futile.logger::flog.threshold("FATAL", name = "kube_install")
futile.logger::flog.threshold("FATAL", name = "kube_progress")
futile.logger::flog.threshold("FATAL", name = "kube_errors")
test_that("build dummy pkgs", {
deps <- list(
C = "A",
D = "B",
E = c("A", "B"),
F = "E",
G = NULL
)
lib_path <- tempdir()
bin_path <- tempdir()
logs_path<- tempdir()
## remove all files in the temp directory
do.call(file.remove,
list(list.files(lib_path, full.names = TRUE, recursive = TRUE))
)
param <- BiocParallel::SnowParam(2)
## No error for all pkgs
result <- with_mock(
kube_install_single_package = function(...) {},
kube_install(lib_path, bin_path, logs_path, deps,
BPPARAM = param)
)
expect_identical(result, list())
## Build with single error
result <- with_mock(
kube_install_single_package =
function(pkg, ...) if (pkg %in% "A") simpleError(pkg),
kube_install(lib_path, bin_path, logs_path, deps,
BPPARAM = param)
)
expect_identical(sort(names(result)), c("A", "C", "E", "F"))
## Build with multiple errors
result <- with_mock(
kube_install_single_package =
function(pkg, ...) if (pkg %in% c("A", "B")) simpleError(pkg),
kube_install(lib_path, bin_path, logs_path, deps,
BPPARAM = param)
)
expect_identical(sort(names(result)), c("A", "B", "C", "D", "E", "F"))
})
test_that("build pkgs", {
deps0 <- c("agilp","AMOUNTAIN", "ASAFE", "BAC")
l <- rep(list(NULL), length(deps0))
names(l) <- deps0
lib_path <- tempdir()
bin_path <- tempdir()
logs_path<- tempdir()
## remove all files in the temp directory
do.call(file.remove,
list(list.files(lib_path, full.names = TRUE, recursive = TRUE))
)
p <- BiocParallel::SnowParam(2)
res <- kube_install(lib_path,
bin_path,
logs_path,
l,
p
)
files <- list.files(lib_path, full.names = TRUE)
expect_equal(sum(grepl(".out$", files)), length(deps0))
## 4 success + 1 final PACKAGES.gz i.e length(deps0) + 1
## [1] "/tmp/RtmpMcUYkQ/agilp_3.27.0_R_x86_64-pc-linux-gnu.tar.gz"
## [2] "/tmp/RtmpMcUYkQ/AMOUNTAIN_1.21.0_R_x86_64-pc-linux-gnu.tar.gz"
## [3] "/tmp/RtmpMcUYkQ/ASAFE_1.21.0_R_x86_64-pc-linux-gnu.tar.gz"
## [4] "/tmp/RtmpMcUYkQ/BAC_1.55.0_R_x86_64-pc-linux-gnu.tar.gz"
## [5] "/tmp/RtmpMcUYkQ/PACKAGES.gz"
expect_equal(sum(grepl(".gz$", files)), length(deps0) + 1)
})
futile.logger::flog.threshold("INFO", name = "kube_install")
futile.logger::flog.threshold("INFO", name = "kube_progress")
futile.logger::flog.threshold("INFO", name = "kube_errors")
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