KEGGSOAP package: I can't retrieve KEGG pathway diagrams
0
0
Entering edit mode
Paolo Sonego ▴ 140
@paolo-sonego-3256
Last seen 8.4 years ago
Italy
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 hgu133a KEGGSOAP • 686 views
ADD COMMENT

Login before adding your answer.

Traffic: 527 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6