KEGGgraph fails on a KEGG XML file

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Rajarshi Guha ▴ 120

@rajarshi-guha-3531

Last seen 8.6 years ago

Hi, I'm using KEGGgraph on R 2.9.0 (64 bit) on OS X 10.5.7. When trying to read in the KEGG XML for hsa00051, I get the following message: > parseKGML2Graph('hsa00051.xml', genesOnly=FALSE) Error in UseMethod("xmlAttrs", node) : no applicable method for "xmlAttrs" Has anybody seen this before? -- Rajarshi Guha NIH Chemical Genomics Center

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ADD COMMENT • link updated 14.8 years ago by Jitao David Zhang ▴ 340 • written 14.8 years ago by Rajarshi Guha ▴ 120

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Chris Fjell ▴ 60

@chris-fjell-3696

Last seen 10.3 years ago

I've used KEGGgraph successfully on OS X and I recall seeing this. Can you give a link to the 'hsa00051.xm' file and I'll try to replicate the error. Remeber to give your session info as per the posting guidelines. -Chris Rajarshi Guha wrote: Hi, I'm using KEGGgraph on R 2.9.0 (64 bit) on OS X 10.5.7. When trying to read in the KEGG XML for hsa00051, I get the following message: parseKGML2Graph('hsa00051.xml', genesOnly=FALSE) Error in UseMethod("xmlAttrs", node) : no applicable method for "xmlAttrs" Has anybody seen this before?

ADD COMMENT • link 14.8 years ago Chris Fjell ▴ 60

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Seth Falcon ▴ 150

@seth-falcon-2443

Last seen 10.3 years ago

On 3/5/10 11:57 AM, Rajarshi Guha wrote: > Hi, I'm using KEGGgraph on R 2.9.0 (64 bit) on OS X 10.5.7. When > trying to read in the KEGG XML for hsa00051, I get the following > message: > >> parseKGML2Graph('hsa00051.xml', genesOnly=FALSE) > Error in UseMethod("xmlAttrs", node) : > no applicable method for "xmlAttrs" > > > Has anybody seen this before? That error looks slightly familiar. I would try installing the latest XML package. And I would also recommend upgrading to the latest R release and installing the newer Bioconductor packages. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user

ADD COMMENT • link 14.8 years ago Seth Falcon ▴ 150

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Jitao David Zhang ▴ 340

@jitao-david-zhang-3188

Last seen 7.9 years ago

Hi dear Rajarshi Guha, This is probably caused by an oder version of XML package. Please update it. Best wishes, David 2010/3/5 Rajarshi Guha <rajarshi.guha@gmail.com> > Hi, I'm using KEGGgraph on R 2.9.0 (64 bit) on OS X 10.5.7. When > trying to read in the KEGG XML for hsa00051, I get the following > message: > > > parseKGML2Graph('hsa00051.xml', genesOnly=FALSE) > Error in UseMethod("xmlAttrs", node) : > no applicable method for "xmlAttrs" > > > Has anybody seen this before? > > -- > Rajarshi Guha > NIH Chemical Genomics Center > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Biological Statistics and Computational Biology Ph.D. Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]

ADD COMMENT • link 14.8 years ago Jitao David Zhang ▴ 340

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Indeed. With the latest XML package it works fine On Mar 7, 2010, at 5:36 AM, Jitao David Zhang wrote: > Hi dear Rajarshi Guha, > > This is probably caused by an oder version of XML package. Please > update it. > > Best wishes, > David > > 2010/3/5 Rajarshi Guha <rajarshi.guha at="" gmail.com=""> > Hi, I'm using KEGGgraph on R 2.9.0 (64 bit) on OS X 10.5.7. When > trying to read in the KEGG XML for hsa00051, I get the following > message: > > > parseKGML2Graph('hsa00051.xml', genesOnly=FALSE) > Error in UseMethod("xmlAttrs", node) : > no applicable method for "xmlAttrs" > > > Has anybody seen this before? > > -- > Rajarshi Guha > NIH Chemical Genomics Center > > _______________________________________________ > 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 > > > > -- > Jitao David Zhang > Biological Statistics and Computational Biology Ph.D. > Division of Molecular Genome Analysis > DKFZ, Heidelberg D-69120, Germany > > http://www.NextBioMotif.com/ ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov

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