[BioC] Error loading GO.db

Thu Jun 6 19:49:20 CEST 2013

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/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
>