Hi Xiaojiang, On 02/24/2011 06:32 AM, XIAOJIANG XU wrote: > Hi Herve, > I try to install package "BSgenome.Mmusculus.UCSC.mm9", but BSgenome > show me that it is not available. It's in the previous version. Do you > know why? How can I install it? Thanks. This is better asked on the mailing list (cc'ed). I get this on a fresh R session: > library(BSgenome) > grep("Mmusculus", available.genomes(type="source"), value=TRUE) BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). [1] "BSgenome.Mmusculus.UCSC.mm8" "BSgenome.Mmusculus.UCSC.mm9" with both BioC-2.7/R-2.12 (current release) and BioC-2.8/R-2.13 (current devel), so at least the source packages are available. However, if you are on Mac, the situation seems to be a little bit more complicated and confusing. If I remember correctly, it was decided that, starting with BioC-2.7/R-2.12, the project would drop support for Tiger (i.e. stop building binaries on a Tiger machine). This was just following CRAN's authority on that matter, which dropped support for Tiger starting with R-2.12. The consequence of this is that, if you try to get the list of packages that are available on CRAN for Tiger, it works with R < 2.12: > nrow(available.packages(type="mac.binary")) [1] 2240 but not with R >= 2.12: > nrow(available.packages(type="mac.binary")) Warning: unable to access index for repository http://cran.fhcrc.org/bin/macosx/universal/contrib/2.12 [1] 0 Now available.genomes() should give something consistent with this but it doesn't. With R 2.11: > library(BSgenome) > available.genomes(type="mac.binary") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). Warning: unable to access index for repository http://www.bioconductor.org/packages/2.6/data/annotation/bin/macosx/un iversal/contrib/2.11 character(0) And it seems that I get this problem whatever version of BioC/R I use (I tried with 2.11, 2.12 and 2.13) when in fact, it should work properly with R < 2.12 :-/ So I'll need to check on our end what is going on. Now if you are on Leopard (or Snow Leopard), things look good with BioC devel: > grep("Mmusculus", available.genomes(type="mac.binary.leopard"), value=TRUE) BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). [1] "BSgenome.Mmusculus.UCSC.mm8" "BSgenome.Mmusculus.UCSC.mm9" and they don't look too bad with BioC release: > grep("Mmusculus", available.genomes(type="mac.binary.leopard"), value=TRUE) BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). [1] "BSgenome.Mmusculus.UCSC.mm8" except that, as you can see, mm9 is missing. I will also need to check this on our end. In the mean time, if your machine is set up to install packages from source, you can still use 'type="source"' in available.packages(), available.genomes() and biocLite(). Sorry for the inconvenience. We'll post again here when we have an update on the 2 issues spotted above. H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319