Re: [Bioc-devel] BiocParallel Variable Not Found

2020-03-17 Thread Dario Strbenac
Good day, I am not sure how to fix my package properly, even with the good example. A link to the specific part of my function is https://github.com/DarioS/ClassifyR/blob/e35899caceb401691990136387a517f4c3b57d5e/R/runTests.R#L567 and the example in the help page of runTestsEasyHard function tri

Re: [Bioc-devel] BiocParallel Variable Not Found

2020-03-17 Thread Martin Morgan
The question is a bit abstract for me to understand and it might be better to point to actual code in a git repository or similar... Inside a package, something like fun = function(x, y, ...) { c(x, y, length(as.list(...))) } user_visible <- function(x, ...) { y = 1 internal_functi

Re: [Bioc-devel] BiocParallel Variable Not Found

2020-03-17 Thread Dario Strbenac
Good day, Thanks for the examples which demonstrate the issue. Do you have other recommendations if, inside the loop, another function in the package is being called and the variable being passed is the ellipsis? There are only a couple of variables which might be provided by the user collected

Re: [Bioc-devel] BiocParallel Variable Not Found

2020-03-17 Thread Martin Morgan
Windows uses separate processes that do not share memory (SnowParam()), whereas linux / mac by default use forked processes that share the original memory (MulticoreParam()). So > y = 1 > param = MulticoreParam() > res = bplapply(1:2, function(x) y, BPPARAM=param) works because the function can