Problem with KEGGgraph
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Fraser Sim ▴ 270
@fraser-sim-3567
Last seen 8.1 years ago
Dear all, I'm having a problem with KEGGgraph. It appears the problem is located on the KEGG servers as I am unable to download the xml directly using IE/Firefox. Here's the code: > library(KEGGgraph) > url <- getKGMLurl('04330', organism = "hsa") > url [1] ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml > parseKGML(url) failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" Error: 1: failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] hgu133plus2.db_2.2.11 org.Hs.eg.db_2.2.11 Rgraphviz_1.21.11 [4] KEGGgraph_1.0.0 graph_1.22.2 XML_2.3-0 [7] KEGG.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [10] AnnotationDbi_1.6.1 Biobase_2.4.1 rcom_2.2-1 [13] rscproxy_1.3-1 loaded via a namespace (and not attached): [1] annotate_1.22.0 genefilter_1.24.2 splines_2.9.1 survival_2.35-4 [5] tools_2.9.1 xtable_1.5-5 > Thanks, Fraser
Organism hgu133plus2 KEGGgraph Organism hgu133plus2 KEGGgraph • 1.1k views
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Tony Chiang ▴ 570
@tony-chiang-1769
Last seen 8.1 years ago
Hi Fraser, Works for me: > 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/hsa0 4330.xml " > parseKGML(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) ------------------------------------------------------------ This might have something to do with your internet connection, since it does not seem to be either the package nor the repository (but I am using a different version of R so this is not exactly a reproduction of your code). > sessionInfo() R version 2.11.0 Under development (unstable) (2009-10-04 r49936) i386-apple-darwin10.0.0 locale: [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGGgraph_1.1.12 Rgraphviz_1.23.5 graph_1.23.7 XML_2.6-0 loaded via a namespace (and not attached): [1] tools_2.11.0 Cheers, --Tony On Tue, Oct 13, 2009 at 7:59 AM, Fraser Sim <fjsim@buffalo.edu> wrote: > Dear all, > > I'm having a problem with KEGGgraph. It appears the problem is located on > the KEGG servers as I am unable to download the xml directly using > IE/Firefox. > > Here's the code: > > > library(KEGGgraph) > > url <- getKGMLurl('04330', organism = "hsa") > > url > [1] ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml > > parseKGML(url) > failed to load external entity > "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" > Error: 1: failed to load external entity > "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" > > sessionInfo() > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] hgu133plus2.db_2.2.11 org.Hs.eg.db_2.2.11 Rgraphviz_1.21.11 > [4] KEGGgraph_1.0.0 graph_1.22.2 XML_2.3-0 > [7] KEGG.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [10] AnnotationDbi_1.6.1 Biobase_2.4.1 rcom_2.2-1 > [13] rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 genefilter_1.24.2 splines_2.9.1 survival_2.35-4 > [5] tools_2.9.1 xtable_1.5-5 > > > > Thanks, > Fraser > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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Hi Tony, >From your sessionInfo, It looks like your using the devel branch of Bioconductor (2.11). Can you check with the current release version? My internet seems fine now as I am able to see the xml file if I link directly to the ftp site in IE. I still get the error in R. Cheers, Fraser From: tc.fhcrc@gmail.com [mailto:tc.fhcrc@gmail.com] On Behalf Of Tony Chiang Sent: Tuesday, October 13, 2009 11:30 AM To: Fraser Sim Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Problem with KEGGgraph Hi Fraser, Works for me: > 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) 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) ------------------------------------------------------------ This might have something to do with your internet connection, since it does not seem to be either the package nor the repository (but I am using a different version of R so this is not exactly a reproduction of your code). > sessionInfo() R version 2.11.0 Under development (unstable) (2009-10-04 r49936) i386-apple-darwin10.0.0 locale: [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGGgraph_1.1.12 Rgraphviz_1.23.5 graph_1.23.7 XML_2.6-0 loaded via a namespace (and not attached): [1] tools_2.11.0 Cheers, --Tony On Tue, Oct 13, 2009 at 7:59 AM, Fraser Sim <fjsim@buffalo.edu> wrote: Dear all, I'm having a problem with KEGGgraph. It appears the problem is located on the KEGG servers as I am unable to download the xml directly using IE/Firefox. Here's the code: > library(KEGGgraph) > url <- getKGMLurl('04330', organism = "hsa") > url [1] ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml > parseKGML(url) failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" Error: 1: failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] hgu133plus2.db_2.2.11 org.Hs.eg.db_2.2.11 Rgraphviz_1.21.11 [4] KEGGgraph_1.0.0 graph_1.22.2 XML_2.3-0 [7] KEGG.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [10] AnnotationDbi_1.6.1 Biobase_2.4.1 rcom_2.2-1 [13] rscproxy_1.3-1 loaded via a namespace (and not attached): [1] annotate_1.22.0 genefilter_1.24.2 splines_2.9.1 survival_2.35-4 [5] tools_2.9.1 xtable_1.5-5 > Thanks, Fraser _______________________________________________ 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 [[alternative HTML version deleted]]
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Hi, Fraser, I used R2.10.0 (whose beta version is released today) and KEGGgraph1.1.12, and it works just fine. When I used KEGGgraph_1.1.0 on R-2.9, I got the same error message as you got. Anyhow, it seems your version of KEGGgraph seems old, even for R-2.9. You can first try to update your package on R-2.9. If it still doesn't work, you can try to upgrade R to R-2.10. Hope this helps. Cheers, Chao-Jen > sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-11 r49665) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGGgraph_1.1.12 Rgraphviz_1.23.4 graph_1.23.2 XML_2.5-0 Fraser Sim wrote: > Hi Tony, > > > > >From your sessionInfo, It looks like your using the devel branch of > Bioconductor (2.11). Can you check with the current release version? > > > > My internet seems fine now as I am able to see the xml file if I link > directly to the ftp site in IE. I still get the error in R. > > > > Cheers, > > Fraser > > > > From: tc.fhcrc at gmail.com [mailto:tc.fhcrc at gmail.com] On Behalf Of Tony > Chiang > Sent: Tuesday, October 13, 2009 11:30 AM > To: Fraser Sim > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem with KEGGgraph > > > > Hi Fraser, > > Works for me: > > >> 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) >> > 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) > ------------------------------------------------------------ > > This might have something to do with your internet connection, since it does > not seem to be either the package nor the repository (but I am using a > different version of R so this is not exactly a reproduction of your code). > > >> sessionInfo() >> > R version 2.11.0 Under development (unstable) (2009-10-04 r49936) > i386-apple-darwin10.0.0 > > locale: > [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] KEGGgraph_1.1.12 Rgraphviz_1.23.5 graph_1.23.7 XML_2.6-0 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Cheers, > --Tony > > On Tue, Oct 13, 2009 at 7:59 AM, Fraser Sim <fjsim at="" buffalo.edu=""> wrote: > > Dear all, > > I'm having a problem with KEGGgraph. It appears the problem is located on > the KEGG servers as I am unable to download the xml directly using > IE/Firefox. > > Here's the code: > > >> library(KEGGgraph) >> url <- getKGMLurl('04330', organism = "hsa") >> url >> > [1] ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml > >> parseKGML(url) >> > failed to load external entity > "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" > Error: 1: failed to load external entity > "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04330.xml" > >> sessionInfo() >> > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] hgu133plus2.db_2.2.11 org.Hs.eg.db_2.2.11 Rgraphviz_1.21.11 > [4] KEGGgraph_1.0.0 graph_1.22.2 XML_2.3-0 > [7] KEGG.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [10] AnnotationDbi_1.6.1 Biobase_2.4.1 rcom_2.2-1 > [13] rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 genefilter_1.24.2 splines_2.9.1 survival_2.35-4 > [5] tools_2.9.1 xtable_1.5-5 > > > Thanks, > Fraser > > _______________________________________________ > 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 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
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