The example code (in svn at least) looks like it needs
BSgenome.Mmusculus.UCSC.mm9, not GenomicFeatures. Maybe you're talking about
the contextDistribution example, which could be considered
deprecated/obsolete, until I figure out how chipseq should interact with the
new generation of GenomicFeatures.

Michael

On Mon, Apr 5, 2010 at 3:38 PM, Kunbin Qu <KQu@genomichealth.com> wrote:

> Hi,
>
> I was trying to run the diffPeakSummary example code in chipseq. It
> needs to install GenomicFeatures.Mmusculus.UCSC.mm9. When I tried to
> install it, it gave the following error messages. Please help, thanks.
>
> -Kunbin
>
>
> >
> install.packages("/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar
> .gz", type="source")
> inferring 'repos = NULL' from the file name
> * Installing *source* package ?GenomicFeatures.Mmusculus.UCSC.mm9? ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: rtracklayer
> Loading required package: RCurl
> Loading required package: bitops
> Warning: Multiple methods tables found for 'duplicated'
> Warning: Multiple methods tables found for 'unique'
> Warning: Multiple methods tables found for 'sort'
> Warning: Multiple methods tables found for 'rank'
> Warning in namespaceImportFrom(self, asNamespace(ns)) :
>  replacing previous import: .__C__Dups
> Warning in namespaceImportFrom(self, asNamespace(ns)) :
>  replacing previous import: match
> Warning in namespaceImportFrom(self, asNamespace(ns)) :
>  replacing previous import: summary
> Warning in namespaceImportFrom(self, asNamespace(ns)) :
>  replacing previous import: .__C__Dups
> Warning in namespaceImportFrom(self, asNamespace(ns)) :
>  replacing previous import: match
> ** help
> *** installing help indices
>  >>> Building/Updating help pages for package
> 'GenomicFeatures.Mmusculus.UCSC.mm9'
>     Formats: text html latex example
>
>
> ******* Syntax error: \enumerate in
> /-----
> A data frame with 16026 observations on the following 4 variables.
> \enumeratenormal-bracket12bracket-normal\-----
> ERROR: building help failed for package
> ?GenomicFeatures.Mmusculus.UCSC.mm9?
> * Removing
> ?/mnt/opt/R/R-2.9.2/x86_64-unknown-linux-gnu/lib64/R/library/GenomicFeat
> ures.Mmusculus.UCSC.mm9?
> Warning message:
> In
> install.packages("/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar
> .gz",  :
>  installation of package
> '/home/kqu/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1.tar.gz' had non-zero
> exit status
> > sessionInfo()
> R version 2.9.2 (2009-08-24)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
> ON=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.13 chipseq_0.2.1
>
> [3] ShortRead_1.2.1                    lattice_0.17-26
>
> [5] BSgenome_1.12.5                    Biostrings_2.12.10
>
> [7] IRanges_1.4.16
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.1 grid_2.9.2    hwriter_1.2   tools_2.9.2
> >
>
>
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