.0.3 XML_3.98-1.1 XMLRPC_0.3-0 _________________________________ Suzy Stiegelmeyer, PhD Computational Biologist Bioinformatics Syngenta Biotechnology, Inc. 3054 Cornwallis Rd Research Triangle Park, NC 27709 USA phone +1 919 281 7472 suzy.stiegelmeyer@syngenta.com<mailto:suzy.stiegelmeyer@syngenta.com> www.syngenta.com<http: www.syngenta.com=""/> This message may contain confidential information. If yo...{{dropped:7}}
Moved Permanently
>The document has moved href="http://amigo.geneontology.org/visualize">here.
> </body></html> > > Looking in the code it has the default server as webserver <- > http://amigo.geneontology.org/cgi-bin/amigo/visualize. > I tried a new webserver according to the "moved permanently message" > above, but no luck. > > pngamigo=getAmigoTree(goIDs=ids,color="pink",filename="grmzm2g323024 > > _bp.png",picType="png",webserver="http://amigo.geneontology.org/visu > > alize",saveResult=T) > Error: Internal Server Error > I think that not only has the URL moved, but the API of the web service has changed. So the Ramigo maintainer (CC'd) needs to fix the package. It's broken in both release and devel. Dan > So, any ideas? Happy Friday BTW. > Thanks, > Suzy > > > sessionInfo() > R version 3.0.3 (2014-03-06) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] > LC_TIME=English_United States.1252 > > 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 car_2.0-19 > > loaded via a namespace (and not attached): > [1] BiocGenerics_0.8.0 graph_1.40.1 igraph_0.7.0 > MASS_7.3-30 nnet_7.3-7 > [6] parallel_3.0.3 png_0.1-7 RCurl_1.95-4.1 > RCytoscape_1.12.0 stats4_3.0.3 > [11] tcltk_3.0.3 tools_3.0.3 XML_3.98-1.1 > XMLRPC_0.3-0 > _________________________________ > > Suzy Stiegelmeyer, PhD > Computational Biologist > Bioinformatics > > Syngenta Biotechnology, Inc. > 3054 Cornwallis Rd > Research Triangle Park, NC > 27709 > USA > > phone +1 919 281 7472 > > suzy.stiegelmeyer at syngenta.com<mailto:suzy.stiegelmeyer at="" syngenta.com=""> > www.syngenta.com<http: www.syngenta.com=""/> > > > > > This message may contain confidential information. If > yo...{{dropped:7}} > > _______________________________________________ > 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 > This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.