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

[Dan Tenenbaum]

----- Original Message -----
> From: "Sine Katharina Zambach" <sine.katharina.zambach at regionh.dk>
> To: bioconductor at r-project.org
> Sent: Monday, September 30, 2013 7:24:14 AM
> Subject: [BioC] 'AnnotationDbi'  1.23.24 is required by ‘GO.db’ in Windows
> 
> 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”
> (...)
> 

This version should be available soon. In the meantime, try:

biocLite("AnnotationDbi", type="source")

Dan


> 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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