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

Tue, Sep 23, 2014 10:55 AM

Hi Herve,

No joy:

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
  3.1.0.
Installing package(s) 'ReportingTools'
trying URL '
http://bioconductor.org/packages/2.14/bioc/src/contrib/ReportingTools_2.4.0.tar.gz
'
Content type 'application/x-gzip' length 2570348 bytes (2.5 Mb)
opened URL
==================================================
downloaded 2.5 Mb

* installing *source* package ?ReportingTools? ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning 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?)
Warning 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?)
Warning: found methods to import for function ?summary? but not the generic
itself
Warning 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?)
Warning: found methods to import for function ?summary? but not the generic
itself
in method for ?objectToHTML? with signature ?object="ggbio"?: no definition
for class ?ggbio?
Note: no visible binding for '<<-' assignment to '.reportDirectory'
Note: no visible binding for '<<-' assignment to '.reportDirectory'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning 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?)
Warning 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?)
Warning: found methods to import for function ?summary? but not the generic
itself
Warning 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?)
Warning: found methods to import for function ?summary? but not the generic
itself
* DONE (ReportingTools)

And when I load ReportingTools I still get the 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: found methods to import for function ?summary? but not the generic
itself
4: 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?)
5: found methods to import for function ?summary? but not the generic
itself

R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ReportingTools_2.4.0 AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2
[4] Biobase_2.24.0       BiocGenerics_0.10.0  RSQLite_0.11.4
[7] DBI_0.3.0            knitr_1.6            BiocInstaller_1.14.2

loaded via a namespace (and not attached):
 [1] annotate_1.42.1          AnnotationForge_1.6.1    BatchJobs_1.3

 [4] BBmisc_1.7               BiocParallel_0.6.1       biomaRt_2.20.0

 [7] Biostrings_2.32.1        biovizBase_1.12.3        bitops_1.0-6

[10] brew_1.0-6               BSgenome_1.32.0          Category_2.30.0

[13] checkmate_1.4            cluster_1.15.2           codetools_0.2-9

[16] colorspace_1.2-4         DESeq2_1.4.5             dichromat_2.0-0

[19] digest_0.6.4             edgeR_3.6.8              evaluate_0.5.5

[22] fail_1.2                 foreach_1.4.2            formatR_1.0

[25] Formula_1.1-2            genefilter_1.46.1        geneplotter_1.42.0

[28] GenomicAlignments_1.0.6  GenomicFeatures_1.16.2   GenomicRanges_1.16.4

[31] ggbio_1.12.10            ggplot2_1.0.0            GO.db_2.14.0

[34] GOstats_2.30.0           graph_1.42.0             grid_3.1.0

[37] gridExtra_0.9.1          GSEABase_1.26.0          gtable_0.1.2

[40] Hmisc_3.14-4             hwriter_1.3.1            IRanges_1.22.10

[43] iterators_1.0.7          lattice_0.20-29          latticeExtra_0.6-26

[46] limma_3.20.9             locfit_1.5-9.1           MASS_7.3-34

[49] Matrix_1.1-4             munsell_0.4.2            PFAM.db_2.14.0

[52] plyr_1.8.1               proto_0.3-10             RBGL_1.40.1

[55] RColorBrewer_1.0-5       Rcpp_0.11.2
 RcppArmadillo_0.4.400.0
[58] RCurl_1.95-4.3           reshape2_1.4             R.methodsS3_1.6.1

[61] R.oo_1.18.0              Rsamtools_1.16.1         rtracklayer_1.24.2

[64] R.utils_1.33.0           scales_0.2.4             sendmailR_1.1-2

[67] splines_3.1.0            stats4_3.1.0             stringr_0.6.2

[70] survival_2.37-7          tools_3.1.0
 VariantAnnotation_1.10.5
[73] XML_3.98-1.1             xtable_1.7-3             XVector_0.4.0

[76] zlibbioc_1.10.0

Jim

On Tue, Sep 23, 2014 at 1:43 PM, Herv? Pag?s <hpages at fhcrc.org> wrote:

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 | 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?

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

--
Herv? Pag?s

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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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

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