Problems with install.packages when Ncpus > 1
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.
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