Hi Jim, On 09/23/2014 09:42 AM, James W. MacDonald wrote:
There is an issue on the support site having to do with the inability to import the summary function from the namespaces from the packages listed in the subject line. I see the same problem/errors with my affycoretools package.When you load ReportingTools, you get the following warnings: Warning messages: 1: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, : No generic function found corresponding to requested imported methods for "summary" from package "AnnotationDbi" (malformed exports?) 2: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, : No generic function found corresponding to requested imported methods for "summary" from package "Category" (malformed exports?) 3: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, : No generic function found corresponding to requested imported methods for "summary" from package "GOstats" (malformed exports?) Is this because of the following changes? ------------------------------------------------------------------------ r94092 | hpa...@fhcrc.org | 2014-09-12 18:02:34 -0700 (Fri, 12 Sep 2014) | 7 lines Changed paths: M /trunk/madman/Rpacks/AnnotationDbi/DESCRIPTION M /trunk/madman/Rpacks/AnnotationDbi/NAMESPACE M /trunk/madman/Rpacks/AnnotationDbi/R/createAnnObjs-utils.R M /trunk/madman/Rpacks/AnnotationDbi/R/createAnnObjs.NCBIORG_DBs.R M /trunk/madman/Rpacks/AnnotationDbi/R/methods-Inparanoid.R M /trunk/madman/Rpacks/AnnotationDbi/R/methods-Inparanoid8.R M /trunk/madman/Rpacks/AnnotationDbi/R/methods-geneCentricDbs.R - Drop dependency on IRanges (stuff from IRanges needed by AnnotationDbi is now in S4Vectors). - Add dependency on stats4 and import summary() from it. This is an S4 generic and AnnotationDbi defines and exports S4 methods for it. - Address the "A package almost never needs to use ::: for its own objects" NOTE from 'R CMD check'. which included Index: NAMESPACE =================================================================== --- NAMESPACE (revision 94000) +++ NAMESPACE (working copy) @@ -1,11 +1,11 @@ import(methods) import(utils) +importFrom(stats4, summary) import(Biobase) import(DBI) import(RSQLite) import(BiocGenerics) -importFrom(S4Vectors, isTRUEorFALSE, isSingleString, metadata) -importFrom(IRanges, elementLengths) +importFrom(S4Vectors, isTRUEorFALSE, isSingleString, metadata, elementLengths) importFrom(GenomeInfoDb, genomeStyles, extractSeqlevels, mapSeqlevels) exportClasses( @@ -169,9 +169,6 @@ intraIDMapper, idConverter, - #Needs to be exported from RSQLite - summary, - ## AnnotationDb metadata, so it appears summary is no longer exported?
Yes, no need to export summary from AnnotationDbi because summary() is a generic defined in the stats4 package. Before I made that change, AnnotationDbi was implicitly promoting base::summary() to an S4 generic which was then a different generic from stats4::summary(). Having these 2 distinct summary() generics was causing the usual troubles when a user had AnnotationDbi and stats4 in their search path. Also it was breaking the attract package in some obscure way. The warnings you get when you load ReportingTools will hopefully go away if you reinstall the package. Let me know if it doesn't. Hope this helps, H.
Best, Jim
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
