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
>
______________________________________________________________________
The contents of this electronic message, including any attachments, are
intended only for the use of the individual or entity to which they are
addressed and may contain confidential information. If you are not the intended
recipient, you are hereby notified that any use, dissemination, distribution,
or copying of this message or any attachment is strictly prohibited. If you
have received this transmission in error, please send an e-mail to
[email protected] and delete this message, along with any
attachments, from your computer.
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
