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message("Testing bpmapply")
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()
{
cl <- parallel::makeCluster(2)
doParallel::registerDoParallel(cl)
params <- list(
serial=SerialParam(),
snow=SnowParam(2),
dopar=DoparParam()
)
if (.Platform$OS.type != "windows")
params$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)
}
# test names and simplify
x <- setNames(1:5, letters[1:5])
for (param in params) {
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)
}
}
}
# 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)
}
# test empty input
for (param in params) {
current <- quiet(bpmapply(identity, BPPARAM=param))
checkIdentical(list(), current)
}
## clean up
foreach::registerDoSEQ()
parallel::stopCluster(cl)
closeAllConnections()
}
test_bpmapply_symbols <- function()
{
cl <- parallel::makeCluster(2)
doParallel::registerDoParallel(cl)
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
foreach::registerDoSEQ()
parallel::stopCluster(cl)
closeAllConnections()
TRUE
}
test_bpmapply_named_list <- function()
{
X <- list()
Y <- character()
checkIdentical(X, bpmapply(identity))
checkIdentical(X, bpmapply(identity, X))
checkIdentical(mapply(identity, Y), bpmapply(identity, Y))
checkIdentical(X, bpmapply(identity, USE.NAMES = FALSE))
checkIdentical(X, bpmapply(identity, X, USE.NAMES = FALSE))
checkIdentical(X, bpmapply(identity, Y, USE.NAMES = FALSE))
names(X) <- names(Y) <- character()
checkIdentical(X, bpmapply(identity, X))
checkIdentical(X, bpmapply(identity, Y))
checkIdentical(list(), bpmapply(identity, X, USE.NAMES = FALSE))
checkIdentical(list(), bpmapply(identity, Y, USE.NAMES = FALSE))
Y1 <- setNames(letters, letters)
Y2 <- setNames(letters, LETTERS)
checkIdentical(mapply(identity, Y1), bpmapply(identity, Y1))
checkIdentical(mapply(identity, Y2), bpmapply(identity, Y2))
X <- list(c(a = 1))
checkIdentical(X, bpmapply(identity, X, SIMPLIFY = FALSE))
X <- list(a = 1:2)
checkIdentical(X, bpmapply(identity, X, SIMPLIFY = FALSE))
X <- list(a = 1:2, b = 1:4)
checkIdentical(X, bpmapply(identity, X, SIMPLIFY = FALSE))
X <- list(A = c(a = 1:3))
checkIdentical(X, bpmapply(identity, X, SIMPLIFY = FALSE))
X <- list(A = c(a = 1, b=2), B = c(c = 1, d = 2))
checkIdentical(X, bpmapply(identity, X, SIMPLIFY = FALSE))
## named arguments to bpmapply
Y <- 1:3
checkIdentical(Y, bpmapply(identity, x = Y))
}
test_transposeArgsWithIterations <- function() {
.transposeArgsWithIterations <- BiocParallel:::.transposeArgsWithIterations
## list() when `mapply()` invoked with no arguments, `mapply(identity)`
checkIdentical(
list(),
.transposeArgsWithIterations(list(), USE.NAMES = TRUE)
)
checkIdentical(
list(),
.transposeArgsWithIterations(list(), USE.NAMES = FALSE)
)
## list(X) when `mapply()` invoked with one argument, `mapply(identity, X)`
X <- list()
XX <- list(X)
checkIdentical(list(), .transposeArgsWithIterations(XX, USE.NAMES = TRUE))
checkIdentical(list(), .transposeArgsWithIterations(XX, USE.NAMES = FALSE))
## `mapply(identity, character())` returns a _named_ list()
X <- character()
XX <- list(X)
checkIdentical(
setNames(list(), character()),
.transposeArgsWithIterations(XX, TRUE)
)
checkIdentical(list(), .transposeArgsWithIterations(XX, FALSE))
## named arguments to mapply() are _not_ names of return value...
X <- list()
XX <- list(x = X)
checkIdentical(list(), .transposeArgsWithIterations(XX, TRUE))
checkIdentical(list(), .transposeArgsWithIterations(XX, FALSE))
## ...except if the argument is a character()
X <- character()
XX <- list(x = X)
checkIdentical(
setNames(list(), character()),
.transposeArgsWithIterations(XX, TRUE)
)
checkIdentical(list(), .transposeArgsWithIterations(XX, FALSE))
## with multiple arguments, names are from the first argument
XX <- list(c(a = 1, b = 2, c = 3), c(d = 4, e = 5, f = 6))
checkIdentical(
setNames(list(list(1, 4), list(2, 5), list(3, 6)), letters[1:3]),
.transposeArgsWithIterations(XX, TRUE)
)
checkIdentical(
list(list(1, 4), list(2, 5), list(3, 6)),
.transposeArgsWithIterations(XX, FALSE)
)
## ...independent of names on the arguments
XX <- list(A = c(a = 1, b = 2, c = 3), B = c(d = 4, e = 5, f = 6))
checkIdentical(
list(a = list(A=1, B=4), b = list(A=2, B=5), c = list(A=3, B=6)),
.transposeArgsWithIterations(XX, TRUE)
)
checkIdentical(
list(list(A=1, B=4), list(A=2, B=5), list(A=3, B=6)),
.transposeArgsWithIterations(XX, FALSE)
)
## when the first argument is an unnamed character vector, names
## are values
XX <- list(A = c("a", "b", "c"), B = 1:3)
checkIdentical(
list(
a = list(A="a", B=1L), b = list(A="b", B=2L), c = list(A="c", B=3L)
),
.transposeArgsWithIterations(XX, TRUE)
)
checkIdentical(
list(list(A="a", B=1L), list(A="b", B=2L), list(A="c", B=3L)),
.transposeArgsWithIterations(XX, FALSE)
)
## ...except if there are names on the first vector...
XX <- list(A = setNames(letters[1:3], LETTERS[1:3]), B = 1:3)
checkIdentical(
list(
A = list(A="a", B=1L), B = list(A="b", B=2L), C = list(A="c", B=3L)
),
.transposeArgsWithIterations(XX, TRUE)
)
checkIdentical(
list(list(A="a", B=1L), list(A="b", B=2L), list(A="c", B=3L)),
.transposeArgsWithIterations(XX, FALSE)
)
}
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