Question: KEGGSOAP
0
gravatar for Ricardo Silva
7.6 years ago by
Ricardo Silva110
Ricardo Silva110 wrote:
Hi, I would like to know if I can have access to zzz.R file of KEGGSOAP. best regards Ricardo
keggsoap • 563 views
ADD COMMENTlink modified 7.6 years ago by Ricardo Silva20 • written 7.6 years ago by Ricardo Silva110
Answer: KEGGSOAP
0
gravatar for Martin Morgan
7.6 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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 at 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
ADD COMMENTlink written 7.6 years ago by Martin Morgan ♦♦ 23k
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]]
ADD REPLYlink written 7.6 years ago by Ricardo Silva110
Answer: KEGGSOAP
0
gravatar for Ricardo Silva
7.6 years ago by
Ricardo Silva20 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]]
ADD COMMENTlink written 7.6 years ago by Ricardo Silva20
Answer: KEGGSOAP
0
gravatar for Ricardo Silva
7.6 years ago by
Ricardo Silva110
Ricardo Silva110 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]]
ADD COMMENTlink written 7.6 years ago by Ricardo Silva110
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]]
ADD REPLYlink written 7.6 years ago by Marc Carlson7.2k
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