Error loading GO.db
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@anne-deslattes-mays-5977
Last seen 9.5 years ago
United States
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/d ownloaded_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? 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
Annotation GO Annotation GO • 5.2k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
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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/bi n/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 /downloaded_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
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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 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/b in/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//RtmppQR5 na/downloaded_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
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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. 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/downl oaded_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 >
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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
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Dear Martin, I had the same problem. > > Another option might be > > biocLite(c("AnnotationDbi", "GO.db"), type="source") > With this loading Go.db is finally working under R 3.0.0 on MacOSX Thanks a lot! Eszter -- Eszter Ari Institut für Populationsgenetik Vetmeduni Vienna Veterinärplatz 1 1210 Wien, Austria [[alternative HTML version deleted]]
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On 06/11/2013 02:23 AM, Ari Eszter wrote: > Dear Martin, > > I had the same problem. > >> >> Another option might be >> >> biocLite(c("AnnotationDbi", "GO.db"), type="source") >> > > With this loading Go.db is finally working under R 3.0.0 on MacOSX Hi Eszter and others reading the thread -- Glad that works for you. It's likely that other packages that use reference classes will have the same problem, and some of these will require the 'devel' tools (C compiler, etc) to install with type="source". In the long run it's better to find the time to update to R-3.0.1. Martin > > Thanks a lot! > > Eszter > > > > _______________________________________________ > 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
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@anne-deslattes-mays-5991
Last seen 6.4 years ago
United States
Hi Dan, I do as you say and still get the error.... Would that I could unlink the two :-<. I am on a Mac book Pro -- OSX 10.8.3, Error : .onLoad failed in loadNamespace() for 'GO.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found In addition: Warning message: package ?AnnotationDbi? was built under R version 3.0.1 Error: package or namespace load failed for ?ReportingTools? Anne
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States
On Wed, Jun 12, 2013 at 1:20 PM, Anne Deslattes Mays <adeslat at="" sbresearchllc.com=""> wrote: > Hi Dan, > > I do as you say and still get the error.... > Would that I could unlink the two :-<. > > I am on a Mac book Pro -- OSX 10.8.3, > > Error : .onLoad failed in loadNamespace() for 'GO.db', details: > call: get(name, envir = asNamespace(pkg), inherits = FALSE) > error: object '.setDummyField' not found > In addition: Warning message: > package ?AnnotationDbi? was built under R version 3.0.1 > Error: package or namespace load failed for ?ReportingTools? > The warning suggests you are still running R-3.0.0; we recommend updating to 3.0.1. Dan > > Anne > > _______________________________________________ > 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
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