Hi,

I found following error when I tried running the following example code from regioneR vignette. 

pt_Rad21_5k_vs_Ctcf <- permTest(A=HepG2_Rad21_5K, B=HepG2_Ctcf, ntimes=1000,
                                randomize.function=circularRandomizeRegions,
                                evaluate.function=numOverlaps, count.once=TRUE,
                                + genome="hg19", mc.set.seed=FALSE, mc.cores=4)

Error in if (alt == "less") { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In mclapply(c(1:ntimes), randomize_and_evaluate, ...) :
  all scheduled cores encountered errors in user code
2: In mean.default(rand.ev, na.rm = TRUE) :
  argument is not numeric or logical: returning NA

Thank you

I just run the full example in and it run without errors for me.  If you take a closer look at the error message it produced you can see it said

1: In mclapply(c(1:ntimes), randomize_and_evaluate, ...) : all scheduled cores encountered errors in user code

That means that all parallel jobs sent errored. However you cannot see the exact problem, since when running in parallel the errors get hidden.

I would recommend making sure you downloaded all needed data (with the code in the prior page in the vignette) and the running without parallel execution (and a lower number of permutations, so it finishes faster) with this:

pt_Rad21_5k_vs_Ctcf <- permTest(A=HepG2_Rad21_5K, B=HepG2_Ctcf, ntimes=10,
                                randomize.function=circularRandomizeRegions,
                                evaluate.function=numOverlaps, count.once=TRUE,
                                genome="hg19", force.parallel = FALSE)

With this, more clear and evident error messages should appear.

Part of permTest is to determine what the alternative hypothesis is, and if you don't specify the alternative, it will figure it out by itself (which is sort of bootleg - you shouldn't decide on the test based on your data, but whatever). It does this by looking at the mean of the randomized data (which is captured in a variable called rand.ev).

You have a warning and an error that in essence tell you what the problem is. The warning is

In mean.default(rand.ev, na.rm = TRUE) :
  argument is not numeric or logical: returning NA

Which can be translated to 'when I generated random data, the results aren't numeric, so what's up with that?'. This probably means that you are feeding character data into permTest, but only you can know that for sure. I get the same warning if I do something like

> mean(c(1,2,3,"a"))
[1] NA
Warning message:
In mean.default(c(1, 2, 3, "a")) :
  argument is not numeric or logical: returning NA

The error is

Error in if (alt == "less") { : missing value where TRUE/FALSE needed

which comes from a test

if(alternative == "auto") {
alt <- ifelse(orig.ev < mean(rand.ev, na.rm=TRUE), "less", "greater")

and you have a missing value because rand.ev isn't numeric, as the warning already noted, so in this case alt won't be less or greater, it will be NA, so when you do the test of alt == "less", you get the error because  NA == "less", returns NA, not TRUE or FALSE.