[Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats

[James W. MacDonald]

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 | hpages at 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?

Best,

Jim




-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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