[BioC] Error loading GO.db
Dan Tenenbaum
dtenenba at fhcrc.org
Thu Jun 6 18:43:46 CEST 2013
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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