[Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats
James W. MacDonald
jmacdon at uw.edu
Tue Sep 23 19:55:28 CEST 2014
Hi Herve,
No joy:
> biocLite("ReportingTools")
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
> sessionInfo()
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, Hervé Pagès <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
>>
>>
>>
>>
>>
> --
> 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: 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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