[BioC] Error loading GO.db
Martin Morgan
mtmorgan at fhcrc.org
Thu Jun 6 20:22:17 CEST 2013
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/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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