[BioC] 'AnnotationDbi' 1.23.24 is required by ‘GO.db’ in Windows

[Sine Katharina Zambach]

Hi Bioconductor forum,

I get a strange error message when working with the Bioconductor Gene Ontology-packages.
I have done the following:
➢ source("http://bioconductor.org/biocLite.R")
➢ biocLite("GO.db")

The problem is that GO.db is dependant on AnnotationDbi in a later version than 1.23.23, and when I load GO.db using
> biocLite("GO.db")
(...)
“Warning: dependency ‘AnnotationDbi (>= 1.23.24)’ is not available”
(...)

but when I load AnnotationDbi it says:
> biocLite("AnnotationDbi")
" There is a binary version available (and will be installed) but the
  source version is later:
                        binary          source
AnnotationDbi   1.23.23         1.23.25”

Can I suppress the installation of the binary version such that I get an appropriate version of AnnotationDbi? Or do you have any other suggestions? (Except changing to Linux :-))
I have tried with several versions of R and I use Windows XP as platform. R version 2.15 works ok, but using that, I have problems with getting the newer packages to work.
My colleague, who uses Linux and R 3.0.1, has no problems with GO.db or any of the other packages using AnnotationDbi  – and he also "only" has AnnotationDbi 1.23.23.

Best wishes,

Sine Zambach

Results from traceback and sessionInfo:

> traceback()
3: stop(gettextf("package %s %s is loaded, but %s %s is required by %s",
       sQuote(pkg), current, z$op, target, sQuote(pkgname)), call. = FALSE,
       domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(GO.db)

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252    LC_MONETARY=Danish_Denmark.1252
[4] LC_NUMERIC=C                    LC_TIME=Danish_Denmark.1252

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] VariantAnnotation_1.7.47 Rsamtools_1.13.44        Biostrings_2.29.19       GenomicRanges_1.13.45
 [5] XVector_0.1.4            IRanges_1.19.38          ontoCAT_1.13.0           rJava_0.9-4
 [9] DOSE_1.99.6              ggplot2_0.9.3.1          GOSemSim_1.19.3          RSQLite_0.11.4
[13] DBI_0.2-7                Rcpp_0.10.4              Rgraphviz_2.5.6          graph_1.39.3
[17] Matrix_1.0-14            lattice_0.20-23          AnnotationDbi_1.23.23    Biobase_2.21.7
[21] BiocGenerics_0.7.5       DAVIDQuery_1.21.0        RCurl_1.95-4.1           bitops_1.0-6
[25] BiocInstaller_1.11.4

loaded via a namespace (and not attached):
 [1] biomaRt_2.17.3          BSgenome_1.29.1         colorspace_1.2-3        dichromat_2.0-0
 [5] digest_0.6.3            DO.db_2.6.0             GenomicFeatures_1.13.43 GO.db_2.10.1
 [9] gtable_0.1.2            igraph_0.6.5-2          labeling_0.2            MASS_7.3-29
[13] munsell_0.4.2           plyr_1.8                proto_0.3-10            qvalue_1.35.0
[17] RColorBrewer_1.0-5      reshape2_1.2.2          rtracklayer_1.21.12     scales_0.2.3
[21] stats4_3.0.2            stringr_0.6.2           tcltk_3.0.2             tools_3.0.2
[25] XML_3.98-1.1            zlibbioc_1.7.0




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