[Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats
James W. MacDonald
jmacdon at uw.edu
Tue Sep 23 20:57:52 CEST 2014
Exactly! And re-installing the various packages didn't result in any
version changes, so it's a mystery as to why there was a problem in the
first place.
On Tue, Sep 23, 2014 at 2:24 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
> Also note that, according to the sessionInfo() you sent, it seems you
> were using the release. I've no idea how you could get these warnings
> with the release since the changes I made recently to AnnotationDbi,
> Category, and GOstats are in devel only...
>
> H.
>
> On 09/23/2014 11:05 AM, James W. MacDonald wrote:
>
>> 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
>> <mailto: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
>> <mailto: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 <mailto: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 <mailto:hpages at fhcrc.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>>
>>
>>
>> --
>> 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
>>
>
> --
> 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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