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") if (isDevAndInteractive) { 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' if (isWindows()) { (Install("Require", repos = "https://predictiveecology.r-univierse.dev", 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(unloadNamespace("SpaDES.project")) test <- testWarnsInUsePleaseChange(warns) expect_true(test) # 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 <- 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 <- ip[LibPath == persLibPathOld] # 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)) 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 anyBad <- any(pkgDT[!Package %in% "Require", good %in% FALSE]) 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)", "rgeos", "RhpcBLASctl", "robustbase", "RSQLite", "scales", "sf", "snow", "sp", "SpaDES.core", "SpaDES.tools", "spatialEco", "stats", "terra", "tidyr", "viridis" ) otherPkgs <- c("archive", "details", "DBI", "s-u/fastshp", "logging", "RPostgres", "slackr") 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$Package) a <- attr(out[[i]], "Require") expect_true(length(allInstalled) == 0) if (!getOption("Require.usePak") %in% TRUE) { out1Attr <- attr(out[[1]], "Require") out2Attr <- attr(out[[2]], "Require") # some sort of test about whether anything was installed; pick reproducible as a random pkg testthat::expect_true( sum(grepl("reproducible", out1Attr$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) } testthat::expect_true(st[[1]]["elapsed"]/st[[2]]["elapsed"] > 15) # WAY faster -- though st1 is not that slow b/c local binaries } })