[BioC] Error loading GO.db
James W. MacDonald
jmacdon at u.washington.edu
Thu Jun 6 19:32:08 CEST 2013
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/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/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
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--
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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