On 06.10.2012 18:02, Winston Chang wrote:
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.
The question isn't about whether these are valid make options. I
realize that '-j <n>' is a valid option for make, just like Ncpus is a
valid option for install.packages. The question is whether that option
is unexpectedly resulting in failed compiles for some packages.
I think Brian answered this already:
Not unexpectedly. It fails in case when a package installation requires
another package and that is installed at the same time or not yet
installed. Such things happen when install time dependencies are not
correctly declared. R CMD check finds (at least most of) such
declaration errors nowadays.
Uwe Ligges
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, I'll take a closer look at these those cross dependencies.
-Winston
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