README.md

bettermcExt

The bettermcExt package provides extensions of the bettermc package which are not allowed on CRAN.

Installation of the Latest Release

# install.packages("remotes")
remotes::install_github("gfkse/bettermcExt", remotes::github_release())

Overloading parallel::mclapply() With bettermc::mclapply()

Enable the use of bettermc::mclapply() by third-party packages originally using mclapply() from the parallel package, e.g. doMC or rstan. This is achieved by replacing the mclapply-function in various environments, which violates the following CRAN policy:

A package must not tamper with the code already loaded into R: any attempt to change code in the standard and recommended packages which ship with R is prohibited. Altering the namespace of another package should only be done with the agreement of the maintainer of that package.

Example: Making doMC Reproducible

doMC::registerDoMC(2L)

# fix mc.set.seed arg to NA in order to avoid modifications by doMC:::doMC
bettermcExt::overload_mclapply(imports = "doMC", fixed_args = list(mc.set.seed = NA))

set.seed(123)
ret1 <- foreach::`%dopar%`(foreach::foreach(i = 1:4), runif(1))
set.seed(123)
ret2 <- foreach::`%dopar%`(foreach::foreach(i = 1:4), runif(1))
stopifnot(identical(ret1, ret2))

bettermcExt::undo_overload_mclapply(imports = "doMC")

# back to using parallel::mclapply under the hood -> seeding has no effect
set.seed(123)
ret3 <- foreach::`%dopar%`(foreach::foreach(i = 1:4), runif(1))
set.seed(123)
ret4 <- foreach::`%dopar%`(foreach::foreach(i = 1:4), runif(1))
stopifnot(identical(ret3, ret4))

## Error: identical(ret3, ret4) is not TRUE

Example: Making rstan::sampling() Reproducible

Note that rstan::sampling() uses mclapply() only in a non-interactive session.

bettermcExt::overload_mclapply(parallel_namespace = TRUE)

m <- rstan::stan_model(model_code = 'parameters {real y;} model {y ~ normal(0,1);}')

set.seed(456)
capture.output(f1 <- rstan::sampling(m, iter = 100, cores = 2), file = "/dev/null")
set.seed(456)
capture.output(f2 <- rstan::sampling(m, iter = 100, cores = 2), file = "/dev/null")
stopifnot(identical(rstan::extract(f1), rstan::extract(f2)))

bettermcExt::undo_overload_mclapply(parallel_namespace = TRUE)

# back to using parallel::mclapply under the hood -> seeding has no effect
set.seed(456)
capture.output(f3 <- rstan::sampling(m, iter = 100, cores = 2), file = "/dev/null")
set.seed(456)
capture.output(f4 <- rstan::sampling(m, iter = 100, cores = 2), file = "/dev/null")
stopifnot(identical(rstan::extract(f3), rstan::extract(f4)))

## Error: identical(rstan::extract(f3), rstan::extract(f4)) is not TRUE