From ligges at statistik.tu-dortmund.de  Sat Oct  6 19:02:42 2012
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Sat, 06 Oct 2012 19:02:42 +0200
Subject: [Rd] Problems with install.packages when Ncpus > 1
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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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[Rd] Problems with install.packages when Ncpus > 1
Uwe Ligges