Re: [Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats
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 | hpa...@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: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats
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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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_0.3.0knitr_1.6BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] annotate_1.42.1 AnnotationForge_1.6.1BatchJobs_1.3 [4] BBmisc_1.7 BiocParallel_0.6.1 biomaRt_2.20.0 [7] Biostrings_2.32.1biovizBase_1.12.3bitops_1.0-6 [10] brew_1.0-6 BSgenome_1.32.0 Category_2.30.0 [13] checkmate_1.4cluster_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_1.4.2formatR_1.0 [25] Formula_1.1-2genefilter_1.46.1geneplotter_1.42.0 [28] GenomicAlignments_1.0.6 GenomicFeatures_1.16.2 GenomicRanges_1.16.4 [31] ggbio_1.12.10ggplot2_1.0.0GO.db_2.14.0 [34] GOstats_2.30.0 graph_1.42.0 grid_3.1.0
Re: [Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats
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 jmac...@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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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_0.3.0knitr_1.6BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] annotate_1.42.1 AnnotationForge_1.6.1BatchJobs_1.3 [4] BBmisc_1.7 BiocParallel_0.6.1 biomaRt_2.20.0 [7] Biostrings_2.32.1biovizBase_1.12.3bitops_1.0-6 [10] brew_1.0-6 BSgenome_1.32.0 Category_2.30.0 [13] checkmate_1.4cluster_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
