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all_positive_integers <- function(N) sample(.Machine$integer.max, N, replace=TRUE)
are_PCs_equal <- function(first, second, tol=1e-8)
# Check if PCs are equal (other than sign).
{
expect_identical(dim(first), dim(second))
relative <- first/second
expect_true(all(colSums(relative > 0) %in% c(0, nrow(first))))
expect_true(all(abs(abs(relative)-1) < tol))
}
# Because SnowParam() is too slow, yet MulticoreParam() fails on Windows.
# See discussion at https://github.com/Bioconductor/BiocParallel/issues/98.
safeBPParam <- function(nworkers) {
if (.Platform$OS.type=="windows") {
BiocParallel::SerialParam()
} else {
BiocParallel::MulticoreParam(nworkers)
}
}
# Using ExactParam to avoid the trouble of setting the seed for all SVD-related tests.
options(BiocSingularParam.default=BiocSingular::ExactParam())
# Adding a test to flush out any uncontrolled parallelization.
library(BiocParallel)
failgen <- setRefClass("FailParam",
contains="BiocParallelParam",
fields=list(),
methods=list())
FAIL <- failgen()
register(FAIL)
library(DelayedArray)
setAutoBPPARAM(FAIL)
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