[BioC] WGCNA

[Peter Langfelder]

As far as I know, RStudio has problems with parallel calculations that
fork R processes (such as those called by parallel or
foreach/doParallel on machines where fork is available). The WGCNA
function pickSoftThreshold uses this parallelization. The correlation
functions use multithreading from within C code, which does not fork
the entire R session. That's why corFast etc in WGCNA work fine but
pickSoftThreshold does not.

Hope this clears up any lingering confusion.

Also see inline below

On Sun, Feb 16, 2014 at 12:26 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

>
>
> Also I don't see where the error message is coming from (who is printing
> "task 1 failed - " ?)


I believe this is printed by foreach/doParallel but here I could be wrong.



HTH,

Peter

>
> I have a vague recollection that the x[["Version"]] (which comes from
> getAnywhere("print.sessionInfo")) has to do with multiple installed versions
> of a package, but again it would be good to get to the bottom of this
> problem.
>
> Martin