/usr/lib/R/site-library/BiocParallel/unitTests/test_bpmapply.R is in r-bioc-biocparallel 1.12.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 | quiet <- suppressWarnings
test_bpmapply_MoreArgs_names <- function()
{
## https://github.com/Bioconductor/BiocParallel/issues/51
f <- function(x, y) x
target <- bpmapply(f, 1:3, MoreArgs=list(x=1L))
checkIdentical(rep(1L, 3), target)
}
test_bpmapply_Params <- function()
{
if (.Platform$OS.type != "windows") {
doParallel::registerDoParallel(2)
params <- list(serial=SerialParam(),
snow=SnowParam(2),
dopar=DoparParam(),
batchjobs=BatchJobsParam(2, progressbar=FALSE),
mc <- MulticoreParam(2))
x <- 1:10
y <- rev(x)
f <- function(x, y) x + y
expected <- x + y
for (param in params) {
current <- quiet(bpmapply(f, x, y, BPPARAM=param))
checkIdentical(expected, current)
closeAllConnections()
}
# test names and simplify
x <- setNames(1:5, letters[1:5])
for (param in params) {
for (catch.errors in c(FALSE, TRUE)) {
bpcatchErrors(param) <- catch.errors
for (SIMPLIFY in c(FALSE, TRUE)) {
for (USE.NAMES in c(FALSE, TRUE)) {
expected <- mapply(identity, x,
USE.NAMES=USE.NAMES,
SIMPLIFY=SIMPLIFY)
current <- quiet(bpmapply(identity, x,
USE.NAMES=USE.NAMES,
SIMPLIFY=SIMPLIFY,
BPPARAM=param))
checkIdentical(expected, current)
closeAllConnections()
}
}
}
}
# test MoreArgs
x <- setNames(1:5, letters[1:5])
f <- function(x, m) { x + m }
expected <- mapply(f, x, MoreArgs=list(m=1))
for (param in params) {
current <- quiet(bpmapply(f, x, MoreArgs=list(m=1), BPPARAM=param))
checkIdentical(expected, current)
closeAllConnections()
}
# test empty input
for (param in params) {
current <- quiet(bpmapply(identity, BPPARAM=param))
checkIdentical(list(), current)
closeAllConnections()
}
## clean up
env <- foreach:::.foreachGlobals
rm(list=ls(name=env), pos=env)
closeAllConnections()
TRUE
} else TRUE
}
test_bpmapply_symbols <- function()
{
doParallel::registerDoParallel(2)
params <- list(serial=SerialParam(),
snow=SnowParam(2),
dopar=DoparParam())
if (.Platform$OS.type != "windows")
params$mc <- MulticoreParam(2)
x <- list(as.symbol(".XYZ"))
expected <- mapply(as.character, x)
for (param in names(params)) {
current <- bpmapply(as.character, x, BPPARAM=params[[param]])
checkIdentical(expected, current)
}
## clean up
env <- foreach:::.foreachGlobals
rm(list=ls(name=env), pos=env)
closeAllConnections()
TRUE
}
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