Hi David, Thanks. That doesn?t solve the problem though, try to get the KEGG pathway ?hsa03010? using >getCategoryIndepKGMLurl(?03010?,organism = ?hsa?) It doesn?t produce a valid html link. It should find ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/hsa/hsa03010. xml? which is correct but because 'getKGMLurl' returns the invalid ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 03010. xml?, it then returns ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/metabolic/organisms/hsa/hsa0301 0.xml? which does not exist. Note the substitution of "_" with "-". I?m pretty sure it?s a bug in getKGMLurl. Thanks, Fraser From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: Monday, November 23, 2009 5:58 AM To: Fraser Sim Cc: bioc Subject: Re: [BioC] KEGGgraph bug Hi Fraser, ? Thanks for the reporting.? The reason for this is that since April 2009 the KEGG server saves the non-metabolic and metabolic pathways in two different sub-directory separatedly, and so far as I know there is no way to tell whether the pathway is metabolic alone from the pathway id. Therefore 'getKGMLurl' can NOT garantee to return the correct address. However, 'retrieveKGML' tries both metabolic and non-metabolic pathway directories, therefore it is able to download the file remotely. ? To retrieve the URL for a pathway, use 'getCategoryIndepKGMLurl' function, which tries both non-metabolic and metabolic directories. 'getKGMLurl' will be hidden from the next release. ? I hope my answer solves your question. ? Best wishes, David 2009/11/20 Fraser Sim <fjsim at="" buffalo.edu=""> I have found a problem with how 'getKGMLurl' constructs the URL for retrieving the KGML files. It looks like the '_' should be '-' in non_metabolic portion of the generated url. I am using the current release versions, R2.10.0 and KEGGgraph 1.2.0. Thanks, Fraser > library(KEGGgraph) Loading required package: XML Loading required package: graph Attaching package: 'graph' ? ? ? ?The following object(s) are masked from package:XML : ? ? ? ? addNode Loading required package: Rgraphviz Loading required package: grid > url <- getKGMLurl('04330', organism = "hsa") > url [1] "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" > parseKGML(url) failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" Error: 1: failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" > parseKGML(gsub("_","-",url)) KEGG Pathway [ Title ]: Notch signaling pathway [ Name ]: path:hsa04330 [ Organism ]: hsa [ Number ] :04330 [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04330.png [ Link ] :http://www.genome.jp/kegg-bin/show_pathway?hsa04330 ------------------------------------------------------------ Statistics: ? ? ? ?30 node(s) ? ? ? ?16 edge(s) ? ? ? ?0 reaction(s) ------------------------------------------------------------ > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 ? ?LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United States.1252 attached base packages: [1] grid ? ? ?stats ? ? graphics ?grDevices datasets ?utils ? ? methods base other attached packages: [1] KEGGgraph_1.2.0 ?Rgraphviz_1.24.0 graph_1.24.0 ? ? XML_2.6-0 rcom_2.2-1 ? ? ? rscproxy_1.3-1 loaded via a namespace (and not attached): [1] tools_2.10.0 > _______________________________________________ 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/

Hi Fraser, I believe that David fixed this bug a couple weeks ago. Please use biocLite() to update and let us know if there are any further issues. Marc Fraser Sim wrote: > Hi David, > > Thanks. That doesn?t solve the problem though, try to get the KEGG pathway > ?hsa03010? using > > >> getCategoryIndepKGMLurl(?03010?,organism = ?hsa?) >> > > It doesn?t produce a valid html link. It should find > ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/hsa/hsa03010. > xml? which is correct but because 'getKGMLurl' returns the invalid > ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/h sa03010. > xml?, it then returns > ?ftp://ftp.genome.jp/pub/kegg/xml/kgml/metabolic/organisms/hsa/hsa03 010.xml? > which does not exist. > > Note the substitution of "_" with "-". I?m pretty sure it?s a bug in > getKGMLurl. > > Thanks, > Fraser > > From: Jitao David Zhang [mailto:davidvonpku at gmail.com] > Sent: Monday, November 23, 2009 5:58 AM > To: Fraser Sim > Cc: bioc > Subject: Re: [BioC] KEGGgraph bug > > Hi Fraser, > > Thanks for the reporting. The reason for this is that since April 2009 > the KEGG server saves the non-metabolic and metabolic pathways in two > different sub-directory separatedly, and so far as I know there is no way to > tell whether the pathway is metabolic alone from the pathway id. Therefore > 'getKGMLurl' can NOT garantee to return the correct address. However, > 'retrieveKGML' tries both metabolic and non-metabolic pathway directories, > therefore it is able to download the file remotely. > > To retrieve the URL for a pathway, use 'getCategoryIndepKGMLurl' function, > which tries both non-metabolic and metabolic directories. 'getKGMLurl' will > be hidden from the next release. > > I hope my answer solves your question. > > Best wishes, > David > 2009/11/20 Fraser Sim <fjsim at="" buffalo.edu=""> > I have found a problem with how 'getKGMLurl' constructs the URL for > retrieving the KGML files. It looks like the '_' should be '-' in > non_metabolic portion of the generated url. I am using the current release > versions, R2.10.0 and KEGGgraph 1.2.0. > > Thanks, > Fraser > > >> library(KEGGgraph) >> > Loading required package: XML > Loading required package: graph > > Attaching package: 'graph' > > > The following object(s) are masked from package:XML : > > addNode > > Loading required package: Rgraphviz > Loading required package: grid > >> url <- getKGMLurl('04330', organism = "hsa") >> url >> > [1] > "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/h sa04330. > xml" > >> parseKGML(url) >> > failed to load external entity > "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/h sa04330. > xml" > Error: 1: failed to load external entity > "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/h sa04330. > xml" > >> parseKGML(gsub("_","-",url)) >> > KEGG Pathway > [ Title ]: Notch signaling pathway > [ Name ]: path:hsa04330 > [ Organism ]: hsa > [ Number ] :04330 > [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04330.png > [ Link ] :http://www.genome.jp/kegg-bin/show_pathway?hsa04330 > ------------------------------------------------------------ > Statistics: > 30 node(s) > 16 edge(s) > 0 reaction(s) > ------------------------------------------------------------ > >> sessionInfo() >> > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > base > > other attached packages: > [1] KEGGgraph_1.2.0 Rgraphviz_1.24.0 graph_1.24.0 XML_2.6-0 > rcom_2.2-1 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > _______________________________________________ > 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 > > > >