Question: KEGGSOAP package: I can't retrieve KEGG pathway diagrams
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gravatar for Paolo Sonego
10.4 years ago by
Paolo Sonego140
Italy
Paolo Sonego140 wrote:
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: library(KEGGSOAP) url <- color.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263"), c("#ff0000", "#00ff00"), c("#ffff00", "yellow")) url [1] "http://soap.genome.jp/tmp/mark_pathway_www3_api21891/eco00260.gif" library(EBImage) im.gif <- readImage (url) R: no data returned `http://soap.genome.jp/tmp/mark_pathway_www3_api588/eco00260.gif' @ url.c/ReadURLImage/224. 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: http://soap.genome.jp/tmp/mark_pathway_www3_api21891/eco00260.gif ---------------------------- My R session info: > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: C 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) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 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. Regards, Paolo
hgu133a keggsoap • 487 views
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