/usr/lib/R/site-library/BiocParallel/unitTests/test_bpvalidate.R is in r-bioc-biocparallel 1.4.0-1.
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 | library(Rsamtools)
test_bpvalidate_library <- function()
{
fun <- function(fl, ...) {
countBam(fl)
}
res <- suppressMessages(bpvalidate(fun))
checkIdentical(names(res$inPath), "countBam")
checkIdentical(res$unknown, character())
}
test_bpvalidate_args <- function()
{
param <- ScanBamParam(flag=scanBamFlag(isMinusStrand=FALSE))
fun <- function(fl, ...) {
library(Rsamtools)
countBam(fl, param=param)
}
res <- bpvalidate(fun)
checkIdentical(unname(res$inPath), list())
checkIdentical(res$unknown, "param") ## no .GlobalEnv; param -> unknown
fun <- function(fl, ..., param) {
library(Rsamtools)
countBam(fl, param=param)
}
res <- bpvalidate(fun)
checkIdentical(unname(res$inPath), list())
checkIdentical(res$unknown, character())
}
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