[BioC] Packaging bioconductor

Seth Falcon sfalcon at fhcrc.org
Fri Sep 23 19:55:01 CEST 2005

On 23 Sep 2005, ghibo at mandriva.com wrote:
> How to call install.packages() in batch mode? i.e. either without
> X11 as well as without manual interaction. I.e. there shouldn't be
> opened like the tcl/tk interface window which is opened when calling
> install.packages() once started R interactively.

This only happens if you have not specified the repos argument.
However, some packages may not install properly without a connection
to an X server.  On our build system we use something like this:

   ## Start a virtual X server, used by R for running tests.
   /usr/X11R6/bin/Xvfb :9 -screen 0 800x600x16&
   export DISPLAY=:9.0

> Furthermore the 'repos' can't be an URL (even local), but at most a
> path (I can rsync the src dir and then put all the pkg files in a
> single dir, from which it will install), otherwise the package
> building won't work.

Not sure I understand your requirement.  Why can't you setup a local
dir as a CRAN-style repository and use a file:// type URL?  That would
be the easiest way.

We do have a patch pending that would allow install.packages to print
out the installation order and this would give you most of what you'd
need to install everything without using a repository.  Unfortunately,
we haven't had time to make this available.

+ seth

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