On 06/06/2013 10:49 AM, Dan Tenenbaum wrote: > On Thu, Jun 6, 2013 at 10:32 AM, James W. MacDonald > <jmacdon at="" u.washington.edu=""> wrote: >> Hi Dan, >> >> I can reproduce it: >> >>> library(GO.db) >> Loading required package: AnnotationDbi >> Loading required package: BiocGenerics >> Loading required package: parallel >> >> Attaching package: ?BiocGenerics? >> >> The following objects are masked from ?package:parallel?: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from ?package:stats?: >> >> xtabs >> >> The following objects are masked from ?package:base?: >> >> anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, >> Filter, Find, get, intersect, lapply, Map, mapply, match, mget, >> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, >> rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist >> >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> Loading required package: DBI >> >> Error : .onLoad failed in loadNamespace() for 'GO.db', details: >> call: get(name, envir = asNamespace(pkg), inherits = FALSE) >> error: object '.setDummyField' not found >> Error: package or namespace load failed for ?GO.db? >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 >> [4] Biobase_2.20.0 BiocGenerics_0.6.0 >> >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.18.1 stats4_3.0.0 >>> packageDescription("GO.db") >> Package: GO.db >> Title: A set of annotation maps describing the entire Gene Ontology >> Description: A set of annotation maps describing the entire Gene >> Ontology assembled using data from GO >> Version: 2.9.0 >> Author: Marc Carlson >> Maintainer: Biocore Data Team <biocannotation at="" lists.fhcrc.org=""> >> Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.21.13) >> Imports: methods, AnnotationDbi >> License: Artistic-2.0 >> biocViews: AnnotationData, FunctionalAnnotation >> Packaged: 2013-03-08 20:42:40 UTC; mcarlson >> Built: R 3.0.0; ; 2013-03-29 01:39:43 UTC; unix >> >> -- File: C:/Users/bioinf_admin/R/win- library/3.0/GO.db/Meta/package.rds >> > > I can reproduce it with R 3.0.0 but not 3.0.1. Therefore I suggest > upgrading to R-3.0.1. Another option might be biocLite(c("AnnotationDbi", "GO.db"), type="source") I *think* that these can be built w/out special tools. There was a change between R 3.0.0 and 3.0.1 in the implementation of reference classes. The binary packages built under 3.0.1 contain serialized representations appropriate for R 3.0.1, and break when used with 3.0.0. $ svn log -r62487 ---------------------------------------------------------------------- -- r62487 | jmc | 2013-04-03 14:56:23 -0700 (Wed, 03 Apr 2013) | 4 lines Clean up active binding to assign fields, won't be fooled by functions in the package environment for the class. Also fixes a bug that did not check the class of the initial assignment of a read-only field. Martin > Dan > > >> Best, >> >> Jim >> >> >> >> >> On 6/6/2013 12:43 PM, Dan Tenenbaum wrote: >>> >>> Hi Anne, >>> >>> >>> >>> On Wed, Jun 5, 2013 at 11:39 PM, Anne Deslattes Mays >>> <ad376 at="" georgetown.edu=""> wrote: >>>> >>>> Dear annotation team, >>>> >>>> Thanks for the awesome work you do -- I try to load >>>> biocLite("ReportingTools") and get an error regarding GO.db >>>> GO.db says it depends upon AnnotationDbi >>>> I load biocLite("AnnotationDbi") >>>> >>>> I try to load biocLite("GO.db") and get an error >>>> >>>>> biocLite("GO.db") >>>> >>>> BioC_mirror: http://bioconductor.org >>>> Using Bioconductor version 2.12 >>>> (BiocInstaller 1.10.1), R version 3.0.0. >>>> Installing package(s) 'GO.db' >>>> trying URL >>>> 'http://bioconductor.org/packages/2.12/data/annotation/bin/macosx /contrib/3.0/GO.db_2.9.0.tgz' >>>> Content type 'application/x-gzip' length 25061115 bytes (23.9 Mb) >>>> opened URL >>>> ================================================== >>>> downloaded 23.9 Mb >>>> >>>> >>>> The downloaded binary packages are in >>>> >>>> /var/folders/q_/snn7m1m53y161gssz9flysm00000gn/T//RtmppQR5na/down loaded_packages >>>>> >>>>> library(GO.db) >>>> >>>> Error : .onLoad failed in loadNamespace() for 'GO.db', details: >>>> call: get(name, envir = asNamespace(pkg), inherits = FALSE) >>>> error: object '.setDummyField' not found >>>> Error: package or namespace load failed for ?GO.db? >>>> >>> I can't reproduce this using the same OS and R/BioC versions, but I'm >>> not clear on the all the commands you entered in order to get to this >>> point. What happens if you start a fresh R session with >>> >>> R --vanilla >>> >>> and then do: >>> >>> library(ReportingTools) >>> ? >>> >>> Or, if ReportingTools is not installed: >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("ReportingTools") >>> library(ReportingTools) >>> >>> If I understand you correctly, you are just trying to load >>> ReportingTools and the issues with GO.db and AnnotationDbi are just >>> impediments to that goal. >>> >>> Dan >>> >>> >>>> Best regards, >>>> >>>> Anne >>>> >>>> Here is my sessionInfo >>>> >>>> R version 3.0.0 (2013-04-03) >>>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] affy_1.38.1 BiocInstaller_1.10.1 RSQLite_0.11.4 >>>> [4] DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.0 >>>> [7] BiocGenerics_0.6.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.28.0 annotate_1.38.0 AnnotationForge_1.2.1 >>>> [4] Category_2.26.0 edgeR_3.2.3 genefilter_1.42.0 >>>> [7] graph_1.38.2 grid_3.0.0 GSEABase_1.22.0 >>>> [10] IRanges_1.18.1 limma_3.16.5 preprocessCore_1.22.0 >>>> [13] RBGL_1.36.2 splines_3.0.0 stats4_3.0.0 >>>> [16] survival_2.37-4 tools_3.0.0 XML_3.95-0.2 >>>> [19] xtable_1.7-1 zlibbioc_1.6.0 >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793