Error in .testGOFraâ me(x, organism)
Diwan [guest]
guest at bioconductor.org
Tue Mar 19 20:06:45 CET 2013
Hi Valerie,
Thank you.Now I am able to use GOframe without any error.
Initially I installed the âAnnotationDbiâ and I assumed that âbiocLite("AnnotationDbi")â will install the latest version.
> source("http://bioconductor.org/biocLite.R")
> biocLite("AnnotationDbi")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.9.
Installing package(s) 'AnnotationDbi'
trying URL 'http://bioconductor.org/packages/2.10/bioc/src/contrib/AnnotationDbi_1.18.4.tar.gz'
But I was using Bioconductor version 2.10 . I am able to install AnnotationDbi 1.20.7 after upgrading to version 2.11. I also updated the other older packages
'Biobase', 'GO.db', 'GSEABase', 'org.Rn.eg.db'. Now I don't get any error.
Thank you for your time and help.
Diwan
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.8.3 KEGG.db_2.8.0 GSEABase_1.20.2 rat2302.db_2.8.1 org.Rn.eg.db_2.8.1
[6] annotate_1.36.0 GOstats_2.24.0 graph_1.34.0 Category_2.24.0 GO.db_2.8.0
[11] RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] AnnotationForge_1.0.3 genefilter_1.38.0 IRanges_1.16.6 parallel_2.15.2 RBGL_1.34.0
[6] splines_2.15.2 stats4_2.15.2 survival_2.37-4 tools_2.15.2 XML_3.95-0.2
[11] xtable_1.7-1
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