tests/testthat/test_kube_install.R

In Bioconductor/BiocKubeInstall: Build R / Bioconductor package binaries using Kubernetes on a cloud service

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")