Question: Error in getAmigoTree (RamiGO package)
0
gravatar for suzy.stiegelmeyer@syngenta.com
5.2 years ago by
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}}
ramigo • 823 views
ADD COMMENTlink modified 5.2 years ago by Dan Tenenbaum8.2k • written 5.2 years ago by suzy.stiegelmeyer@syngenta.com40
Answer: Error in getAmigoTree (RamiGO package)
0
gravatar for Dan Tenenbaum
5.2 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
----- Original Message ----- > From: "suzy stiegelmeyer" <suzy.stiegelmeyer at="" syngenta.com=""> > To: bioconductor at r-project.org > Sent: Friday, March 14, 2014 12:48:55 PM > Subject: [BioC] Error in getAmigoTree (RamiGO package) > > 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 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="grmzm2g3230 24_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 >
ADD COMMENTlink written 5.2 years ago by Dan Tenenbaum8.2k
Hi again, I think I have found a work around by editing the source code. In the file getAmigoTree.R, change the following: Change line 1 from getAmigoTree <- function(goIDs, color, pvalues, pcolors = c("white","tomato"), psplit = c(1,0.25,0.1,0.05,0.001), filename, picType = "png", modeType = "advanced", webserver, saveResult = TRUE) to getAmigoTree <- function(goIDs, color, pvalues, pcolors = c("white","tomato"), psplit = c(1,0.25,0.1,0.05,0.001), filename, picType = "png", modeType = "amigo", webserver, saveResult = TRUE) Line 4 from webserver <-"http://amigo.geneontology.org/cgi-bin/amigo/visualize" to webserver <-"http://amigo.geneontology.org/visualize" Change line 37 from if(modeType != "advanced"){ to if(modeType != "amigo"){ -Suzy -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Friday, March 14, 2014 3:53 PM To: Stiegelmeyer Suzy USRE Cc: bioconductor at r-project.org; Markus Schroeder Subject: Re: [BioC] Error in getAmigoTree (RamiGO package) ----- Original Message ----- > From: "suzy stiegelmeyer" <suzy.stiegelmeyer at="" syngenta.com=""> > To: bioconductor at r-project.org > Sent: Friday, March 14, 2014 12:48:55 PM > Subject: [BioC] Error in getAmigoTree (RamiGO package) > > 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> > 301 Moved Permanently > </head><body> >

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.
ADD REPLYlink written 5.2 years ago by suzy.stiegelmeyer@syngenta.com40
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