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?
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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