[Bioc-sig-seq] example(diffPeakSummary) in chipseq

[Kunbin Qu]

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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