[BioC] Problem with KEGGgraph
Chao-Jen Wong
cwon2 at fhcrc.org
Tue Oct 13 22:02:15 CEST 2009
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/hsa04330.
> 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
>
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--
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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