[Rd] Problems with install.packages when Ncpus > 1

[Prof Brian Ripley]

On 06/10/2012 05:42, Winston Chang wrote:
> I have a Ubuntu Linux 12.04.1 machine running R 2.15.1. I'm trying to
> run tests building packages, so install.packages() is trying to
> install about about 1000 packages from source. I'm running into some
> strange issues that seem related to using values for Ncpus other than 1.
>
> When I use Ncpus=32, about 260 of the packages fail to install. When I
> tried again with Ncpus=2, more of them get installed, and there were
> only 234 failed packages. I tried it again with Ncpus=1, after which
> there were only 142 failed packages. (I think these remaining failed
> packages are due to missing external dependencies, like RODBC, Java,
> and various development libraries, so these aren't a concern at the
> moment.)
>
> In the code for install.packages, I see that if Ncpus>1, it passes the
> Ncpus to make, as in 'make -k -j 32'. Is it possible that these
> packages are failing because of this option to make?

It is perfectly correct option: please do your homework before posting 
as the posting guide asked of you.
>
> Has anyone else run into this issue before?

Yes.  It is due to missing dependencies between packages.   I find this 
works well on CRAN *provided* that the BioC repositories are also 
selected so that dependencies can be traced via BioC dependencies. 
However, BioC does have a fair few missing dependencies in its packages 
(run R CMD check over BioC to see them).

Take a look at the logs of the failed packages.  One I see frequently is 
that ddgraph fails because it depends indirectly on RBGL which takes a 
long time to install and is still being done.

>
> Thanks!
> -Winston


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595