Question: KEGGSOAP - Error in xmlName(node[[1]]) : no applicable method for "xmlName"
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gravatar for michael watson IAH-C
14.6 years ago by
michael watson IAH-C3.4k wrote:
Hi I sorted out the proxy problem with a rather embarassingly easy call to Sys.putenv(). Anyway, now I have lots of KEGGSOAP functions working but I get the following error: > get.pathways.by.genes("stm:STM0002") Error in xmlName(node[[1]]) : no applicable method for "xmlName" I get this error for any gene I enter. In fact, stm:STM0002 is in a pathway, it's in "stm00260 Glycine, serine and threonine metabolism". I also got lots of warnings from a previous call: > get.genes.by.organism("stm",1,10) Type: string & length = 10 [1] "stm:STM0001" "stm:STM0002" "stm:STM0003" "stm:STM0004" "stm:STM0005" "stm:STM0006" [7] "stm:STM0007" "stm:STM0008" "stm:STM0009" "stm:STM0010" Warning messages: 1: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 2: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 3: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 4: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 5: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 6: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 7: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 8: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 9: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, 10: Don't understand the SOAP type `string' yet in: fromSOAP(x, root = root, converters = converters, findReturn = FALSE, Any help would be very much appreciated! Thanks Mick
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