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Question: gene2pathway retrain() error: species \'hsa\' unknown
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6.4 years ago by
Guest User12k
Guest User12k wrote:
Hi, when using retrain() in the gene2pathway library I get the following error: library(gene2pathway) > retrain() Retrieving KEGG information via SOAP ... xmlns: URI SOAP/KEGG is not absolute xmlns: URI SOAP/KEGG is not absolute Fehler in gene2pathway:::buildTrainingSet(minnmap = minnmap, level1Only = level1Only, : Organism 'hsa' is unknown in KEGG! Please refer to <url:http: www.genome.jp="" kegg-bin="" create_kegg_menu=""> for a complete list of supported organisms. library(gene2pathway) leads to the following output: Warnmeldungen: 1: Class "VirtualSOAPClass" is defined (with package slot ???SSOAP???) but no metadata object found to revise subclass information---not exported? Making a copy in package ???.GlobalEnv??? 2: Class "VirtualXMLSchemaClass" is defined (with package slot ???XMLSchema???) but no metadata object found to revise subclass information---not exported? Making a copy in package ???.GlobalEnv??? I have no idea how to solve that problem... Best regards Carl -- output of sessionInfo(): > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] gene2pathway_2.10.0 keggorthology_2.8.0 hgu95av2.db_2.7.1 [4] org.Hs.eg.db_2.7.1 org.Dm.eg.db_2.7.1 RSQLite_0.11.1 [7] DBI_0.2-5 AnnotationDbi_1.18.1 Biobase_2.16.0 [10] BiocGenerics_0.2.0 RBGL_1.32.1 graph_1.34.0 [13] KEGGSOAP_1.30.0 biomaRt_2.12.0 kernlab_0.9-14 loaded via a namespace (and not attached): [1] codetools_0.2-8 IRanges_1.14.3 RCurl_1.91-1 SSOAP_0.8-0 [5] stats4_2.15.0 tools_2.15.0 XML_3.9-4 XMLSchema_0.7-2 -- Sent via the guest posting facility at bioconductor.org.
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