%dopar% error after several iterations

Question

I've been trying to get a parallelized foreach loop running in R, it works fine for approximately ten iterations but then crashes, showing the error:

Error in { : task 7 failed - "missing value where TRUE/FALSE needed"
Calls: %dopar% -> <Anonymous>
Execution halted

I append the results of each loop to a file, which does show the output to be as expected. My script is as followed,using the combn_sub function from this post:

LBRA <- fread(
 input      = "LBRA.012",
 data.table = FALSE)
str_bra <- nrow(LBRA)

br1sums <- colSums(LBRA)
b1non <- which(br1sums == 0)

LBRA_trim <- LBRA[,-b1non]

library(foreach)
library(doMC)
registerDoMC(28)

foreach(X = seq(2, (nrow(LBRA)-1))) %dopar% {
  com <- combn_sub(
   x    = nrow(LBRA),
   m    = X,
   nset = 1000)

  out_in <- matrix(
   ncol = 2,
   nrow = 1)
   colnames(out) <- c("SNPs", "k")

    for (A in seq(1, ncol(com))){
      rowselect <- com[, A]

      sub <- LBRA_trim[rowselect, ]
      subsum <- colSums(sub)

      length <- length(which(subsum != 0)) - 1
      out_in <- rbind(out_in, c(length, X))
    }

  write.table(
   file   = "plateau.csv",
   sep    = "\t",
   x      = out_in,
   append = TRUE)
}

Answer 1

I had a similar problem with my foreach call...

tmpcol <- foreach(j = idxs:idxe, .combine=cbind) %dopar% { imp(j) }

Error in { : task 18 failed - "missing value where TRUE/FALSE needed"

Changing the .errorhandling parameter only ignores the error

tmpcol <- foreach(j = idxs:idxe, .combine=cbind, .errorhandling="pass") %dopar% { imp(j) }

Warning message:
In fun(accum, result.18) :
  number of rows of result is not a multiple of vector length (arg 2)

I suggest running the function in your foreach call for X=7. The problem in my case was my function, imp(j), was throwing an error (for j=18, it was hitching on an NA calculation) which resulted in the vague output from foreach.