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 <hpa...@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 <jmac...@uw.edu >> <mailto: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-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 <hpa...@fhcrc.org >> <mailto:hpa...@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 | hpa...@fhcrc.org <mailto: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 <mailto:hpa...@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: hpa...@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel