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

James W. MacDonald jmacdon at uw.edu
Tue Sep 23 20:05:05 CEST 2014


Never mind. Installing all of GOstats, Category, AnnotationDbi and
ReportingTools fixed the issue.

Thanks,

Jim



On Tue, Sep 23, 2014 at 1:55 PM, James W. MacDonald <jmacdon at uw.edu> wrote:

> 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
>



-- 
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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