Hello,

I have been trying to use bumphunter on my 450k data and I have been
running into some problems with the smooth function using the option of
loessByCluster.  I have tired both other smoothing functions
runmedByCluster and locfitByCluster and these perform correctly however I
get this error when trying to use loessByCluster.

Error in { :
  task 1 failed - "NA/NaN/Inf in foreign function call (arg 1)"

I have called bumphunter with the following function:

### Run all chromosomes together

chr_locs <- ordered by chromosome genomic location
chr_chr <- chromosome information
chr_clusters <- clusterMaker(chr_chr, chr_locs, maxGap = 400)

logtrans <- log transformed beta-values

chr_bumphunter <- bumphunter(logtrans,
  design matrix with first column of "1" and second column with membership
comparing 6 (0) samples to 89 samples (1),
  chr_chr, chr_locs, chr_clusters, smoothFunction = loessByCluster, smooth
= TRUE)

This error always occurs when I am trying to do the permutations, never on
the normal data.  This is the output from bumphunter.

bumphunterEngine: Using a single core (backend: doSEQ, version: 1.4.2)
bumphunterEngine: Computing coefficients.
bumphunterEngine: Smoothing coefficients.
bumphunterEngine cutoff: 1.123
bumphunterEngine: Finding regions.
bumphunterEngine: Performing 100 permutations.
bumphunterEngine: Computing marginal permutation p-values.
bumphunterEngine: Smoothing permutation coefficients.

After which I see the error above.  I have tired checking the
logtransformed beta-values to see if I have any NAs or 1 but there aren't
any.  Any idea what this error is coming from?  I do have some very, very
small numbers approaching zero but I have tired even to change these to
0.001 and it does not fix the error.  Furthermore, it's only in the
permutation portion where this error occurs so I thought this might not be
the problem.

Any ideas what's going on?

Thanks!

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