[Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats
Hervé Pagès
hpages at fhcrc.org
Tue Sep 23 20:24:50 CEST 2014
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
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