On 09/04/2010 01:38 PM, David Winsemius wrote: > (Caveat: I am not a bioc user.) The error messages suggest that you > are missing dependencies. I looked at the documentation for > GenomeGraphs and it does not list any dependencies, but I have no way > of knowing how careful > packageDescription("GenomeGraphs")$Depends [1] "methods, biomaRt, grid"
and likewise for biomaRt. Also at http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html for the current (release) version, or replacing 'release' with '2.5' (from the original poster's biocLite invocation) for the version relevant to R-2.10 <http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html> > or knowledgeable the authors may or may not have bben when they > composed that document. The fact that you are Not sure what 'that document' means, but if it's the package vignette or reference manual then that's not the appropriate place for stating package dependencies -- like all R packages, this information belongs in the package DESCRIPTION file, with dependencies enforced at installation time. Also the Bioconductor build system only makes available packages that do not produce errors on R CMD build and R CMD check, i.e., packages that have fully specified their dependencies. And the build system is versioned, so the original poster is getting (Bioconductor) packages that are appropriate for their system (though CRAN packages come from CRAN and so are not versioned in sync with R). > posting to the wrong mailing list and are not including what version > of linux (although there is a hint it may be RedHat5) you are running > suggests you could be fairly new at this. > > Is biocLite the correct function for installing a bioc package? It > appears it may be, but I'm wondering if there is an Yes it is. It does install dependencies, to the same extent that install.packages() does; biocLite is a wrapper around install.packages that inserts the appropriate (for the R version) Bioconductor repositories in front of CRAN repositories. Likely the original poster has an installed version of the XML package, but it is not installed correctly or the installation has become compromised in some way, e.g., by removing or updating libxml in the operating system. Your advice -- install (or otherwise troubleshoot) XML -- is likely part of the right solution, but since XML comes from the R repository and is therefore only known to build with the current version of R, it makes sense for the original poster to update their version of R first. Martin > argument for dependencies as there is in install.packages() that you > need to set to TRUE? If biocLite has a ,... in its argument list (and > the error message suggests that it does) then you may get better > results with the same call with an addition of dependencies=TRUE. > > Or you could first install the packages that are reported missing: XML > and biomaRt, and then try again as you did before. > > Links to the bioc mailing lists can be found here: > > http://www.bioconductor.org/help/index.html > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.