Hi All, I am running into a problem with KEGGgraph package. After loading all libraries and downloading hsa05200.xml I run: cancerKGML <- system.file("hsa05200.xml",package="KEGGgraph"); but then, on running cancerG <- parseKGML2Graph(cancerKGML,expandGenes=TRUE); I get: Error: XML content does not seem to be XML, nor to identify a file name '' Any ideas? Many thanks, Eric -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.7.1 KEGG.db_2.7.1 RSQLite_0.11.2 [4] DBI_0.2-5 AnnotationDbi_1.18.4 Biobase_2.16.0 [7] BiocGenerics_0.2.0 KEGGgraph_1.12.0 graph_1.34.0 [10] XML_3.95-0.1 loaded via a namespace (and not attached): [1] IRanges_1.14.4 stats4_2.15.0 tools_2.15.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Eric, I see a couple of difficulties in your (nicely) provided code. Try this: dir(system.file("extdata",package="KEGGgraph")) and you will see that hsa05200 is not amongh the 14 xml files included with the package. Two suggestions: 1) If you wished to load one of those 14, you might have more success with this slight variation on what you wrote: filename <- system.file("extdata","hsa04010.xml",package="KEGGgraph") stopifnot(file.exists(filename)) Note that "extdata" needs to be included in the file path system.file helps you create. 2) To obtain files which are not included in the KEGGgraph package, take a look at ?retrieveKGML I hope this helps. - Paul On Jan 29, 2013, at 8:48 AM, eric [guest] wrote: > > > Hi All, > > I am running into a problem with KEGGgraph package. After loading > all libraries and downloading hsa05200.xml I run: > > cancerKGML <- system.file("hsa05200.xml",package="KEGGgraph"); > > but then, on running > > cancerG <- parseKGML2Graph(cancerKGML,expandGenes=TRUE); > > I get: > Error: XML content does not seem to be XML, nor to identify a file name '' > > Any ideas? Many thanks, > Eric > > > > > > -- output of sessionInfo(): > > R version 2.15.0 (2012-03-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] org.Hs.eg.db_2.7.1 KEGG.db_2.7.1 RSQLite_0.11.2 > [4] DBI_0.2-5 AnnotationDbi_1.18.4 Biobase_2.16.0 > [7] BiocGenerics_0.2.0 KEGGgraph_1.12.0 graph_1.34.0 > [10] XML_3.95-0.1 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 stats4_2.15.0 tools_2.15.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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

Hello, If you check the value of "cancerKGML" , it turns out to be an empty string. Actually the file does not exist. For an working example, use system.file("extdata/hsa05210.xml", package="KEGGgraph"). Or use your own KGML file. Best wishes, David -----Original Message----- From: eric [guest] [mailto:guest@bioconductor.org] Sent: Dienstag, 29. Januar 2013 17:49 To: bioconductor at r-project.org; aetc23_98 at yahoo.com Cc: Zhang, Jitao David {PNBE~Basel} Subject: KEGGgraph problem Hi All, I am running into a problem with KEGGgraph package. After loading all libraries and downloading hsa05200.xml I run: cancerKGML <- system.file("hsa05200.xml",package="KEGGgraph"); but then, on running cancerG <- parseKGML2Graph(cancerKGML,expandGenes=TRUE); I get: Error: XML content does not seem to be XML, nor to identify a file name '' Any ideas? Many thanks, Eric -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.7.1 KEGG.db_2.7.1 RSQLite_0.11.2 [4] DBI_0.2-5 AnnotationDbi_1.18.4 Biobase_2.16.0 [7] BiocGenerics_0.2.0 KEGGgraph_1.12.0 graph_1.34.0 [10] XML_3.95-0.1 loaded via a namespace (and not attached): [1] IRanges_1.14.4 stats4_2.15.0 tools_2.15.0 -- Sent via the guest posting facility at bioconductor.org.