KEGGSOAP returning blank pages

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Daniel Brewer ★ 1.9k

@daniel-brewer-1791

Last seen 9.6 years ago

Hello, I had KEGGSOAP working well a few months ago, but now when I try to do anything the returned URL is just a blank page. For example: library(KEGGSOAP) mark.pathway.by.objects("path:hsa04110",c("hsa:595","hsa:7157")) [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api23284/hsa04110.gif" Am I doing something wrong is this a problem at KEGG's servers? Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

Cancer KEGGSOAP Cancer KEGGSOAP • 988 views

ADD COMMENT • link updated 14.7 years ago by Marc Carlson ★ 7.2k • written 14.7 years ago by Daniel Brewer ★ 1.9k

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 7.7 years ago

United States

Hi Daniel, I have been exploring this and the problem does appear to be on the server side. Our code has not changed and worked fine until recently. It is not clear whether their server has indigestion or if they have changed something. But if their API has changed for some reason, I have not been able to find a corresponding change in their documentation to indicate this, so I actually suspect that their server is just misbehaving. I have written to them to let them know that something is amiss. Hopefully this will be resolved soon. Marc Daniel Brewer wrote: > Hello, > > I had KEGGSOAP working well a few months ago, but now when I try to do > anything the returned URL is just a blank page. For example: > > library(KEGGSOAP) > mark.pathway.by.objects("path:hsa04110",c("hsa:595","hsa:7157")) > [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api23284/hsa04110.gif" > > Am I doing something wrong is this a problem at KEGG's servers? > > Thanks > > Dan > >

ADD COMMENT • link 14.7 years ago Marc Carlson ★ 7.2k

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Hi, Daniel, Thank you for pointing the error. We have fixed KEGGSOAP in BioC 2.5. If you can install R development version 2.10.0, then you will be able to download the newest version of KEGGSOAP (v1.19.1) which should give you the graph that you used to get. Listed below is my sessionInfo(). Regards, Chao-Jen > library(KEGGSOAP) > sessionInfo() R version 2.10.0 Under development (unstable) (2009-06-03 r48708) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGGSOAP_1.19.1 loaded via a namespace (and not attached): [1] RCurl_0.98-1 SSOAP_0.4-6 XML_2.5-0 Marc Carlson wrote: > Hi Daniel, > > I have been exploring this and the problem does appear to be on the > server side. Our code has not changed and worked fine until recently. > It is not clear whether their server has indigestion or if they have > changed something. But if their API has changed for some reason, I have > not been able to find a corresponding change in their documentation to > indicate this, so I actually suspect that their server is just > misbehaving. I have written to them to let them know that something is > amiss. Hopefully this will be resolved soon. > > Marc > > > > Daniel Brewer wrote: > >> Hello, >> >> I had KEGGSOAP working well a few months ago, but now when I try to do >> anything the returned URL is just a blank page. For example: >> >> library(KEGGSOAP) >> mark.pathway.by.objects("path:hsa04110",c("hsa:595","hsa:7157")) >> [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api23284/hsa04110.gif" >> >> Am I doing something wrong is this a problem at KEGG's servers? >> >> Thanks >> >> Dan >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org

ADD REPLY • link 14.7 years ago Chao-Jen Wong ▴ 580

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