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Yan Jiao ▴ 140
@yan-jiao-4354
Last seen 8.1 years ago
Hi I'm trying to ues retrieveKGML from KEGGgraph package: retrieveKGML(pathwayid="05211", organism="hsa", destfile=tmp) Warning message: In download.file(kgml, destfile = destfile, method = method, ...) : download had nonzero exit status colFile <- system.file("extdata/hsa05211.xml",package="KEGGgraph") g <- parseKGML2Graph(colFile) Error: does not seem to be XML, nor to identify a file name as you can see I got warning message, is it ok? I don't think it worked properly, since I got error after I ran parse KGML2Graph, I guess i need to install wget, but can't find wget for win 64. any suggestion? many thanks yan ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}}
KEGGgraph KEGGgraph • 879 views
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@jitao-david-zhang-3188
Last seen 5.7 years ago
Hi dear Yan, You could manually download the file from KEGG server, in case wget does not work out of any reason. Note that system.file function only provides the possibility to access the file delivered together with the package, but not the ones that you download after the installation of KEGGgraph. To do that, (1) download the file to a location (for example, C:/KEGGgraph/ in windows, or /home/username/KEGGgraph in linux) (2) in R, assign the actual file location, for example colFile <- "C:/KEGGgraph/has05211.xml" (3) call paseKGML2Graph(colFile) Best wishes, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > Hi > > > > I'm trying to ues retrieveKGML from KEGGgraph package: > > retrieveKGML(pathwayid="05211", organism="hsa", destfile=tmp) > > Warning message: > > In download.file(kgml, destfile = destfile, method = method, ...) : > > download had nonzero exit status > > colFile <- system.file("extdata/hsa05211.xml",package="KEGGgraph") > > g <- parseKGML2Graph(colFile) > > Error: does not seem to be XML, nor to identify a file name > > > > as you can see I got warning message, is it ok? I don't think it worked > properly, since I got error after I ran parse KGML2Graph, > > I guess i need to install wget, but can't find wget for win 64. > > > > > > any suggestion? > > > > many thanks > > > > yan > > > ********************************************************************** > This email and any files transmitted with it are confide...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Pre-doc staff of Computational Biology and Biostatistics Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]
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Thanks david, One stupid question, I couldn't find hsa05211 on the KEGG server. Where to download? Many thanks yan From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: 29 November 2010 12:42 To: Yan Jiao Cc: bioconductor@r-project.org Subject: Re: [BioC] (no subject) Hi dear Yan, You could manually download the file from KEGG server, in case wget does not work out of any reason. Note that system.file function only provides the possibility to access the file delivered together with the package, but not the ones that you download after the installation of KEGGgraph. To do that, (1) download the file to a location (for example, C:/KEGGgraph/ in windows, or /home/username/KEGGgraph in linux) (2) in R, assign the actual file location, for example colFile <- "C:/KEGGgraph/has05211.xml" (3) call paseKGML2Graph(colFile) Best wishes, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> Hi I'm trying to ues retrieveKGML from KEGGgraph package: retrieveKGML(pathwayid="05211", organism="hsa", destfile=tmp) Warning message: In download.file(kgml, destfile = destfile, method = method, ...) : download had nonzero exit status colFile <- system.file("extdata/hsa05211.xml",package="KEGGgraph") g <- parseKGML2Graph(colFile) Error: does not seem to be XML, nor to identify a file name as you can see I got warning message, is it ok? I don't think it worked properly, since I got error after I ran parse KGML2Graph, I guess i need to install wget, but can't find wget for win 64. any suggestion? many thanks yan ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}} _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Jitao David Zhang Pre-doc staff of Computational Biology and Biostatistics Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}}
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