Message-ID: <CAFOpNVFDkJ_TSTobYiitiKvDZcgKLTrp50xwj-VqXfUKt4QEKA@mail.gmail.com>
Date: 2012-10-06T16:02:18Z
From: Winston Chang
Subject: Problems with install.packages when Ncpus > 1
In-Reply-To: <506FC724.6050207@stats.ox.ac.uk>
>> 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