Hi Julie,

There error is pretty clear. The version of BSgenome requires that you have
at least the version of 1.3.79 of IRanges before it can be installed
properly. The fix is then to just update your IRanges (and whatever other
packages that might need updating in the downstream, if there is need).

tc

On Sat, Dec 12, 2009 at 12:31 PM, Julie Zhu <julie.zhu@umassmed.edu> wrote:

> Hi Herve,
>
> I encountered problem loading Bsgenome. Please let me know how to fix it.
> The ChIPpeakAnno package I am working on relies on Bsgenome. Thank you very
> much for your help!
>
> Best regards,
>
> Julie
>
> > library(BSgenome)
> Error: package 'IRanges' 1.3.49 is loaded, but >= 1.3.79 is required by
> 'BSgenome'
> In addition: Warning message:
> package 'BSgenome' claims to be built under R version 2.10.0 but is missing
> some help files and needs to be re-installed
>
>
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-apple-darwin8.11.1
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] Biostrings_2.13.30            IRanges_1.3.49
> multtest_2.1.2                biomaRt_2.1.0
>  [5] mogene10stv1.r3.xdacdf_1.24.0 makecdfenv_1.24.0
> affyio_1.14.0                 mogene10stv1.r3cdf_2.5.0
>  [9] annaffy_1.17.1                KEGG.db_2.3.5
> GO.db_2.3.5
> RSQLite_0.7-1
> [13] DBI_0.2-4                     AnnotationDbi_1.8.1
> affxparser_1.18.0             affy_1.23.5
> [17] Biobase_2.5.5
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-3           preprocessCore_1.8.0 RCurl_0.98-1
> splines_2.10.0       survival_2.35-7      tools_2.10.0
> [7] XML_2.3-0
> >
>
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