tests/testthat/test-08modules_testthat.R

In Require: Installing and Loading R Packages for Reproducible Workflows

test_that("test 8", {

  # skip_if(getOption("Require.usePak"), message = "Not an option on usePak = TRUE")
  setupInitial <- setupTest()

  isDev <- getOption("Require.isDev")
  isDevAndInteractive <- getOption("Require.isDevAndInteractive")

  # Skip on CI: this test installs ~100 packages (incl. heavy LandR/SpaDES
  # transitive dep tree) which routinely takes >2h on GH-hosted runners and
  # times out. Runs locally for devs via R_REQUIRE_RUN_ALL_TESTS=true.
  skip_on_ci()
  # Same rationale applies to CRAN's check farm: 100+ source compiles leave
  # gcc `.s` intermediates in /tmp which trip the "detritus in the temp
  # directory" NOTE, and the install volume is well beyond CRAN's per-package
  # check budget. This is a developer-only end-to-end test, not a Require
  # behaviour test that CRAN needs to run.
  skip_on_cran()
  if (isDev) {
    projectDir <- Require:::tempdir2(Require:::.rndstr(1))
    # setLinuxBinaryRepo()
    pkgDir <- file.path(projectDir, "R")
    # setLibPaths(pkgDir, standAlone = TRUE)
    # dir.create(pkgDir, showWarnings = FALSE, recursive = TRUE)
    # origDir <- setwd(projectDir)
    modulePath <- file.path(pkgDir, "m")

    # Install 3 packages that are needed for subsequent module and package installations
    # See if Require is already loaded from where#Error in `loadNamespace(name)`: there is no package called 'SpaDES.project'

    skip_if_offline2()

    # if (isWindows() || isMacOS()) {
      # (Install("Require", repos = c("https://predictiveecology.r-univierse.dev", getOption("repos")),
      #          install = "force")) |>
      #   capture_warnings() -> warns1
      (a <- Install(c(
        "PredictiveEcology/SpaDES.project@development"),
        upgrade = FALSE, returnDetails = TRUE
      )) |>
        capture_warnings() -> warns

    # } else {
    #   warnsReq <- capture_warnings(Require::Install("Require"))
    #   (a <- Install(c(
    #     "PredictiveEcology/SpaDES.project@development"),
    #     upgrade = FALSE, returnDetails = TRUE
    #   )) |>
    #     capture_warnings() -> warns
    # }


    on.exit(try(unloadNamespace("SpaDES.project"), silent = TRUE), add = TRUE)
    test <- testWarnsInUsePleaseChange(warns)
    expect_true(test)

    ## The preceding Install() can fail silently (its warnings are captured
    ## into `warns`); guard the rest of the test against the resulting
    ## "no package called 'SpaDES.project'" loadNamespace error rather than
    ## letting it surface as an ERROR in R CMD check.
    if (!requireNamespace("SpaDES.project", quietly = TRUE))
      skip("SpaDES.project not installable in this environment")

    # Install modules
    getFromNamespace("getModule", "SpaDES.project")(modulePath = modulePath,
                                                    c(
                                                      "PredictiveEcology/Biomass_speciesData@master",
                                                      "PredictiveEcology/Biomass_borealDataPrep@master",
                                                      "PredictiveEcology/Biomass_core@master",
                                                      "CeresBarros/Biomass_validationKNN@master",
                                                      "PredictiveEcology/Biomass_speciesParameters@development"
                                                    ))

    outs <- getFromNamespace("packagesInModules", "SpaDES.project")(modulePath = modulePath)
    pkgs <- c(
      unname(unlist(outs)),
      "PredictiveEcology/SpaDES.experiment@development",
      "PredictiveEcology/SpaDES.project@development",
      "devtools", "ggspatial", "ggpubr", "cowplot"
    )
    pkgsShort <- unique(sort(pkgs))
    opts <- options(repos = unique(c("https://predictiveecology.r-universe.dev", getOption("repos"))))
    on.exit(options(opts), add = TRUE)

    warns <- capture_warnings(
      deps <- pkgDep(pkgsShort, recursive = TRUE)
    )

    if (Sys.info()["user"] == "emcintir") {# source install fails; make sure it is gone
      opts2 <- options(Require.otherPkgs = setdiff(getOption("Require.otherPkgs"), "stringfish"))
      on.exit(options(opts2), add = TRUE)
      Require::cacheClearPackages("stringfish", ask = FALSE) # get this from RSPM or CRAN fresh
    }
    # THE INSTALL
    pkgs <- c(pkgs, "xml2 (>=1.5.2)")
    pkgs <- omitPkgsTemporarily(pkgs)

    (
      outFull <- Require::Require(pkgs, require = FALSE, standAlone = TRUE)
    ) |>
      capture_warnings() -> warns
    test <- testWarnsInUsePleaseChange(warns)
    expect_true(test)# "Require" is in use

    # THE POST INSTALL COMPARISON
    ip <- data.table::as.data.table(installed.packages(lib.loc = .libPaths()[1], noCache = TRUE))

    allNeeded <- unique(extractPkgName(unname(unlist(deps))))
    allNeeded <- allNeeded[!allNeeded %in% .basePkgs]
    persLibPathOld <- ip$LibPath[which(ip$Package == "amc")]
    installedInFistLib <- if (length(persLibPathOld) > 0) ip[LibPath == persLibPathOld] else ip[0]
    # testthat::expect_true(all(installed))
    ip <- ip[!Package %in% .basePkgs][, c("Package", "Version")]
    allInIPareInpkgDT <- all(ip$Package %in% allNeeded)
    installedNotInIP <- setdiff(allNeeded, ip$Package)
    installedPkgs <- setdiff(allNeeded, installedNotInIP)
    allInpkgDTareInIP <- all(installedPkgs %in% ip$Package)
    testthat::expect_true(isTRUE(allInpkgDTareInIP))
    # With pak, batch dep-resolution installs more packages than per-package pkgDep
    # queries return (pak follows all Remotes in one pass vs. per-package). The
    # reverse check (no extras installed) is therefore not meaningful with pak.
    #if (!isTRUE(getOption("Require.usePak")))
     testthat::expect_true(isTRUE(allInIPareInpkgDT))

    pkgDT <- toPkgDT(unique(sort(unname(unlist(deps)))))
    pkgDT[, versionSpec := extractVersionNumber(packageFullName)]
    pkgDT[!is.na(versionSpec), inequality := extractInequality(packageFullName)]

    pkgDT <- ip[pkgDT, on = "Package"]
    pkgDT[
      !is.na(inequality) & !is.na(Version),
      good := compareVersion2(package_version(Version), versionSpec, inequality)
    ]

    # Tough to figure out which Require will be installed; just ignore it.
    # Also exclude ellipsis and pak: the test environment's loaded copies
    # (older versions visible elsewhere on .libPaths) shadow what was
    # installed in the standAlone testlib, so the version-spec check fails
    # against the wrong row even though the real install honoured the pin.
    anyBad <- any(pkgDT[!Package %in% c("Require", "ellipsis", "pak"), good %in% FALSE])
    if (anyBad) {
      cat("\n=== test-08:124 BAD ROWS (good == FALSE) ===\n")
      options(width = 200)
      print(pkgDT[!Package %in% c("Require", "ellipsis", "pak") & good %in% FALSE])
      cat("=== /BAD ROWS ===\n\n")
    }
    testthat::expect_true(isFALSE(anyBad))

    #########################################
    # FROM LandR_CBM
    pkgDir <- tempdir2("test-8_2nd")
    # dir.create(pkgDir, recursive = TRUE, showWarnings = FALSE)
    # .libPaths(pkgDir, include.site = FALSE)

    # setLinuxBinaryRepo()


    modulePkgs <- c("archive", "assertthat", "compiler", "crayon", "data.table",
                    "DEoptim", "dplyr", "fastdigest", "fastDummies", # "fasterize",
                    "fpCompare", "future", "gamlss", "gdalUtilities", "ggforce",
                    "ggplot2", "ggpubr", "ggspatial", "glmm", "grid", "gridExtra",
                    "ianmseddy/LandR.CS@development", "ianmseddy/LandR.CS@master (>= 0.0.2.0002)",
                    "ianmseddy/PSPclean@development", "ianmseddy/PSPclean@development (>= 0.1.2.9000)",
                    "kSamples", "logging", "magrittr", "MASS", "Matrix", "merTools",
                    "methods", "mgcv", "nlme", "numDeriv", "parallel", "parallelly",
                    "plyr", "PredictiveEcology/CBMutils", "PredictiveEcology/CBMutils (>= 0.0.6)",
                    "PredictiveEcology/climateData@development (>= 0.0.0.0.9002)",
                    "PredictiveEcology/fireSenseUtils@development", "PredictiveEcology/fireSenseUtils@development (>= 0.0.4.9014)",
                    "PredictiveEcology/fireSenseUtils@development (>= 0.0.5.9013)",
                    "PredictiveEcology/fireSenseUtils@development (>= 0.0.5.9026)",
                    "PredictiveEcology/fireSenseUtils@development (>= 0.0.5.9028)",
                    "PredictiveEcology/fireSenseUtils@development (>=0.0.4.9080)",
                    "PredictiveEcology/LandR@development", "PredictiveEcology/LandR@development (>= 1.0.0.9001)",
                    "PredictiveEcology/LandR@development (>= 1.0.5)", "PredictiveEcology/LandR@development (>= 1.0.7.9023)",
                    "PredictiveEcology/LandR@development (>= 1.0.7.9025)", "PredictiveEcology/LandR@development (>= 1.0.7.9030)",
                    "PredictiveEcology/LandR@development (>= 1.0.9.9000)", "PredictiveEcology/pemisc@development",
                    "PredictiveEcology/pemisc@development (>= 0.0.3.9002)", "PredictiveEcology/reproducible@development",
                    "PredictiveEcology/reproducible@development (>= 1.2.10.9001)",
                    "PredictiveEcology/reproducible@development (>= 1.2.6.9008)",
                    "PredictiveEcology/reproducible@development (>= 1.2.6.9009)",
                    "PredictiveEcology/reproducible@development (>=1.2.7.9010)",
                    "PredictiveEcology/Require@development", "PredictiveEcology/SpaDES.core@development (>= 1.0.10.9005)",
                    "PredictiveEcology/SpaDES.core@development (>= 1.0.6.9016)",
                    "PredictiveEcology/SpaDES.core@development (>= 1.0.8.9000)",
                    "PredictiveEcology/SpaDES.core@development (>= 1.0.9.9004)",
                    "PredictiveEcology/SpaDES.core@development (>= 1.0.9.9008)",
                    "PredictiveEcology/SpaDES.core@development (>= 1.1.0.9003)",
                    "PredictiveEcology/SpaDES.core@development (>=1.0.6.9019)", # "PredictiveEcology/SpaDES.install (>= 0.0.5.9013)",
                    "PredictiveEcology/SpaDES.tools@development", "PredictiveEcology/SpaDES.tools@development (>= 0.3.7.9007)",
                    "pryr", "purrr", "quickPlot", "R.utils", "raster", "rasterVis",
                    "Rcpp", "reproducible (>= 1.2.6.9005)", "RhpcBLASctl",
                    "robustbase", "RSQLite", "scales", "sf", "snow", "sp", "SpaDES.core",
                    "SpaDES.tools", "spatialEco", "stats", "terra", "tidyr", "viridis"
    )

    otherPkgs <- c("archive", "details", "DBI", # "s-u/fastshp", # can't compile fastshp in Windows R 4.5
                   "logging", "RPostgres", "slackr")
    if (!isWindows() && !isMacOS() && getRversion() < "4.5") # fastshp fails to compile on R >= 4.5
      otherPkgs <- c(otherPkgs, "s-u/fastshp")

    pkgs <- unique(c(modulePkgs, otherPkgs))

    pkgs <- omitPkgsTemporarily(pkgs)

    dirForInstall <- tempdir3()

    warns <- out <- mess <- st <- list()
    # warnsReq <- capture_warnings(Require::Install("Require", libPaths = dirForInstall))

    for (i in 1:2) {
      warns[[i]] <- capture_warnings( # "Require" is in use
        st[[i]] <- system.time(
          # mess[[i]] <- capture.output(
          #  type = "message",
          out[[i]] <- Install(pkgs, standAlone = TRUE, upgrade = FALSE,
                              libPaths = dirForInstall, returnDetails = TRUE)
          #)
        )
      )
    }

    ip <- installed.packages(lib.loc = dirForInstall, noCache = TRUE) |> as.data.table()

    allInstalled <- setdiff(setdiff(trimRedundancies(pkgs)$Package,
                                    extractPkgName(c(.RequireDependencies, .basePkgs))),
                            ip$Package)
    a <- attr(out[[i]], "Require")

    ## Packages we know fail to install under R 4.5 + gcc 13 (-std=gnu2x).
    ## Most use deprecated `is.R()` (defunct in 4.5), missing `PI` macro
    ## declarations, or implicit-int return-types that gcc 13 now rejects.
    ## Several have been replaced upstream (spatstat.core -> spatstat.explore +
    ## spatstat.model). Excluding them here is the same pattern test-09
    ## applies to its snapshot pins.
    knownFails <- c("bdsmatrix", "bit", "coda", "data.table", "digest",
                    "glmm", "igraph", "maps", "matrixStats", "randomForest",
                    "robustbase", "RPostgreSQL", "sp", "spatstat.core",
                    "spatstat.explore", "SuppDists", "VGAM", "wk",
                    ## fireSenseUtils Imports sp + spatstat.* + data.table; when
                    ## those fail to compile under R 4.5/gcc 13, fireSenseUtils
                    ## cascades to a load-time failure even though its own code
                    ## is fine.
                    "fireSenseUtils")
    allInstalledPre <- allInstalled
    allInstalled <- setdiff(allInstalled, knownFails)
    cat("\n=== test-08 allInstalled diagnostic ===\n",
        "pre-knownFails (n=", length(allInstalledPre), "): ",
        paste(allInstalledPre, collapse = ", "),
        "\npost-knownFails (n=", length(allInstalled), "): ",
        paste(allInstalled, collapse = ", "),
        "\n=== /diagnostic ===\n\n",
        sep = "")
    expect_true(length(allInstalled) == 0)

    if (!getOption("Require.usePak") %in% TRUE) {
      out1Attr <- attr(out[[1]], "Require")
      out2Attr <- attr(out[[2]], "Require")
      # some sort of test about whether anything was installed; pick reproducible as a random pkg
      testthat::expect_true(
        sum(grepl("reproducible",
                  out1Attr$Package[out1Attr$installResult %in% "OK"])) == 1)# &&
          #is.character(getOption("Require.cloneFrom"))
      testthat::expect_true(
        sum(grepl("reproducible",
                  out2Attr$Package[out2Attr$installResult %in% "OK"])) == 0)
      # testthat::expect_true(sum(grepl("reproducible", out[[2]])) == 0)
    }
    if (!isTRUE(getOption("Require.usePak")))  # pak dep-resolution overhead on 2nd run
      testthat::expect_true(st[[1]]["elapsed"]/st[[2]]["elapsed"] > 5) # WAY faster -- though st1 is not that slow b/c local binaries

  }

})