test_that("test 3", { setupInitial <- setupTest() # on.exit(endTest(setupInitial)) isDev <- getOption("Require.isDev") # Test misspelled warns <- capture_warnings( err <- try(silent = TRUE, out <- capture.output(type = "message", lala <- Require("data.tt") ) ) ) test <- testWarnsInUsePleaseChange(warns) if (!getOption("Require.usePak", TRUE)) testthat::expect_true(any(grepl("could not be installed", warns))) # {out, "simpleWarning")}) # for coverages that were missing pkgDTEmpty <- Require:::toPkgDT(character()) out <- Require:::installedVers(pkgDTEmpty) # pkgDep("data.table", purge = FALSE) if (!isDev) { pkgDep("data.table", purge = TRUE) } if (isTRUE(tryCatch(packageVersion("fpCompare"), error = function(e) "0.0.0") < "0.2.5")) { # aaaa <<- 1 # on.exit(rm(aaaa, envir= .GlobalEnv)) Require::Install(c("fpCompare (>= 0.2.4)", "PredictiveEcology/fpCompare@development (>= 0.2.4.9000)"), install= "force") expect_true(packVer("fpCompare", lib.loc = .libPaths()[1]) > "0.2.4") } # pkgDep2("Require") if (!getOption("Require.usePak", TRUE)) { pkgDepTopoSort(c("data.table"), useAllInSearch = TRUE) pkgDepTopoSort(c("data.table"), useAllInSearch = TRUE, deps = "Require") pkgDepTopoSort(c("Require", "data.table")) pkgDepTopoSort(c("Require", "data.table"), useAllInSearch = TRUE, deps = "Require", returnFull = FALSE, reverse = TRUE ) } if (Sys.info()["user"] == "emcintir") { options( "Require.cachePkgDir" = TRUE, "Require.unloadNamespaces" = FALSE ) } Require("data.table", install = "force", require = FALSE, libPaths = tempdir2("other"), quiet = !(getOption("Require.verbose") >= 1) ) suppressWarnings(Require("Require", install = "force", require = FALSE, libPaths = tempdir2("other") )) pkg <- c("data.table", "data.table") pkgDT <- Require:::toPkgDT(pkg) data.table::set(pkgDT, NULL, "installFrom", "CRAN") data.table::set(pkgDT, NULL, "installed", FALSE) data.table::set(pkgDT, NULL, "installResult", TRUE) data.table::set(pkgDT, NULL, "versionSpec", NA) if (!getOption("Require.usePak", TRUE)) { out <- detachAll("data.table", dontTry = dontDetach()) testthat::expect_true({ isTRUE(out["data.table"] == 1) }) } warn <- tryCatch(Require:::warningCantInstall("devtools"), warning = function(w) w$message) testthat::expect_true({ grepl("you will likely", warn) }) origLP <- setLibPaths(tempdir2("other"), updateRprofile = FALSE) warn <- tryCatch(Require("data.table", require = FALSE), warning = function(w) w$message) silent <- setLibPaths(origLP, updateRprofile = FALSE) # Test the setLibPaths with changed .Rprofile origDir <- setwd(tempdir2("other")) setLibPaths("newProjectLib", updateRprofile = TRUE) # set a new R package library locally setLibPaths() # reset it to original setwd(origDir) ## setup # setupTestDir <- normPath(tempdir2("setupTests")) # ccc <- checkPath(file.path(setupTestDir, ".cache"), create = TRUE) # out2222 <- capture.output(setup(setupTestDir, RPackageCache = ccc)) # testthat::expect_true(identical(getOption("Require.cachePkgDir"), ccc)) ## TODO: warnings in readLines() cannot open DESCRIPTION file # out2222 <- capture.output(setupOff()) # Require:::messageVerbose("This is getOption('Require.cachePkgDir'): ", Require:::cacheGetOptionCachePkgDir(), # verboseLevel = 0) # RPackageCacheSysEnv <- Sys.getenv("R_REQUIRE_PKG_CACHE") # if (identical(RPackageCacheSysEnv, "FALSE") ) { # testthat::expect_true(identical(NULL, cacheGetOptionCachePkgDir())) # } else { # if (!(is.null(Require:::cacheGetOptionCachePkgDir()) || Require:::cacheGetOptionCachePkgDir() == "FALSE")) # testthat::expect_true(identical(normPath(Require:::cacheGetOptionCachePkgDir()), normPath(Require::cachePkgDir()))) # } # reset options after setupOff() # secondTry <- normPath(file.path(setupTestDir, ".cacheSecond")) # opt22 <- options("Require.cachePkgDir" = secondTry) # ccc <- checkPath(secondTry, create = TRUE) # out2222 <- capture.output(setup(setupTestDir, RPackageCache = ccc)) ## TODO: warnings in file() cannot open DESCRIPTION files # testthat::expect_true(identical(Require:::cacheGetOptionCachePkgDir(), ccc)) # out2222 <- capture.output(setupOff()) # testthat::expect_true(identical(Require:::cacheGetOptionCachePkgDir(), secondTry)) # BECAUSE THIS IS A MANUAL OVERRIDE of options; doesn't return Sys.getenv ooo <- options(Require.cachePkgDir = TRUE) testthat::expect_true(identical(cacheGetOptionCachePkgDir(), cachePkgDir())) ooo <- options(Require.cachePkgDir = FALSE) testthat::expect_true(identical(cacheGetOptionCachePkgDir(), NULL)) ooo <- options(Require.cachePkgDir = tempdir()) testthat::expect_true(identical(cacheGetOptionCachePkgDir(), tempdir())) ooo <- options(Require.cachePkgDir = "default") RPackageCacheSysEnv <- Sys.getenv("R_REQUIRE_PKG_CACHE") if (identical(RPackageCacheSysEnv, "FALSE")) { testthat::expect_true(identical(NULL, cacheGetOptionCachePkgDir())) } else { if (!(is.null(Require:::cacheGetOptionCachePkgDir()) || Require:::cacheGetOptionCachePkgDir() == "FALSE")) { testthat::expect_true(identical(normPath(Require:::cacheGetOptionCachePkgDir()), normPath(Require::cachePkgDir()))) } } ro <- RequireOptions() gro <- getRequireOptions() testthat::expect_true(is.list(ro)) testthat::expect_true(all(startsWith(names(ro), "Require"))) testthat::expect_true(is.list(gro)) testthat::expect_true(all(startsWith(names(gro), "Require"))) # Ensure the "which" for pkgDep are working correctly wh <- expand.grid(suggests = c(TRUE, FALSE), depends = c(TRUE, FALSE), imports = c(TRUE, FALSE), linkingTo = c(TRUE, FALSE)) utilsOut <- list() for (i in c("Suggests", "Imports", "Depends", "LinkingTo")) { lala <- strsplit(gsub("\n", "", utils::packageDescription("Require", fields = i)), ",")[[1]] utilsOut[[i]] <- gsub(x = lala, " ", "") # remove spaces } if (getRversion() >= "4.3.0") { # R 4.2.X and lower don't exist on PEuniverse so this test fails opts <- options(repos = PEUniverseRepo()); on.exit(options(opts), add = TRUE) out2 <- by(wh, seq(NROW(wh)), function(wh1Row) { out <- do.call(pkgDep, append(list("Require"), as.list(wh1Row[1, , drop = TRUE])))[[1]] o2 <- tools::toTitleCase(names(wh1Row)[unlist(wh1Row)]) if (length(o2)) { pkgs <- gsub(x = unname(unlist(utilsOut[o2])), " ", "") # remove spaces out <- gsub(x = out, " ", "") # remove spaces # out <- setdiff(out, grep("R\\(.+", pkgs, value = TRUE, invert = TRUE)) } setdiff(out, "remotes") # remotes was removed in version 0.2.6.9020 }) localDeps <- DESCRIPTIONFileDeps(system.file("DESCRIPTION", package = "Require"), which = c("Suggests", "Imports", "Depends")) locals <- setdiff(extractPkgName(localDeps), .basePkgs) testArgs <- setdiff(locals, unique(extractPkgName(unname(unlist(as.list(out2)))))) # not sure why roxygen2 was not in it before; fpCompare is new, not yet on PEUniverse testArgs <- setdiff(testArgs, c("roxygen2", "rmarkdown", "fpCompare")) testthat::expect_identical(testArgs, character()) } if (isDev) { # this was a bug created a warning when there was a package not on CRAN, but there # were multiple repos; ffbase is no longer on CRAN # can't quiet this down on linux because ffbase is not binary but rest are ... # install.packages won't do both types quiet = TRUE for some reason warns1 <- capture_warnings( Install("ff", # verbose = 0, repos = c(RSPM = urlForPositPACKAGES, CRAN = "https://cloud.r-project.org" )) ) expect_identical(character(0), warns1) } if (isWindows()) { # test the new approach that installs outside R session -- is fine on Linux-alikes withr::local_options(Require.installPackagesSys = FALSE) ver <- "0.2.4"; ineq <- "<" Install(paste0("fpCompare (", ineq, ver, ")"), install = "force") ip <- installed.packages(noCache = TRUE) |> as.data.table() expect_true(compareVersion2(ip[Package %in% "fpCompare"]$Version, ver, inequality = ineq)) #packageVersion("fpCompare") # doesn't update immediately ineq <- ">=" warns <- capture_warnings( Install(paste0("fpCompare (", ineq, ver, ")"), install = "force")) ip <- installed.packages(noCache = TRUE) |> as.data.table() expect_true(compareVersion2(ip[Package %in% "fpCompare"]$Version, ver, inequality = ineq)) # Require("fpCompare (>=0.2.4)", install = "force")) # packageVersion("fpCompare") if (!getOption("Require.usePak", TRUE)) { withr::local_options(Require.installPackagesSys = TRUE) mess <- capture_messages(Require("fpCompare (>=0.2.4)", install = "force", require = FALSE)) warnsAfter <- capture_warnings(packageVersion("fpCompare")) # expect_true(grepl(.txtMsgIsInUse, warns)) expect_false(isTRUE(grepl(.txtMsgIsInUse, warnsAfter))) } warns <- capture_warnings( # fpCompare namespace cannot be unloaded: cannot open file? # and also restarting interuupted promise evaluation try(detach("package:fpCompare", unload = TRUE), silent = TRUE) # some are not attaching ) } if (FALSE) { pkgs <- c("fpCompare", "rlang", "cli", "crayon", "stringr", "lobstr") a <- unique(extractPkgName(unlist(unname(pkgDep(pkgs))))) cacheClearPackages(a, ask = F) library(sys); library(waldo) setLibPaths(tempdir3()) try(remove.packages(a)) options(Require.installPackagesSys = 1L) ipBefore <- installed.packages(lib.loc = .libPaths()[1], noCache = TRUE) system.time(Install(pkgs, verbose = 1)) # system.time(install.packages(pkgs)) ipAfter <- installed.packages(lib.loc = .libPaths()[1], noCache = TRUE) } if (FALSE) { # benchmark pak and Require library(Require) options(Require.installPackagesSys = 2, Require.cloneFrom = Sys.getenv("R_LIBS_USER")) setLinuxBinaryRepo() pkgsKeep <- c('rlang', "R6", "cli", "withr", "magrittr", "data.table") Install(pkgsKeep) pkgs <- c("PredictiveEcology/fpCompare", "PredictiveEcology/reproducible@modsForLargeArchives", "rlang", "purrr", "ggplot2") a <- pkgDep(pkgs) N = 4 # st <- list() st[["Require"]] <- system.time(replicate(N, { try(remove.packages(setdiff(extractPkgName(unname(unlist(a))), pkgsKeep))) cacheClearPackages(ask = F) Install(pkgs) })) st[["pak"]] <- system.time(replicate(N, { try(remove.packages(setdiff(extractPkgName(unname(unlist(a))), pkgsKeep))) pak::cache_clean() pak::pkg_install(pkgs, ask = FALSE) })) Map(x = st, function(x) x[[3]]/N) # min lq mean median uq max neval #13.759182 13.873962 13.999130 13.98874 14.11910 14.24947 3 # 7.367775 8.914831 9.495963 10.46189 10.56006 10.65823 3 } if (getRversion() >= "4.3.0") { # R 4.2.x and below can't seem to build many of the PE ecosystem from src # Mistakenly have a partial repos, i.e., without getOption("repos") -- This failed previously Jul 2, 2024 dir44 <- tempdir2(.rndstr(1)) silence <- dir.create(dir44, recursive = TRUE, showWarnings = FALSE) on.exit(unlink(dir44, recursive = TRUE), add = TRUE) warns <- capture_warnings( Require::Install("LandR", repos = "predictiveecology.r-universe.dev", libPaths = dir44, standAlone = TRUE) ) test <- testWarnsInUsePleaseChange(warns) expect_true(test) } ooo <- options(Require.cachePkgDir = NULL) testthat::expect_true(identical(cacheGetOptionCachePkgDir(), NULL)) options(ooo) })