[BioC] WGCNA

[Peter Langfelder]

Hi Martin,

if you simply run pickSoftThreshold without calling enableWGCNAThreads
before, the function is run in a single-worker mode. To reproduce the
error, you have to call enableWGCNAThreads with an argument of 2 or
more.

For a reproducible example, you can run the first two sections of
WGCNA Tutorial I at
http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html.
Sorry, I don't have a quick simulated example ready but could cook one
up.

I am actually not sure whether this problem also occurs on Windows,
since the cluster parallelization is very different from the forking
on linux. I am only aware of it through bug reports of WGCNA users
(who usually email me directly).

Peter



On Sun, Feb 16, 2014 at 6:30 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
> but from my original mail pickSoftThreshold 'worked for me' under Rstudio on
> Windows (output below, again); maybe I didn't invoke it in a way that would
> trigger the error, so a reproducible illustration would help (me). Also on
> Windows (platform of the original post) the parallel package doesn't fork,
> e.g., from ?mcfork
>
>      These are low-level functions, not available on Windows, and not
>      exported from the namespace.
>
> or ?mclapply
>
>      It relies on forking and hence is not available on Windows unless
>      'mc.cores = 1'.
>
> Do you mean something less literally forking, like spawning a new process?
> Maybe from
>
>   http://stackoverflow.com/questions/20704235
>
> the solution is as simple as adding .packages="WGCNA" to your foreach calls?
>
>
>> x = pickSoftThreshold(data)
> trace: .C("checkAvailableMemoryForR", size = as.double(size), PACKAGE =
> "WGCNA")
> trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx =
> as.integer(ncol(x)),
>     y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick),
>     cosineX = as.integer(cosineX), cosineY = as.integer(cosineY),
>     res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err),
>     nThreads = as.integer(nThreads), verbose = as.integer(verbose),
>     indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE =
> "WGCNA")
> trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), ncolx =
> as.integer(ncol(x)),
>     y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick),
>     cosineX = as.integer(cosineX), cosineY = as.integer(cosineY),
>     res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err),
>     nThreads = as.integer(nThreads), verbose = as.integer(verbose),
>     indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE =
> "WGCNA")
>    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.   max.k.
> 1      1    0.173 -11.00        0.98400 4.02e+01  4.02e+01 4.45e+01
> 2      2    0.326  -8.45        0.95700 5.04e+00  5.04e+00 6.12e+00
> 3      3    0.241  -4.30        0.95300 8.01e-01  8.02e-01 1.05e+00
> 4      4    0.348  -4.04        0.95000 1.49e-01  1.49e-01 2.25e-01
> 5      5    0.513  -3.74        0.90400 3.15e-02  3.09e-02 5.77e-02
> 6      6    0.697  -3.72        0.92600 7.32e-03  6.99e-03 1.70e-02
> 7      7    0.811  -3.26        0.93300 1.85e-03  1.70e-03 5.55e-03
> 8      8    0.893  -2.92        0.95700 4.99e-04  4.32e-04 1.97e-03
> 9      9    0.923  -2.67        0.94400 1.43e-04  1.15e-04 7.35e-04
> 10    10    0.958  -2.38        0.96500 4.34e-05  3.15e-05 2.85e-04
> 11    12    0.910  -2.07        0.88600 4.50e-06  2.59e-06 4.55e-05
> 12    14    0.325  -3.02        0.21800 5.31e-07  2.29e-07 7.58e-06
> 13    16    0.219  -3.01        0.00942 6.88e-08  2.06e-08 1.29e-06
> 14    18    0.206  -3.06        0.03550 9.53e-09  1.93e-09 2.29e-07
> 15    20    0.227  -2.97        0.02620 1.39e-09  1.85e-10 4.11e-08
>
>
>
>
>>
>> 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
>
>
>
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