[BioC] Error loading GO.db

[Dan Tenenbaum]

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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