So bug fixes for this package should now have propagated to both release and devel. Updating the package via biocLite() should be all you need to do. biocLite("KEGGSOAP") Marc On 08/23/2012 10:55 AM, Marc Carlson wrote: > Hi Jenny, > > It seems that you have found a bug in KEGGSOAP that has crept in from > changes in one of it's dependencies. I have patched it in the devel > branch and will propagate those changes to release as soon as I can > verify that there will not be other fallout for packages that depend > on KEGGSOAP. I have also added unit tests to prevent this kind of > nasty surprise from staying hidden in the future. > > Marc > > > On 08/21/2012 07:05 AM, Jenny Kartsaki wrote: >> Hello, >> >> I am a beginner user of KEGGSOAP and for my application i need the >> function >> list.pathways(org) for human organism. >> I have noticed that there are some problems with this function and i >> wanted to know if >> it provides all of the pathways that are on KEGG Pathway database or if >> there is an alternative >> way to take all the pathways. >> >> Furthermore , i want to ask what this warning message means: >> >> Warning message: >> In matrix(unlist(.SOAP(KEGGserver, "list_pathways", .soapArgs = >> list(org = org), : >> data length [255] is not a sub-multiple or multiple of the number >> of rows [128] >> >> >> Thank you , >> >> Jenny >> >> ###################################### >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=Greek_Greece.1253 LC_CTYPE=Greek_Greece.1253 >> LC_MONETARY=Greek_Greece.1253 >> [4] LC_NUMERIC=C LC_TIME=Greek_Greece.1253 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] KEGGSOAP_1.30.0 KEGGgraph_1.12.0 graph_1.34.0 >> XML_3.9-4.1 >> [5] KEGG.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 >> AnnotationDbi_1.18.1 >> [9] Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.7 >> >> loaded via a namespace (and not attached): >> [1] codetools_0.2-8 IRanges_1.14.4 RCurl_1.91-1.1 SSOAP_0.8-0 >> stats4_2.15.1 >> [6] tools_2.15.1 XMLSchema_0.7-2 >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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