Hi Mark, I've added the function that a need to the package (in bold), as a copy of an existing function, bellow, in the KEGGSOAP.R, and then installed the function successfully, but I got this erro message, when I am installing or loading the package Note: Method with signature "PrimitiveSOAPType#list" chosen for function "resolve", target signature "PrimitiveSOAPType#SchemaCollection". "SOAPType#SchemaCollection" would also be valid Note: Method with signature "ArrayType#list" chosen for function "resolve", target signature "ArrayType#SchemaCollection". "SimpleSequenceType#SchemaCollection" would also be valid Mensagens de aviso perdidas: 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’ is there sometinhg more that I've to change? Can I redistribute this package with my own just letting the credits? *get.reactions.by.compound function compound.id) { unlist(.SOAP(KEGGserver, "get_reactions_by_compound", .soapArgs = list(compound_id = compound.id), action = KEGGaction, xmlns = KEGGxmlns, nameSpaces = SOAPNameSpaces(version = KEGGsoapns))) } <environment: namespace:keggsoap="">* * *get.reactions.by.pathway function pathway.id) { unlist(.SOAP(KEGGserver, "get_reactions_by_pathway", .soapArgs = list(pathway_id = pathway.id), action = KEGGaction, xmlns = KEGGxmlns, nameSpaces = SOAPNameSpaces(version = KEGGsoapns))) } <environment: namespace:keggsoap=""> On Sat, Mar 3, 2012 at 12:27 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 03/02/2012 09:46 AM, Ricardo Silva wrote: >> >> Hi, >> I would like to know if I can have access to zzz.R file of KEGGSOAP. > > > individual package files are available in the 'source' .tar.gz file > referenced on this page > > http://bioconductor.org/packages/release/bioc/html/KEGGSOAP.html > > or via svn > > http://bioconductor.org/packages/release/bioc/html/KEGGSOAP.html > > as described here > > http://bioconductor.org/developers/source-control/ > > KEGGSOAP/R/zzz.R contains the definition of a single function, > KEGGSOAP:::.onLoad > > Martin > >> >> best regards >> >> Ricardo >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 [[alternative HTML version deleted]]

Hi Ricardo, Sorry about the delay. Things are going into "release mode" around here, which means we are all extremely busy. These warnings are not really new for KEGGSOAP and I would not worry too much about them. The functions you wrote appear to work just fine and it is possible that others may find them useful. With your permission, I would love to add them to the package. If you provide me with a manual page describing them (with your name as the author) then I will be happy to add them to the existing KEGGSOAP package for you. Marc On 03/07/2012 09:46 AM, Ricardo Silva wrote: > Hi everyone, > > I've added a function that I need to the KEGGSOAP package (in bold), as a > copy of an existing function, bellow, in the KEGGSOAP.R, and then installed > the function successfully, but I got this error message when I am > installing or loading the package > > Note: Method with signature "PrimitiveSOAPType#list" chosen for function > "resolve", > target signature "PrimitiveSOAPType#SchemaCollection". > "SOAPType#SchemaCollection" would also be valid > Note: Method with signature "ArrayType#list" chosen for function "resolve", > target signature "ArrayType#SchemaCollection". > "SimpleSequenceType#SchemaCollection" would also be valid > Mensagens de aviso perdidas: > 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' > > is there sometinhg more that I've to change? Can I redistribute this > package with my own just letting the credits? > > *get.reactions.by.compound > function compound.id) > { > unlist(.SOAP(KEGGserver, "get_reactions_by_compound", .soapArgs = > list(compound_id =compound.id), > action = KEGGaction, xmlns = KEGGxmlns, nameSpaces = > SOAPNameSpaces(version = KEGGsoapns))) > } > <environment: namespace:keggsoap="">* > * > *get.reactions.by.pathway > function pathway.id) > { > unlist(.SOAP(KEGGserver, "get_reactions_by_pathway", .soapArgs = > list(pathway_id =pathway.id), > action = KEGGaction, xmlns = KEGGxmlns, nameSpaces = > SOAPNameSpaces(version = KEGGsoapns))) > } > <environment: namespace:keggsoap=""> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]