[Rd] Problems with install.packages when Ncpus > 1
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Oct 6 07:52:36 CEST 2012
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
> 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.
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
More information about the R-devel