Hi Julie, Let's keep this on the list. First off, you should only send issues to bioc-devel when you are using the devel version of R and Bioc. It seems like you are using the current release version of R and Bioc so you should really send these messages to the Bioc list (which I have copied here and removed the devel list). To answer your question about package dependencies, Martin Morgan routinely answers this particular question on the list...though the question is generally not always asked the same way. The command I always run after installing bioc packages (as per Martin's advice) is source('http://bioconductor.org/biocLite.R') old.packages(repos=biocinstallRepos()) update.packages(repos=biocinstallRepos()) and if I look at ?update.packages, the description tells me: *These functions can be used to automatically compare the version numbers of installed packages with the newest available version on the repositories and update outdated packages on the fly.* So searching the archives of the mailing list is pretty helpful, but sometimes you need to figure out that someone else's question might be relevant even though it is not exactly identical. Anyhow, hope that answers your questions. Cheers, --tc On Sat, Dec 12, 2009 at 1:41 PM, Julie Zhu <julie.zhu@umassmed.edu> wrote: > Thanks Tony! > > It seems that download of a package (Bsgenome) that depends on a newer > version of other packages (IRanges) would not automatically update the > depended package (IRanges). Is this correct? It would be nice to > automatically upgrade the packages it depends on first. > > I tried to install the newest release of IRanges, followed by installing > the newest release of Bsgenome solved the problem. > source("http://bioconductor.org/biocLite.R") > biocLite("IRanges") > biocLite(BSgenome) > > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin8.11.1 > > Best regards, > > Julie > > > > On 12/12/09 4:18 PM, "Tony Chiang" <tchiang@fhcrc.org> wrote: > > Hi Julie, > > There error is pretty clear. The version of BSgenome requires that you have > at least the version of 1.3.79 of IRanges before it can be installed > properly. The fix is then to just update your IRanges (and whatever other > packages that might need updating in the downstream, if there is need). > > tc > > On Sat, Dec 12, 2009 at 12:31 PM, Julie Zhu <julie.zhu@umassmed.edu> > wrote: > > Hi Herve, > > I encountered problem loading Bsgenome. Please let me know how to fix it. > The ChIPpeakAnno package I am working on relies on Bsgenome. Thank you very > much for your help! > > Best regards, > > Julie > > > library(BSgenome) > Error: package 'IRanges' 1.3.49 is loaded, but >= 1.3.79 is required by > 'BSgenome' > In addition: Warning message: > package 'BSgenome' claims to be built under R version 2.10.0 but is missing > some help files and needs to be re-installed > > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin8.11.1 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.13.30 IRanges_1.3.49 > multtest_2.1.2 biomaRt_2.1.0 > [5] mogene10stv1.r3.xdacdf_1.24.0 makecdfenv_1.24.0 > affyio_1.14.0 mogene10stv1.r3cdf_2.5.0 > [9] annaffy_1.17.1 KEGG.db_2.3.5 > GO.db_2.3.5 > RSQLite_0.7-1 > [13] DBI_0.2-4 AnnotationDbi_1.8.1 > affxparser_1.18.0 affy_1.23.5 > [17] Biobase_2.5.5 > > loaded via a namespace (and not attached): > [1] MASS_7.3-3 preprocessCore_1.8.0 RCurl_0.98-1 > splines_2.10.0 survival_2.35-7 tools_2.10.0 > [7] XML_2.3-0 > > > > _______________________________________________ > Bioc-devel@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]]