Common problems

Error "return code from pthread_create() is 22"

There is likely a problem with the openblas library that can be fixed by reinstalling preprocessCore and disabling threading.

BiocManager::install("preprocessCore", configure.args="--disable-threading", force=TRUE)

Note that meffil will still be able to use multiple cores to perform multiple processing after this change.

You can check this in your installation beforehand using the following code.

threading.ok <- function() {
	require(preprocessCore)
	y <- matrix(10+rnorm(100),20,5)
	ret <- tryCatch({normalize.quantiles(y); "correct"}, error=function(e) e$message)
	!grepl("pthread_create", ret)
}

If threading.ok() returns TRUE, then you shouldn't have a problem. If it return FALSE, then you'll need to reinstall preprocessCore with threading disabled as shown above.

Error messages when running meffil.ewas.summary()

When plotting associations, meffil.ewas.summary() attempts to fit several different models, some of these may fail with the following error message:

Error in chol.default(K) :
  the leading minor of order 3 is not positive definite

These errors are nothing to worry about. The function will simply omit these from the output and continue generating other outputs. We have decided to retain the error messages to indicate that statistics for some associations may be missing from the report.