Hi,

I'm getting this error when using the BSmooth function in bsseq:

covs <- list.files(indir, pattern="\\.bismark.cov$", full.names=TRUE, recursive=TRUE)
bsobj <- read.bismark(files=covs, sampleNames=names(covs), fileType="cov")
fit <- BSmooth(bsobj, mc.cores=ncores, parallelBy="sample", verbose=TRUE)
[BSmooth] preprocessing ... done in 101.7 sec
[BSmooth] smoothing by 'sample' (mc.cores = 16, mc.preschedule = FALSE)
Error in sum(sapply(res, inherits, "try-error")) :
  invalid 'type' (list) of argument
traceback()
6: mclapply(seq(along = sampleNames), function(sIdx) {
       ptime1 <- proc.time()
       tmp <- lapply(clusterIdx, function(jj) {
           try(smooth(idxes = jj, sampleIdx = sIdx))
       })
       coef <- do.call(c, lapply(tmp, function(xx) xx$coef))
       se.coef <- do.call(c, lapply(tmp, function(xx) xx$se.coef))
       ptime2 <- proc.time()
       stime <- (ptime2 - ptime1)[3]
       if (verbose) {
           cat(sprintf("[BSmooth] sample %s (out of %d), done in %.1f sec\n",
               sampleNames[sIdx], length(sampleNames), stime))
       }
       return(list(coef = coef, se.coef = se.coef))
   }, mc.preschedule = mc.preschedule, mc.cores = mc.cores)
5: BSmooth(bsobj, mc.cores = ncores, parallelBy = "sample", verbose = TRUE) at 07differentialMethylation.R#30
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("07differentialMethylation.R", echo = TRUE)

However I can't reproduce this with the BS.cancer.ex data.

Do you have any idea about what might be causing that error?

I'm using R 3.2.2, Bioconductor 3.2 and bsseq 1.6.0

Thank you,

Enrico