[BioC] Offline Installation of Packages and Dependencies

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Dec 4 17:19:51 CET 2012

Forgot to reply all

Most of the R commands for managing packages has a repos argument.  You can do
  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
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.


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
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