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 <[email protected]> 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 > > > > > ______________________________________________________________________ > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
