[BioC] Packaging bioconductor

Giuseppe Ghibò ghibo at mandriva.com
Fri Sep 23 21:32:03 CEST 2005

Seth Falcon ha scritto:

> 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&
>    xvfb_pid=$!
>    export DISPLAY=:9.0

Yes, I had already used the Xvfb in my current R-bioconductor-1.4 RPM
package because one package was needing it.

>>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.

Well, I could use file://`pwd` or file://$RPM_BUILD_DIR, but
how to have that in the install.packages(), I mean would a
command line like:

	R CMD install.packages(repos=file://`pwd`) -l %{buildroot}%{_libdir}/R/library

produce the installed tree into %{buildroot}%{_libdir}/R/library?

> 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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