tests/testthat/test_install.R

In BiocManager: Access the Bioconductor Project Package Repository

context("install()")

test_that("Arguments are validated", {
    expect_error(
        install("foo", "bar"),
        "all '...' arguments to 'install\\(\\)' must be named"
    )
    expect_error(install(TRUE), "is.character\\(pkgs\\) is not TRUE")
    expect_error(install(ask="foo"), "is.logical\\(ask\\) is not TRUE")
})

test_that("Helpers filter the right packages", {
    .install_filter_r_repos <- BiocManager:::.install_filter_r_repos
    .install_filter_github_repos <- BiocManager:::.install_filter_github_repos

    r <- "foo"
    http <- c("http://foo.bar/baz", "https://foo.bar/baz")
    github <- c("foo/bar", "foo/bar@baz")
    all <- c(r, http, github)

    expect_identical(c(r, http), .install_filter_r_repos(all))
    expect_identical(github, .install_filter_github_repos(all))
})

test_that(".install_repos() works", {
    .skip_if_misconfigured()
    skip_if_offline()
    repos <- repositories()
    old_pkgs <- matrix(
        c("pkgB", "/home/user/dir"), 1, 2,
        dimnames=list("pkgB", c("Package", "LibPath")))
    inst_pkgs <- matrix(
        c("pkgA", "/home/user/dir"), 1, 2,
        dimnames=list("pkgA", c("Package", "LibPath")))
    expect_identical(
        character(0),
        .install_repos(
            character(), old_pkgs, inst_pkgs, repos = repos, force = FALSE
        )
    )
})

test_that(".install_github() works", {
    .skip_if_misconfigured()
    skip_if_offline()
    repos <- repositories()
    expect_identical(
        character(0),
        .install_github(character(), repos = repos, update = FALSE, ask = TRUE)
    )
})

test_that("Versions are checked in install", {
    expect_error(install(version = "0.1"))
    expect_error(install(1:3))
    expect_error(install(NA))
    expect_error(install(c("BioStrings", "S4Vectors", NA)))
    expect_error(install(site_repository = c("string1", "string2")))
    expect_error(install(TRUE))
    expect_error(install(ask = "No"))
    expect_error(install(ask = c("No", "Yes", NA)))
    expect_error(install(version = c("3.7", "3.6")))
    expect_error(install(version = character()))
    expect_error(install(version = ""))
    expect_error(install(version = "3.4.2"))
})

test_that("pkgs are not re-downloaded when force=FALSE", {
    .filter <- BiocManager:::.install_filter_up_to_date

    old_pkgs <- matrix(
        c("pkgB", "/home/user/dir"), 1, 2,
        dimnames=list("pkgB", c("Package", "LibPath")))
    inst_pkgs <- matrix(
        c("pkgA", "pkgB", "/home/user/dir", "/home/user/dir"), 2, 2,
        dimnames=list(c("pkgA", "pkgB"), c("Package", "LibPath")))

    # installed and not old
    expect_warning(.filter("pkgA", inst_pkgs, old_pkgs, FALSE))
    # installed and not old but force
    expect_identical(.filter("pkgA", inst_pkgs, old_pkgs, TRUE), "pkgA")

    # installed and old
    expect_identical(.filter("pkgB", inst_pkgs, old_pkgs, FALSE), "pkgB")
    expect_identical(.filter("pkgB", inst_pkgs, old_pkgs, TRUE), "pkgB")

    # not installed and no info on old
    expect_identical(.filter("pkgC", inst_pkgs, old_pkgs, FALSE), "pkgC")
})

context("install(update = TRUE) filters un-updatable packages")

test_that("masked packages are filtered", {
    .filter <- BiocManager:::.package_filter_masked

    pkgs0 <- matrix(
        character(), 0, 2,
        dimnames=list(NULL, c("Package", "LibPath")))

    expect_identical(pkgs0, .filter(pkgs0))

    paths <- c(tempfile(), tempfile())
    for (path in paths) dir.create(path)
    oLibPaths <- .libPaths()
    on.exit(.libPaths(oLibPaths))
    .libPaths(paths)

    pkgs <- matrix(
        c("Foo", "Bar", "Baz", "Bim", paths, paths), 4, 2,
        dimnames=list(c("Foo", "Bar", "Baz", "Bim"), c("Package", "LibPath")))
    expect_identical(pkgs, .filter(pkgs))
    expect_identical(pkgs[c(1, 3, 2),], .filter(pkgs[c(1, 3, 2),]))

    pkgs <- matrix(
        c("Foo", "Bar", "Foo", paths, paths[2]), 3, 2,
        dimnames=list(c("Foo", "Bar", "Foo"), c("Package", "LibPath")))
    expect_identical(pkgs[1:2,], .filter(pkgs))
    pkgs <- pkgs[3:1,]
    expect_identical(pkgs[2:3,], .filter(pkgs))
})

test_that("unwriteable packages are not considered", {
    .filter <- BiocManager:::.package_filter_unwriteable
    ## setup
    dir.create(p0 <- tempfile())
    on.exit(unlink(p0, recursive=TRUE))

    pkgs0 <- matrix(
        character(), 0, 2,
        dimnames=list(NULL, c("Package", "LibPath")))

    pkgs <- pkgs0
    expect_identical(pkgs, .filter(pkgs, NULL))
    expect_identical(pkgs, .filter(pkgs, character()))
    expect_identical(pkgs, .filter(pkgs, tempdir()))

    pkgs <- matrix(c("Foo", p0), 1, byrow=TRUE,
                   dimnames=list("Foo", c("Package", "LibPath")))
    expect_identical(pkgs, .filter(pkgs, NULL))
    expect_identical(pkgs, .filter(pkgs, p0))

    p1 <- tempfile()
    pkgs <- matrix(c("Foo", p1), 1, byrow=TRUE,
                   dimnames=list("Foo", c("Package", "LibPath")))
    expect_identical(pkgs[FALSE,, drop=FALSE], .filter(pkgs, NULL))
    expect_identical(pkgs[FALSE,, drop=FALSE], .filter(pkgs, p1))
    expect_identical(pkgs, .filter(pkgs, p0))

    pkgs <- matrix(
        c("Foo", p0, "Bar", p1, "Baz", p0), 3, 2, byrow=TRUE,
        dimnames=list(c("Foo", "Bar", "Baz"), c("Package", "LibPath")))
    expect_identical(pkgs[c(1, 3),], .filter(pkgs, NULL))
    expect_identical(pkgs, .filter(pkgs, p0))
    expect_identical(pkgs0, .filter(pkgs, p1))

    expect_message(.filter(pkgs, NULL), "^Installation paths not writeable")

    if (.Platform$OS.type == "windows")
        ## how to create a read-only directory?
        return(TRUE)

    isDirRnW <- dir.create(p2 <- tempfile(), mode="0400") # read but not write
    skip_if_not(isDirRnW)
    pkgs <- matrix(c("Foo", p2), 1, byrow=TRUE,
                   dimnames=list("Foo", c("Package", "LibPath")))
    expect_identical(pkgs0, .filter(pkgs, NULL))

    pkgs <- matrix(
        c("Foo", p0, "Bar", p2, "Baz", p0), 3, 2, byrow=TRUE,
        dimnames=list(c("Foo", "Bar", "Baz"), c("Package", "LibPath")))
    expect_identical(pkgs[c(1, 3),], .filter(pkgs, NULL))
    expect_identical(pkgs0, .filter(pkgs, p2))

    Sys.chmod(p2, mode="0700")
    unlink(p2, recursive=TRUE)
})

test_that("packages can be written", {
    skip("too idiosyncratic for standardized testing")

    lib <- system.file(package="BiocManager", "tests", "cases",
        "lib", "Biobase")
    dir.create(locked <- tempfile())
    file.copy(lib, locked, recursive=TRUE)

    oLibPaths <- .libPaths()
    on.exit(.libPaths(oLibPaths))
    .libPaths(c(locked, .libPaths()))

    Sys.chmod(locked, mode="0500")
    install()
    Sys.chmod(locked, mode="0700")
})

context("install(version =, ask=...) works")

test_that(".install_ask_up_or_down_grade() works non-interactively", {
    skip_if(interactive())
    expect_equal(
        FALSE,
        .install_ask_up_or_down_grade("xx", npkgs = 1L, cmp = 1L, ask = TRUE)
    )
    expect_equal(
        TRUE,
        .install_ask_up_or_down_grade("xx", npkgs = 1L, cmp = 1L, ask = FALSE)
    )
})

test_that("install() fails with different version (non-interactive)", {
    map <- BiocManager:::.version_map()
    incr <- 1L
    version <-
        package_version(paste(version()$major, version()$minor + incr, sep="."))
    expect_error(install(version = version))
})

test_that("install() passes the force argument to .install", {
    .skip_if_misconfigured()
    skip_if_offline()
    expect_true(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['force']]
            },
            `BiocManager:::.version_compare` = function(...) {
                0L
            },
            suppressMessages(
                install(force = TRUE, update = FALSE)
            )
        )
    )
    expect_false(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['force']]
            },
            `BiocManager:::.version_compare` = function(...) {
                0L
            },
            suppressMessages(
                install(force = FALSE, update = FALSE)
            )
        )
    )
    expect_true(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['force']]
            },
            `BiocManager:::.version_compare` = function(...) {
                1L
            },
            `BiocManager:::.install_n_invalid_pkgs` = function(...) {
                0L
            },
            `BiocManager:::.install_updated_version` = function(...) {
                pkgs <<- list(...)[['force']]
            },
            suppressMessages(
                install(force = TRUE, update = FALSE, ask = FALSE)
            )
        )
    )
    expect_false(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['force']]
            },
            `BiocManager:::.version_compare` = function(...) {
                1L
            },
            `BiocManager:::.install_n_invalid_pkgs` = function(...) {
                0L
            },
            `BiocManager:::.install_updated_version` = function(...) {
                pkgs <<- list(...)[['force']]
            },
            suppressMessages(
                install(force = FALSE, update = FALSE, ask = FALSE)
            )
        )
    )
    expect_false(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['update']]
            },
            `BiocManager:::.version_compare` = function(...) {
                1L
            },
            `BiocManager:::.install_n_invalid_pkgs` = function(...) {
                0L
            },
            `BiocManager:::.install_updated_version` = function(...) {
                pkgs <<- list(...)[['update']]
            },
            suppressMessages(
                install(force = FALSE, update = FALSE, ask = FALSE)
            )
        )
    )    
    expect_false(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['ask']]
            },
            `BiocManager:::.version_compare` = function(...) {
                1L
            },
            `BiocManager:::.install_n_invalid_pkgs` = function(...) {
                0L
            },
            `BiocManager:::.install_updated_version` = function(...) {
                pkgs <<- list(...)[['ask']]
            },
            suppressMessages(
                install(force = FALSE, update = FALSE, ask = FALSE)
            )
        )
    )    
    expect_null(
        with_mock(
            `BiocManager:::.install` = function(...) {
                list(...)[['checkBuilt']]
            },
            `BiocManager:::.version_compare` = function(...) {
                1L
            },
            `BiocManager:::.install_n_invalid_pkgs` = function(...) {
                0L
            },
            `BiocManager:::.install_updated_version` = function(...) {
                pkgs <<- list(...)[['checkBuilt']]
            },
            suppressMessages(
                install(
                    force = FALSE, checkBuilt = TRUE,
                    update = FALSE, ask = FALSE
                )
            )
        )
    )
})

test_that("install() without package names passes ... to install.packages", {
    .skip_if_misconfigured()
    object <- FALSE
    with_mock(
        available.packages = function(...) {
            cbind(
                Package = "BiocGenerics", Version = "0.33.0",
                LibPath = .libPaths()[1]
            )
        },
        old.packages = function(...) {
            ## claim that BiocGenerics is out-of-date
            cbind(
                Package = "BiocGenerics", Version = "0.32.0",
                LibPath = .libPaths()[1]
            )
        },
        install.packages = function(pkgs, ..., INSTALL_opts) {
            object <<-
                identical(pkgs, c(Package = "BiocGenerics")) &&
                identical(INSTALL_opts, "--build")
        },
        install(ask = FALSE, INSTALL_opts = "--build")
    )
    expect_true(object)
})