Thank you Kasper. I have got everything working the way I want now. In case anyone wants to know, here are my scripts: ### On the head node #!/usr/bin/env Rscript args = commandArgs(T) rh = R.home() tmp = paste(rh,"/tmp",sep="") if(!file.exists(tmp)) { dir.create(tmp) } source("http://bioconductor.org/biocLite.R") repos = c(biocinstallRepos(),getOption("repos")) pkg = utils:::getDependencies(args,,available.packages(contriburl=cont rib.url(repos))) order = download.packages(pkg, tmp, repos=repos)[,2] write.table(order,paste(tmp,"/pkg_install_order.list",sep=""),col.name s=F,row.names=F,quote=F,sep="\t") ### On the compute node #!/usr/bin/env Rscript rh = R.home() tmp = paste(rh,"/tmp",sep="") if(!file.exists(tmp)) { quit() } pkg = read.table(paste(tmp,"/pkg_install_order.list",sep=""),sep="\t") pkg = as.vector(t(pkg)) install.packages(pkg,repo=NULL) file.remove(pkg) file.remove(paste(tmp,"/pkg_install_order.list",sep="")) Thanks, Nathan Bihlmeyer Human Genetics School of Medicine Johns Hopkins University On Tue, Dec 4, 2012 at 11:19 AM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > Forgot to reply all > > Most of the R commands for managing packages has a repos argument. You can do > library(BiocInstaller) > install.packages(repos = biocinstallRepos()) > Be careful about R versions here, if nodes are different from head. > Also, some commands may not accept a repos argument, but instead a > contriburl argument which you can construct using > contrib.url(biocinstallRepos()) > If you start to grab some of the annotation / experiment data packages > (especially the genomes), watch out that they are much much bigger > than a typical CRAN package. Better make sure /tmp is big enough. > > Kasper > > On Mon, Dec 3, 2012 at 2:10 PM, Nathan Bihlmeyer <nbihlme1 at="" jhmi.edu=""> wrote: >> Hello all, >> >> I am currently working on a HPC cluster that for security reasons does >> not have access to the internet on the compute nodes. Therefore, I >> wish to quickly download package source archives using the head node, >> then compile them on a compute node. >> >> Other details: The head node does not have same shared libraries as >> the compute nodes, so I couldn't compile on that node even if I wanted >> to. All the nodes use the same network-based file system for most >> files (/home etc...). I am using my own compiled version of R 2.15.2. >> >> For non-Bioconductor packages, I have been using the following scripts: >> >> ### On the head node >> #!/usr/bin/env Rscript >> args = commandArgs(T) >> rh = R.home() >> tmp = paste(rh,"/tmp",sep="") >> if(!file.exists(tmp)) { >> dir.create(tmp) >> } >> pkg = utils:::getDependencies(args,,available.packages()) >> download.packages(pkg, tmp) >> >> ### On the compute node >> #!/usr/bin/env Rscript >> rh = R.home() >> tmp = paste(rh,"/tmp",sep="") >> if(!file.exists(tmp)) { >> quit() >> } >> pkg = list.files(tmp,full.names=T) >> install.packages(pkg,repo=NULL) >> file.remove(pkg) >> >> They work well. What I need now is a way to do the same thing with >> Bioconductor packages. I have looked into pkgDepTools; however, the >> package requires a complete dependency graph to be built every time >> the script is run. This takes too long and uses too many resources and >> therefore is not an option on the head node. Also, I can not find a >> way to produce download urls using that package. >> >> Thanks for your help, >> Nathan Bihlmeyer >> Human Genetics >> School of Medicine >> Johns Hopkins University >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor