[BioC] KEGGSOAP package: I can't retrieve KEGG pathway diagrams

Paolo Sonego paolo.sonego at gmail.com
Mon Jul 6 14:52:47 CEST 2009

Dear all,

I need  to retrieve a KEGG pathway diagram using the KEGGSOAP package.
Until now it always works (time ago, thanks to the list, I solved a 
proxy problem to tell the full story).

To check my environment I c & p an example from the 
color.pathway.by.objects function help page:

             url <- color.pathway.by.objects("path:eco00260",
                            c("eco:b0002", "eco:c00263"),
                            c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))


im.gif <- readImage (url)
R: no data returned 
`http://soap.genome.jp/tmp/mark_pathway_www3_api588/eco00260.gif' @ 
Warning message:
In readImage(url) : requested image not found or could not be loaded

Using several browsers I checked the url but I can't get the diagram, at 
most (firefox 3.5) the rendering of the string:


My R session info:
 > sessionInfo()
R version 2.9.0 (2009-04-17)


attached base packages:
[1] grid      splines   stats     graphics  grDevices utils     
datasets  methods   base    

other attached packages:
 [1] hgu133a.db_2.2.12         EBImage_3.0.3             
abind_1.1-0               gplots_2.7.1              
caTools_1.9               gdata_2.4.2             
 [7] gtools_2.6.1              GEOquery_2.8.0            
RCurl_0.98-1              bitops_1.0-4.1            
KEGGSOAP_1.18.0           xtable_1.5-5            
[13] GOstats_2.10.0            graph_1.22.2              
Category_2.10.1           pamr_1.42.0               
survival_2.35-4           cluster_1.12.0          
[19] annaffy_1.16.0            KEGG.db_2.2.11            
GO.db_2.2.11              RSQLite_0.7-1             
DBI_0.2-4                 AnnotationDbi_1.6.1     
[25] genefilter_1.24.2         arrayQualityMetrics_2.2.1 
affyPLM_1.20.0            preprocessCore_1.6.0      
gcrma_2.16.0              Biostrings_2.12.7       
[31] IRanges_1.2.3             AffyExpress_1.10.0        
limma_2.18.2              affy_1.22.0               
Biobase_2.4.1             fortunes_1.3-6          

loaded via a namespace (and not attached):
 [1] GSEABase_1.6.1     RBGL_1.20.0        RColorBrewer_1.0-2 
SSOAP_0.4-6        XML_2.5-3          affyio_1.12.0      
annotate_1.22.0    beadarray_1.12.0 
 [9] hwriter_1.1        lattice_0.17-25    latticeExtra_0.6-1 
marray_1.22.0      simpleaffy_2.20.0  stats4_2.9.0       
tools_2.9.0        vsn_3.12.0

My system information:

uname -a

Linux 2.6.25-gentoo-r7 #2 SMP Wed Nov 5 17:56:30 CET 2008 x86_64 
Intel(R) Xeon(TM) CPU 3.40GHz GenuineIntel GNU/Linux


Same issue on a macbook:

 > sessionInfo()
R version 2.9.1 (2009-06-26)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] EBImage_3.0.3   abind_1.1-0     RCurl_0.98-1    bitops_1.0-4.1
[5] KEGGSOAP_1.18.0 fortunes_1.3-6  xterm256_0.0  

loaded via a namespace (and not attached):
[1] SSOAP_0.4-6 tools_2.9.1 XML_2.5-3

My macbook system information:

Darwin MacBook.local 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 
22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 i386


Any help would appreciated.


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