First R Lab
Matthew Howell
2024-08-31
Reflection Questions
How was the install process? Anything I should know for future students?
The install process was a little stressful. We had clear step-by-step directions for every single step and it felt like I was just trying to keep my head above water. I wish I could say that there was something that could have been done better but my instructor was an extremely clear communicator and provided us with all the resources that we needed. Something to note is that this might be a lot of people’s first time working with a type of coding software.
Have you used any statistical software before?
Yes, I used JASP for my psych stats class last semester.
Installing New Packages
install.packages#("psych")## function (pkgs, lib, repos = getOption("repos"), contriburl = contrib.url(repos,
## type), method, available = NULL, destdir = NULL, dependencies = NA,
## type = getOption("pkgType"), configure.args = getOption("configure.args"),
## configure.vars = getOption("configure.vars"), clean = FALSE,
## Ncpus = getOption("Ncpus", 1L), verbose = getOption("verbose"),
## libs_only = FALSE, INSTALL_opts, quiet = FALSE, keep_outputs = FALSE,
## ...)
## {
## if (!(is.character(type) && length(type) == 1L))
## stop(gettextf("'%s' must be a character string", "type"),
## domain = NA)
## type2 <- .Platform$pkgType
## if (type == "binary") {
## if (type2 == "source")
## stop("type 'binary' is not supported on this platform")
## else type <- type2
## if (type == "both" && (!missing(contriburl) || !is.null(available)))
## stop("specifying 'contriburl' or 'available' requires a single type, not type = \"both\"")
## }
## if (is.logical(clean) && clean)
## clean <- "--clean"
## if (is.logical(dependencies) && is.na(dependencies))
## dependencies <- if (!missing(lib) && length(lib) > 1L)
## FALSE
## else c("Depends", "Imports", "LinkingTo")
## get_package_name <- function(pkg) {
## gsub("_[.](zip|tar[.]gz|tar[.]bzip2|tar[.]xz)", "", gsub(.standard_regexps()$valid_package_version,
## "", basename(pkg)))
## }
## getConfigureArgs <- function(pkg) {
## if (.Platform$OS.type == "windows")
## return(character())
## if (length(pkgs) == 1L && length(configure.args) && length(names(configure.args)) ==
## 0L)
## return(paste0("--configure-args=", shQuote(paste(configure.args,
## collapse = " "))))
## pkg <- get_package_name(pkg)
## if (length(configure.args) && length(names(configure.args)) &&
## pkg %in% names(configure.args))
## config <- paste0("--configure-args=", shQuote(paste(configure.args[[pkg]],
## collapse = " ")))
## else config <- character()
## config
## }
## getConfigureVars <- function(pkg) {
## if (.Platform$OS.type == "windows")
## return(character())
## if (length(pkgs) == 1L && length(configure.vars) && length(names(configure.vars)) ==
## 0L)
## return(paste0("--configure-vars=", shQuote(paste(configure.vars,
## collapse = " "))))
## pkg <- get_package_name(pkg)
## if (length(configure.vars) && length(names(configure.vars)) &&
## pkg %in% names(configure.vars))
## config <- paste0("--configure-vars=", shQuote(paste(configure.vars[[pkg]],
## collapse = " ")))
## else config <- character()
## config
## }
## get_install_opts <- function(pkg) {
## if (!length(INSTALL_opts))
## character()
## else paste(INSTALL_opts[[get_package_name(pkg)]], collapse = " ")
## }
## if (missing(pkgs)) {
## if (!interactive())
## stop("no packages were specified")
## if (.Platform$OS.type == "windows" || .Platform$GUI ==
## "AQUA" || (capabilities("tcltk") && capabilities("X11") &&
## suppressWarnings(tcltk::.TkUp))) {
## }
## else stop("no packages were specified")
## if (is.null(available)) {
## av <- available.packages(contriburl = contriburl,
## method = method, ...)
## if (missing(repos))
## repos <- getOption("repos")
## if (type != "both")
## available <- av
## }
## else av <- available
## if (NROW(av)) {
## pkgs <- select.list(sort(unique(rownames(av))), multiple = TRUE,
## title = "Packages", graphics = TRUE)
## }
## }
## if (.Platform$OS.type == "windows" && length(pkgs)) {
## pkgnames <- get_package_name(pkgs)
## inuse <- search()
## inuse <- sub("^package:", "", inuse[grep("^package:",
## inuse)])
## inuse <- pkgnames %in% inuse
## if (any(inuse)) {
## warning(sprintf(ngettext(sum(inuse), "package %s is in use and will not be installed",
## "packages %s are in use and will not be installed"),
## paste(sQuote(pkgnames[inuse]), collapse = ", ")),
## call. = FALSE, domain = NA, immediate. = TRUE)
## pkgs <- pkgs[!inuse]
## }
## }
## if (!length(pkgs))
## return(invisible())
## if (missing(lib) || is.null(lib)) {
## lib <- .libPaths()[1L]
## if (!quiet && length(.libPaths()) > 1L)
## message(sprintf(ngettext(length(pkgs), "Installing package into %s\n(as %s is unspecified)",
## "Installing packages into %s\n(as %s is unspecified)"),
## sQuote(lib), sQuote("lib")), domain = NA)
## }
## ok <- dir.exists(lib) & (file.access(lib, 2) == 0L)
## if (length(lib) > 1 && any(!ok))
## stop(sprintf(ngettext(sum(!ok), "'lib' element %s is not a writable directory",
## "'lib' elements %s are not writable directories"),
## paste(sQuote(lib[!ok]), collapse = ", ")), domain = NA)
## if (length(lib) == 1L && .Platform$OS.type == "windows") {
## ok <- dir.exists(lib)
## if (ok) {
## fn <- file.path(lib, paste0("_test_dir_", Sys.getpid()))
## unlink(fn, recursive = TRUE)
## res <- try(dir.create(fn, showWarnings = FALSE))
## if (inherits(res, "try-error") || !res)
## ok <- FALSE
## else unlink(fn, recursive = TRUE)
## }
## }
## if (length(lib) == 1L && !ok) {
## warning(gettextf("'lib = \"%s\"' is not writable", lib),
## domain = NA, immediate. = TRUE)
## userdir <- unlist(strsplit(Sys.getenv("R_LIBS_USER"),
## .Platform$path.sep))[1L]
## if (interactive()) {
## ans <- askYesNo(gettext("Would you like to use a personal library instead?"),
## default = FALSE)
## if (!isTRUE(ans))
## stop("unable to install packages")
## lib <- userdir
## if (!file.exists(userdir)) {
## ans <- askYesNo(gettextf("Would you like to create a personal library\n%s\nto install packages into?",
## sQuote(userdir)), default = FALSE)
## if (!isTRUE(ans))
## stop("unable to install packages")
## if (!dir.create(userdir, recursive = TRUE))
## stop(gettextf("unable to create %s", sQuote(userdir)),
## domain = NA)
## .libPaths(c(userdir, .libPaths()))
## }
## }
## else stop("unable to install packages")
## }
## lib <- normalizePath(lib)
## if (length(pkgs) == 1L && missing(repos) && missing(contriburl)) {
## if ((type == "source" && any(grepl("[.]tar[.](gz|bz2|xz)$",
## pkgs))) || (type %in% "win.binary" && endsWith(pkgs,
## ".zip")) || (startsWith(type, "mac.binary") && endsWith(pkgs,
## ".tgz"))) {
## repos <- NULL
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## if (type == "both") {
## if (type2 %in% "win.binary" && endsWith(pkgs, ".zip")) {
## repos <- NULL
## type <- type2
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## else if (startsWith(type2, "mac.binary") && endsWith(pkgs,
## ".tgz")) {
## repos <- NULL
## type <- type2
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## else if (grepl("[.]tar[.](gz|bz2|xz)$", pkgs)) {
## repos <- NULL
## type <- "source"
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## }
## }
## if (length(pkgs) == 1L && is.null(repos) && type == "both") {
## if ((type2 %in% "win.binary" && endsWith(pkgs, ".zip")) ||
## (startsWith(type2, "mac.binary") && endsWith(pkgs,
## ".tgz"))) {
## type <- type2
## }
## else if (grepl("[.]tar[.](gz|bz2|xz)$", pkgs)) {
## type <- "source"
## }
## }
## if (is.null(repos) && missing(contriburl)) {
## tmpd <- destdir
## nonlocalrepos <- any(web <- grepl("^(http|https|ftp)://",
## pkgs))
## if (is.null(destdir) && nonlocalrepos) {
## tmpd <- file.path(tempdir(), "downloaded_packages")
## if (!file.exists(tmpd) && !dir.create(tmpd))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd)), domain = NA)
## }
## if (nonlocalrepos) {
## df <- function(p, destfile, method, ...) download.file(p,
## destfile, method, mode = "wb", ...)
## urls <- pkgs[web]
## for (p in unique(urls)) {
## this <- pkgs == p
## destfile <- file.path(tmpd, basename(p))
## res <- try(df(p, destfile, method, ...))
## if (!inherits(res, "try-error") && res == 0L)
## pkgs[this] <- destfile
## else {
## pkgs[this] <- NA
## }
## }
## }
## }
## if (type == "both") {
## if (type2 == "source")
## stop("type == \"both\" can only be used on Windows or a CRAN build for macOS")
## if (!missing(contriburl) || !is.null(available))
## type <- type2
## }
## getDeps <- TRUE
## if (type == "both") {
## if (is.null(repos))
## stop("type == \"both\" cannot be used with 'repos = NULL'")
## type <- "source"
## contriburl <- contrib.url(repos, "source")
## if (missing(repos))
## repos <- getOption("repos")
## available <- available.packages(contriburl = contriburl,
## method = method, fields = "NeedsCompilation", ...)
## pkgs <- getDependencies(pkgs, dependencies, available,
## lib, ...)
## getDeps <- FALSE
## av2 <- available.packages(contriburl = contrib.url(repos,
## type2), method = method, ...)
## bins <- row.names(av2)
## bins <- pkgs[pkgs %in% bins]
## srcOnly <- pkgs[!pkgs %in% bins]
## binvers <- av2[bins, "Version"]
## hasArchs <- !is.na(av2[bins, "Archs"])
## needsCmp <- !(available[bins, "NeedsCompilation"] %in%
## "no")
## hasSrc <- hasArchs | needsCmp
## srcvers <- available[bins, "Version"]
## later <- as.numeric_version(binvers) < srcvers
## action <- getOption("install.packages.compile.from.source",
## "interactive")
## if (!nzchar(Sys.which(Sys.getenv("MAKE", "make"))))
## action <- "never"
## if (grepl("darwin", R.version$platform) && !length(srcOnly))
## later[later] <- FALSE
## if (any(later)) {
## msg <- ngettext(sum(later), "There is a binary version available but the source version is later",
## "There are binary versions available but the source versions are later")
## cat("\n", paste(strwrap(msg, indent = 2, exdent = 2),
## collapse = "\n"), ":\n", sep = "")
## out <- data.frame(binary = binvers, source = srcvers,
## needs_compilation = hasSrc, row.names = bins,
## check.names = FALSE)[later, ]
## print(out)
## cat("\n")
## if (any(later & hasSrc)) {
## if (action == "interactive" && interactive()) {
## msg <- ngettext(sum(later & hasSrc), "Do you want to install from sources the package which needs compilation?",
## "Do you want to install from sources the packages which need compilation?")
## res <- askYesNo(msg)
## if (is.na(res))
## stop("Cancelled by user")
## if (!isTRUE(res))
## later <- later & !hasSrc
## }
## else if (action == "never") {
## cat(" Binaries will be installed\n")
## later <- later & !hasSrc
## }
## }
## }
## bins <- bins[!later]
## if (length(srcOnly)) {
## s2 <- srcOnly[!(available[srcOnly, "NeedsCompilation"] %in%
## "no")]
## if (length(s2)) {
## msg <- ngettext(length(s2), "Package which is only available in source form, and may need compilation of C/C++/Fortran",
## "Packages which are only available in source form, and may need compilation of C/C++/Fortran")
## msg <- c(paste0(msg, ": "), sQuote(s2))
## msg <- strwrap(paste(msg, collapse = " "), exdent = 2)
## message(paste(msg, collapse = "\n"), domain = NA)
## if (action == "interactive" && interactive()) {
## res <- askYesNo("Do you want to attempt to install these from sources?")
## if (is.na(res))
## stop("Cancelled by user")
## if (!isTRUE(res))
## pkgs <- setdiff(pkgs, s2)
## }
## else if (action == "never") {
## cat(" These will not be installed\n")
## pkgs <- setdiff(pkgs, s2)
## }
## }
## }
## if (length(bins)) {
## if (type2 == "win.binary")
## .install.winbinary(pkgs = bins, lib = lib, contriburl = contrib.url(repos,
## type2), method = method, available = av2, destdir = destdir,
## dependencies = NULL, libs_only = libs_only,
## quiet = quiet, ...)
## else .install.macbinary(pkgs = bins, lib = lib, contriburl = contrib.url(repos,
## type2), method = method, available = av2, destdir = destdir,
## dependencies = NULL, quiet = quiet, ...)
## }
## pkgs <- setdiff(pkgs, bins)
## if (!length(pkgs))
## return(invisible())
## message(sprintf(ngettext(length(pkgs), "installing the source package %s",
## "installing the source packages %s"), paste(sQuote(pkgs),
## collapse = ", ")), "\n", domain = NA)
## flush.console()
## }
## else if (getOption("install.packages.check.source", "yes") %in%
## "yes" && (type %in% "win.binary" || startsWith(type,
## "mac.binary"))) {
## if (missing(contriburl) && is.null(available) && !is.null(repos)) {
## contriburl2 <- contrib.url(repos, "source")
## if (missing(repos))
## repos <- getOption("repos")
## av1 <- tryCatch(suppressWarnings(available.packages(contriburl = contriburl2,
## method = method, ...)), error = function(e) e)
## if (inherits(av1, "error")) {
## message("source repository is unavailable to check versions")
## available <- available.packages(contriburl = contrib.url(repos,
## type), method = method, ...)
## }
## else {
## srcpkgs <- pkgs[pkgs %in% row.names(av1)]
## available <- available.packages(contriburl = contrib.url(repos,
## type), method = method, ...)
## bins <- pkgs[pkgs %in% row.names(available)]
## na <- srcpkgs[!srcpkgs %in% bins]
## if (length(na)) {
## msg <- sprintf(ngettext(length(na), "package %s is available as a source package but not as a binary",
## "packages %s are available as source packages but not as binaries"),
## paste(sQuote(na), collapse = ", "))
## cat("\n ", msg, "\n\n", sep = "")
## }
## binvers <- available[bins, "Version"]
## srcvers <- binvers
## OK <- bins %in% srcpkgs
## srcvers[OK] <- av1[bins[OK], "Version"]
## later <- as.numeric_version(binvers) < srcvers
## if (any(later)) {
## msg <- ngettext(sum(later), "There is a binary version available (and will be installed) but the source version is later",
## "There are binary versions available (and will be installed) but the source versions are later")
## cat("\n", paste(strwrap(msg, indent = 2, exdent = 2),
## collapse = "\n"), ":\n", sep = "")
## print(data.frame(binary = binvers, source = srcvers,
## row.names = bins, check.names = FALSE)[later,
## ])
## cat("\n")
## }
## }
## }
## }
## if (.Platform$OS.type == "windows") {
## if (startsWith(type, "mac.binary"))
## stop("cannot install macOS binary packages on Windows")
## if (type %in% "win.binary") {
## .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
## method = method, available = available, destdir = destdir,
## dependencies = dependencies, libs_only = libs_only,
## quiet = quiet, ...)
## return(invisible())
## }
## have_spaces <- grep(" ", pkgs)
## if (length(have_spaces)) {
## p <- pkgs[have_spaces]
## dirs <- shortPathName(dirname(p))
## pkgs[have_spaces] <- file.path(dirs, basename(p))
## }
## pkgs <- gsub("\\", "/", pkgs, fixed = TRUE)
## }
## else {
## if (startsWith(type, "mac.binary")) {
## if (!grepl("darwin", R.version$platform))
## stop("cannot install macOS binary packages on this platform")
## .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
## method = method, available = available, destdir = destdir,
## dependencies = dependencies, quiet = quiet, ...)
## return(invisible())
## }
## if (type %in% "win.binary")
## stop("cannot install Windows binary packages on this platform")
## if (!file.exists(file.path(R.home("bin"), "INSTALL")))
## stop("This version of R is not set up to install source packages\nIf it was installed from an RPM, you may need the R-devel RPM")
## }
## cmd0 <- file.path(R.home("bin"), "R")
## args0 <- c("CMD", "INSTALL")
## output <- if (quiet)
## FALSE
## else ""
## env <- character()
## tlim <- Sys.getenv("_R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_")
## tlim <- if (!nzchar(tlim))
## 0
## else tools:::get_timeout(tlim)
## outdir <- getwd()
## if (is.logical(keep_outputs)) {
## if (is.na(keep_outputs))
## keep_outputs <- FALSE
## }
## else if (is.character(keep_outputs) && (length(keep_outputs) ==
## 1L)) {
## if (!dir.exists(keep_outputs) && !dir.create(keep_outputs,
## recursive = TRUE))
## stop(gettextf("unable to create %s", sQuote(keep_outputs)),
## domain = NA)
## outdir <- normalizePath(keep_outputs)
## keep_outputs <- TRUE
## }
## else stop(gettextf("invalid %s argument", sQuote("keep_outputs")),
## domain = NA)
## if (length(libpath <- .R_LIBS())) {
## if (.Platform$OS.type == "windows") {
## oldrlibs <- Sys.getenv("R_LIBS")
## Sys.setenv(R_LIBS = libpath)
## on.exit(Sys.setenv(R_LIBS = oldrlibs))
## }
## else env <- paste0("R_LIBS=", shQuote(libpath))
## }
## if (is.character(clean))
## args0 <- c(args0, clean)
## if (libs_only)
## args0 <- c(args0, "--libs-only")
## if (!missing(INSTALL_opts)) {
## if (!is.list(INSTALL_opts)) {
## args0 <- c(args0, paste(INSTALL_opts, collapse = " "))
## INSTALL_opts <- list()
## }
## }
## else {
## INSTALL_opts <- list()
## }
## if (verbose)
## message(gettextf("system (cmd0): %s", paste(c(cmd0, args0),
## collapse = " ")), domain = NA)
## if (is.null(repos) && missing(contriburl)) {
## update <- cbind(path.expand(pkgs), lib)
## for (i in seq_len(nrow(update))) {
## if (is.na(update[i, 1L]))
## next
## args <- c(args0, get_install_opts(update[i, 1L]),
## "-l", shQuote(update[i, 2L]), getConfigureArgs(update[i,
## 1L]), getConfigureVars(update[i, 1L]), shQuote(update[i,
## 1L]))
## status <- system2(cmd0, args, env = env, stdout = output,
## stderr = output, timeout = tlim)
## if (status > 0L)
## warning(gettextf("installation of package %s had non-zero exit status",
## sQuote(update[i, 1L])), domain = NA)
## else if (verbose) {
## cmd <- paste(c(cmd0, args), collapse = " ")
## message(sprintf("%d): succeeded '%s'", i, cmd),
## domain = NA)
## }
## }
## return(invisible())
## }
## tmpd <- destdir
## nonlocalrepos <- !all(startsWith(contriburl, "file:"))
## if (is.null(destdir) && nonlocalrepos) {
## tmpd <- file.path(tempdir(), "downloaded_packages")
## if (!file.exists(tmpd) && !dir.create(tmpd))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd)), domain = NA)
## }
## av2 <- NULL
## if (is.null(available)) {
## filters <- getOption("available_packages_filters")
## if (!is.null(filters)) {
## available <- available.packages(contriburl = contriburl,
## method = method, ...)
## }
## else {
## f <- setdiff(available_packages_filters_default,
## c("R_version", "duplicates"))
## av2 <- available.packages(contriburl = contriburl,
## filters = f, method = method, ...)
## f <- available_packages_filters_db[["R_version"]]
## f2 <- available_packages_filters_db[["duplicates"]]
## available <- f2(f(av2))
## }
## }
## if (getDeps)
## pkgs <- getDependencies(pkgs, dependencies, available,
## lib, ..., av2 = av2)
## foundpkgs <- download.packages(pkgs, destdir = tmpd, available = available,
## contriburl = contriburl, method = method, type = "source",
## quiet = quiet, ...)
## if (length(foundpkgs)) {
## if (verbose)
## message(gettextf("foundpkgs: %s", paste(foundpkgs,
## collapse = ", ")), domain = NA)
## update <- unique(cbind(pkgs, lib))
## colnames(update) <- c("Package", "LibPath")
## found <- pkgs %in% foundpkgs[, 1L]
## files <- foundpkgs[match(pkgs[found], foundpkgs[, 1L]),
## 2L]
## if (verbose)
## message(gettextf("files: %s", paste(files, collapse = ", \n\t")),
## domain = NA)
## update <- cbind(update[found, , drop = FALSE], file = files)
## if (nrow(update) > 1L) {
## upkgs <- unique(pkgs <- update[, 1L])
## DL <- .make_dependency_list(upkgs, available)
## p0 <- .find_install_order(upkgs, DL)
## update <- update[sort.list(match(pkgs, p0)), ]
## }
## if (Ncpus > 1L && nrow(update) > 1L) {
## tlim_cmd <- character()
## if (tlim > 0) {
## if (.Platform$OS.type == "windows" && !nzchar(Sys.getenv("R_TIMEOUT")) &&
## grepl("\\windows\\system32\\", tolower(Sys.which("timeout")),
## fixed = TRUE)) {
## warning("Windows default 'timeout' command is not usable for parallel installs")
## }
## else if (nzchar(timeout <- Sys.which(Sys.getenv("R_TIMEOUT",
## "timeout")))) {
## tlim_cmd <- c(shQuote(timeout), "-s INT", tlim)
## }
## else warning("timeouts for parallel installs require the 'timeout' command")
## }
## args0 <- c(args0, "--pkglock")
## tmpd2 <- file.path(tempdir(), "make_packages")
## if (!file.exists(tmpd2) && !dir.create(tmpd2))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd2)), domain = NA)
## mfile <- file.path(tmpd2, "Makefile")
## conn <- file(mfile, "wt")
## deps <- paste(paste0(update[, 1L], ".ts"), collapse = " ")
## deps <- strwrap(deps, width = 75, exdent = 2)
## deps <- paste(deps, collapse = " \\\n")
## cat("all: ", deps, "\n", sep = "", file = conn)
## aDL <- .make_dependency_list(upkgs, available, recursive = TRUE)
## for (i in seq_len(nrow(update))) {
## pkg <- update[i, 1L]
## fil <- update[i, 3L]
## args <- c(args0, get_install_opts(fil), "-l",
## shQuote(update[i, 2L]), getConfigureArgs(fil),
## getConfigureVars(fil), shQuote(fil), ">", paste0(pkg,
## ".out"), "2>&1")
## cmd <- paste(c("MAKEFLAGS=", tlim_cmd, shQuote(cmd0),
## args), collapse = " ")
## deps <- aDL[[pkg]]
## deps <- deps[deps %in% upkgs]
## deps <- if (length(deps))
## paste(paste0(deps, ".ts"), collapse = " ")
## else ""
## cat(paste0(pkg, ".ts: ", deps), paste("\t@echo begin installing package",
## sQuote(pkg)), paste0("\t@", cmd, " && touch ",
## pkg, ".ts"), paste0("\t@cat ", pkg, ".out"),
## "", sep = "\n", file = conn)
## }
## close(conn)
## cwd <- setwd(tmpd2)
## on.exit(setwd(cwd))
## status <- system2(Sys.getenv("MAKE", "make"), c("-k -j",
## Ncpus), stdout = output, stderr = output, env = env)
## if (status > 0L) {
## pkgs <- update[, 1L]
## tss <- sub("[.]ts$", "", dir(".", pattern = "[.]ts$"))
## failed <- pkgs[!pkgs %in% tss]
## for (pkg in failed) {
## if (file.exists(outfile <- paste0(pkg, ".out")))
## system2("cat", outfile)
## }
## n <- length(failed)
## if (n == 1L)
## warning(gettextf("installation of package %s failed",
## sQuote(failed)), domain = NA)
## else if (n > 1L) {
## msg <- paste(sQuote(failed), collapse = ", ")
## if (nchar(msg) < 40)
## warning(gettextf("installation of %d packages failed: %s",
## n, msg), domain = NA)
## else warning(gettextf("installation of %d packages failed:\n %s",
## n, msg), domain = NA)
## }
## }
## if (keep_outputs) {
## outfiles <- paste0(update[, 1L], ".out")
## file.copy(outfiles[file.exists(outfiles)], outdir,
## overwrite = TRUE)
## }
## file.copy(Sys.glob(paste0(update[, 1L], "*.zip")),
## cwd)
## file.copy(Sys.glob(paste0(update[, 1L], "*.tgz")),
## cwd)
## file.copy(Sys.glob(paste0(update[, 1L], "*.tar.gz")),
## cwd)
## setwd(cwd)
## on.exit()
## unlink(tmpd2, recursive = TRUE)
## }
## else {
## tmpd2 <- tempfile()
## if (!dir.create(tmpd2))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd2)), domain = NA)
## outfiles <- file.path(tmpd2, paste0(update[, 1L],
## ".out"))
## for (i in seq_len(nrow(update))) {
## outfile <- if (keep_outputs)
## outfiles[i]
## else output
## fil <- update[i, 3L]
## args <- c(args0, get_install_opts(fil), "-l",
## shQuote(update[i, 2L]), getConfigureArgs(fil),
## getConfigureVars(fil), shQuote(fil))
## status <- system2(cmd0, args, env = env, stdout = outfile,
## stderr = outfile, timeout = tlim)
## if (!quiet && keep_outputs)
## writeLines(readLines(outfile))
## if (status > 0L)
## warning(gettextf("installation of package %s had non-zero exit status",
## sQuote(update[i, 1L])), domain = NA)
## else if (verbose) {
## cmd <- paste(c(cmd0, args), collapse = " ")
## message(sprintf("%d): succeeded '%s'", i, cmd),
## domain = NA)
## }
## }
## if (keep_outputs)
## file.copy(outfiles, outdir, overwrite = TRUE)
## unlink(tmpd2, recursive = TRUE)
## }
## if (!quiet && nonlocalrepos && !is.null(tmpd) && is.null(destdir))
## cat("\n", gettextf("The downloaded source packages are in\n\t%s",
## sQuote(normalizePath(tmpd, mustWork = FALSE))),
## "\n", sep = "", file = stderr())
## libs_used <- unique(update[, 2L])
## if (.Platform$OS.type == "unix" && .Library %in% libs_used) {
## message("Updating HTML index of packages in '.Library'")
## make.packages.html(.Library)
## }
## }
## else if (!is.null(tmpd) && is.null(destdir))
## unlink(tmpd, TRUE)
## invisible()
## }
## <bytecode: 0x1143d7900>
## <environment: namespace:utils>install.packages#("psychTools")## function (pkgs, lib, repos = getOption("repos"), contriburl = contrib.url(repos,
## type), method, available = NULL, destdir = NULL, dependencies = NA,
## type = getOption("pkgType"), configure.args = getOption("configure.args"),
## configure.vars = getOption("configure.vars"), clean = FALSE,
## Ncpus = getOption("Ncpus", 1L), verbose = getOption("verbose"),
## libs_only = FALSE, INSTALL_opts, quiet = FALSE, keep_outputs = FALSE,
## ...)
## {
## if (!(is.character(type) && length(type) == 1L))
## stop(gettextf("'%s' must be a character string", "type"),
## domain = NA)
## type2 <- .Platform$pkgType
## if (type == "binary") {
## if (type2 == "source")
## stop("type 'binary' is not supported on this platform")
## else type <- type2
## if (type == "both" && (!missing(contriburl) || !is.null(available)))
## stop("specifying 'contriburl' or 'available' requires a single type, not type = \"both\"")
## }
## if (is.logical(clean) && clean)
## clean <- "--clean"
## if (is.logical(dependencies) && is.na(dependencies))
## dependencies <- if (!missing(lib) && length(lib) > 1L)
## FALSE
## else c("Depends", "Imports", "LinkingTo")
## get_package_name <- function(pkg) {
## gsub("_[.](zip|tar[.]gz|tar[.]bzip2|tar[.]xz)", "", gsub(.standard_regexps()$valid_package_version,
## "", basename(pkg)))
## }
## getConfigureArgs <- function(pkg) {
## if (.Platform$OS.type == "windows")
## return(character())
## if (length(pkgs) == 1L && length(configure.args) && length(names(configure.args)) ==
## 0L)
## return(paste0("--configure-args=", shQuote(paste(configure.args,
## collapse = " "))))
## pkg <- get_package_name(pkg)
## if (length(configure.args) && length(names(configure.args)) &&
## pkg %in% names(configure.args))
## config <- paste0("--configure-args=", shQuote(paste(configure.args[[pkg]],
## collapse = " ")))
## else config <- character()
## config
## }
## getConfigureVars <- function(pkg) {
## if (.Platform$OS.type == "windows")
## return(character())
## if (length(pkgs) == 1L && length(configure.vars) && length(names(configure.vars)) ==
## 0L)
## return(paste0("--configure-vars=", shQuote(paste(configure.vars,
## collapse = " "))))
## pkg <- get_package_name(pkg)
## if (length(configure.vars) && length(names(configure.vars)) &&
## pkg %in% names(configure.vars))
## config <- paste0("--configure-vars=", shQuote(paste(configure.vars[[pkg]],
## collapse = " ")))
## else config <- character()
## config
## }
## get_install_opts <- function(pkg) {
## if (!length(INSTALL_opts))
## character()
## else paste(INSTALL_opts[[get_package_name(pkg)]], collapse = " ")
## }
## if (missing(pkgs)) {
## if (!interactive())
## stop("no packages were specified")
## if (.Platform$OS.type == "windows" || .Platform$GUI ==
## "AQUA" || (capabilities("tcltk") && capabilities("X11") &&
## suppressWarnings(tcltk::.TkUp))) {
## }
## else stop("no packages were specified")
## if (is.null(available)) {
## av <- available.packages(contriburl = contriburl,
## method = method, ...)
## if (missing(repos))
## repos <- getOption("repos")
## if (type != "both")
## available <- av
## }
## else av <- available
## if (NROW(av)) {
## pkgs <- select.list(sort(unique(rownames(av))), multiple = TRUE,
## title = "Packages", graphics = TRUE)
## }
## }
## if (.Platform$OS.type == "windows" && length(pkgs)) {
## pkgnames <- get_package_name(pkgs)
## inuse <- search()
## inuse <- sub("^package:", "", inuse[grep("^package:",
## inuse)])
## inuse <- pkgnames %in% inuse
## if (any(inuse)) {
## warning(sprintf(ngettext(sum(inuse), "package %s is in use and will not be installed",
## "packages %s are in use and will not be installed"),
## paste(sQuote(pkgnames[inuse]), collapse = ", ")),
## call. = FALSE, domain = NA, immediate. = TRUE)
## pkgs <- pkgs[!inuse]
## }
## }
## if (!length(pkgs))
## return(invisible())
## if (missing(lib) || is.null(lib)) {
## lib <- .libPaths()[1L]
## if (!quiet && length(.libPaths()) > 1L)
## message(sprintf(ngettext(length(pkgs), "Installing package into %s\n(as %s is unspecified)",
## "Installing packages into %s\n(as %s is unspecified)"),
## sQuote(lib), sQuote("lib")), domain = NA)
## }
## ok <- dir.exists(lib) & (file.access(lib, 2) == 0L)
## if (length(lib) > 1 && any(!ok))
## stop(sprintf(ngettext(sum(!ok), "'lib' element %s is not a writable directory",
## "'lib' elements %s are not writable directories"),
## paste(sQuote(lib[!ok]), collapse = ", ")), domain = NA)
## if (length(lib) == 1L && .Platform$OS.type == "windows") {
## ok <- dir.exists(lib)
## if (ok) {
## fn <- file.path(lib, paste0("_test_dir_", Sys.getpid()))
## unlink(fn, recursive = TRUE)
## res <- try(dir.create(fn, showWarnings = FALSE))
## if (inherits(res, "try-error") || !res)
## ok <- FALSE
## else unlink(fn, recursive = TRUE)
## }
## }
## if (length(lib) == 1L && !ok) {
## warning(gettextf("'lib = \"%s\"' is not writable", lib),
## domain = NA, immediate. = TRUE)
## userdir <- unlist(strsplit(Sys.getenv("R_LIBS_USER"),
## .Platform$path.sep))[1L]
## if (interactive()) {
## ans <- askYesNo(gettext("Would you like to use a personal library instead?"),
## default = FALSE)
## if (!isTRUE(ans))
## stop("unable to install packages")
## lib <- userdir
## if (!file.exists(userdir)) {
## ans <- askYesNo(gettextf("Would you like to create a personal library\n%s\nto install packages into?",
## sQuote(userdir)), default = FALSE)
## if (!isTRUE(ans))
## stop("unable to install packages")
## if (!dir.create(userdir, recursive = TRUE))
## stop(gettextf("unable to create %s", sQuote(userdir)),
## domain = NA)
## .libPaths(c(userdir, .libPaths()))
## }
## }
## else stop("unable to install packages")
## }
## lib <- normalizePath(lib)
## if (length(pkgs) == 1L && missing(repos) && missing(contriburl)) {
## if ((type == "source" && any(grepl("[.]tar[.](gz|bz2|xz)$",
## pkgs))) || (type %in% "win.binary" && endsWith(pkgs,
## ".zip")) || (startsWith(type, "mac.binary") && endsWith(pkgs,
## ".tgz"))) {
## repos <- NULL
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## if (type == "both") {
## if (type2 %in% "win.binary" && endsWith(pkgs, ".zip")) {
## repos <- NULL
## type <- type2
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## else if (startsWith(type2, "mac.binary") && endsWith(pkgs,
## ".tgz")) {
## repos <- NULL
## type <- type2
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## else if (grepl("[.]tar[.](gz|bz2|xz)$", pkgs)) {
## repos <- NULL
## type <- "source"
## message("inferring 'repos = NULL' from 'pkgs'")
## }
## }
## }
## if (length(pkgs) == 1L && is.null(repos) && type == "both") {
## if ((type2 %in% "win.binary" && endsWith(pkgs, ".zip")) ||
## (startsWith(type2, "mac.binary") && endsWith(pkgs,
## ".tgz"))) {
## type <- type2
## }
## else if (grepl("[.]tar[.](gz|bz2|xz)$", pkgs)) {
## type <- "source"
## }
## }
## if (is.null(repos) && missing(contriburl)) {
## tmpd <- destdir
## nonlocalrepos <- any(web <- grepl("^(http|https|ftp)://",
## pkgs))
## if (is.null(destdir) && nonlocalrepos) {
## tmpd <- file.path(tempdir(), "downloaded_packages")
## if (!file.exists(tmpd) && !dir.create(tmpd))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd)), domain = NA)
## }
## if (nonlocalrepos) {
## df <- function(p, destfile, method, ...) download.file(p,
## destfile, method, mode = "wb", ...)
## urls <- pkgs[web]
## for (p in unique(urls)) {
## this <- pkgs == p
## destfile <- file.path(tmpd, basename(p))
## res <- try(df(p, destfile, method, ...))
## if (!inherits(res, "try-error") && res == 0L)
## pkgs[this] <- destfile
## else {
## pkgs[this] <- NA
## }
## }
## }
## }
## if (type == "both") {
## if (type2 == "source")
## stop("type == \"both\" can only be used on Windows or a CRAN build for macOS")
## if (!missing(contriburl) || !is.null(available))
## type <- type2
## }
## getDeps <- TRUE
## if (type == "both") {
## if (is.null(repos))
## stop("type == \"both\" cannot be used with 'repos = NULL'")
## type <- "source"
## contriburl <- contrib.url(repos, "source")
## if (missing(repos))
## repos <- getOption("repos")
## available <- available.packages(contriburl = contriburl,
## method = method, fields = "NeedsCompilation", ...)
## pkgs <- getDependencies(pkgs, dependencies, available,
## lib, ...)
## getDeps <- FALSE
## av2 <- available.packages(contriburl = contrib.url(repos,
## type2), method = method, ...)
## bins <- row.names(av2)
## bins <- pkgs[pkgs %in% bins]
## srcOnly <- pkgs[!pkgs %in% bins]
## binvers <- av2[bins, "Version"]
## hasArchs <- !is.na(av2[bins, "Archs"])
## needsCmp <- !(available[bins, "NeedsCompilation"] %in%
## "no")
## hasSrc <- hasArchs | needsCmp
## srcvers <- available[bins, "Version"]
## later <- as.numeric_version(binvers) < srcvers
## action <- getOption("install.packages.compile.from.source",
## "interactive")
## if (!nzchar(Sys.which(Sys.getenv("MAKE", "make"))))
## action <- "never"
## if (grepl("darwin", R.version$platform) && !length(srcOnly))
## later[later] <- FALSE
## if (any(later)) {
## msg <- ngettext(sum(later), "There is a binary version available but the source version is later",
## "There are binary versions available but the source versions are later")
## cat("\n", paste(strwrap(msg, indent = 2, exdent = 2),
## collapse = "\n"), ":\n", sep = "")
## out <- data.frame(binary = binvers, source = srcvers,
## needs_compilation = hasSrc, row.names = bins,
## check.names = FALSE)[later, ]
## print(out)
## cat("\n")
## if (any(later & hasSrc)) {
## if (action == "interactive" && interactive()) {
## msg <- ngettext(sum(later & hasSrc), "Do you want to install from sources the package which needs compilation?",
## "Do you want to install from sources the packages which need compilation?")
## res <- askYesNo(msg)
## if (is.na(res))
## stop("Cancelled by user")
## if (!isTRUE(res))
## later <- later & !hasSrc
## }
## else if (action == "never") {
## cat(" Binaries will be installed\n")
## later <- later & !hasSrc
## }
## }
## }
## bins <- bins[!later]
## if (length(srcOnly)) {
## s2 <- srcOnly[!(available[srcOnly, "NeedsCompilation"] %in%
## "no")]
## if (length(s2)) {
## msg <- ngettext(length(s2), "Package which is only available in source form, and may need compilation of C/C++/Fortran",
## "Packages which are only available in source form, and may need compilation of C/C++/Fortran")
## msg <- c(paste0(msg, ": "), sQuote(s2))
## msg <- strwrap(paste(msg, collapse = " "), exdent = 2)
## message(paste(msg, collapse = "\n"), domain = NA)
## if (action == "interactive" && interactive()) {
## res <- askYesNo("Do you want to attempt to install these from sources?")
## if (is.na(res))
## stop("Cancelled by user")
## if (!isTRUE(res))
## pkgs <- setdiff(pkgs, s2)
## }
## else if (action == "never") {
## cat(" These will not be installed\n")
## pkgs <- setdiff(pkgs, s2)
## }
## }
## }
## if (length(bins)) {
## if (type2 == "win.binary")
## .install.winbinary(pkgs = bins, lib = lib, contriburl = contrib.url(repos,
## type2), method = method, available = av2, destdir = destdir,
## dependencies = NULL, libs_only = libs_only,
## quiet = quiet, ...)
## else .install.macbinary(pkgs = bins, lib = lib, contriburl = contrib.url(repos,
## type2), method = method, available = av2, destdir = destdir,
## dependencies = NULL, quiet = quiet, ...)
## }
## pkgs <- setdiff(pkgs, bins)
## if (!length(pkgs))
## return(invisible())
## message(sprintf(ngettext(length(pkgs), "installing the source package %s",
## "installing the source packages %s"), paste(sQuote(pkgs),
## collapse = ", ")), "\n", domain = NA)
## flush.console()
## }
## else if (getOption("install.packages.check.source", "yes") %in%
## "yes" && (type %in% "win.binary" || startsWith(type,
## "mac.binary"))) {
## if (missing(contriburl) && is.null(available) && !is.null(repos)) {
## contriburl2 <- contrib.url(repos, "source")
## if (missing(repos))
## repos <- getOption("repos")
## av1 <- tryCatch(suppressWarnings(available.packages(contriburl = contriburl2,
## method = method, ...)), error = function(e) e)
## if (inherits(av1, "error")) {
## message("source repository is unavailable to check versions")
## available <- available.packages(contriburl = contrib.url(repos,
## type), method = method, ...)
## }
## else {
## srcpkgs <- pkgs[pkgs %in% row.names(av1)]
## available <- available.packages(contriburl = contrib.url(repos,
## type), method = method, ...)
## bins <- pkgs[pkgs %in% row.names(available)]
## na <- srcpkgs[!srcpkgs %in% bins]
## if (length(na)) {
## msg <- sprintf(ngettext(length(na), "package %s is available as a source package but not as a binary",
## "packages %s are available as source packages but not as binaries"),
## paste(sQuote(na), collapse = ", "))
## cat("\n ", msg, "\n\n", sep = "")
## }
## binvers <- available[bins, "Version"]
## srcvers <- binvers
## OK <- bins %in% srcpkgs
## srcvers[OK] <- av1[bins[OK], "Version"]
## later <- as.numeric_version(binvers) < srcvers
## if (any(later)) {
## msg <- ngettext(sum(later), "There is a binary version available (and will be installed) but the source version is later",
## "There are binary versions available (and will be installed) but the source versions are later")
## cat("\n", paste(strwrap(msg, indent = 2, exdent = 2),
## collapse = "\n"), ":\n", sep = "")
## print(data.frame(binary = binvers, source = srcvers,
## row.names = bins, check.names = FALSE)[later,
## ])
## cat("\n")
## }
## }
## }
## }
## if (.Platform$OS.type == "windows") {
## if (startsWith(type, "mac.binary"))
## stop("cannot install macOS binary packages on Windows")
## if (type %in% "win.binary") {
## .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
## method = method, available = available, destdir = destdir,
## dependencies = dependencies, libs_only = libs_only,
## quiet = quiet, ...)
## return(invisible())
## }
## have_spaces <- grep(" ", pkgs)
## if (length(have_spaces)) {
## p <- pkgs[have_spaces]
## dirs <- shortPathName(dirname(p))
## pkgs[have_spaces] <- file.path(dirs, basename(p))
## }
## pkgs <- gsub("\\", "/", pkgs, fixed = TRUE)
## }
## else {
## if (startsWith(type, "mac.binary")) {
## if (!grepl("darwin", R.version$platform))
## stop("cannot install macOS binary packages on this platform")
## .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
## method = method, available = available, destdir = destdir,
## dependencies = dependencies, quiet = quiet, ...)
## return(invisible())
## }
## if (type %in% "win.binary")
## stop("cannot install Windows binary packages on this platform")
## if (!file.exists(file.path(R.home("bin"), "INSTALL")))
## stop("This version of R is not set up to install source packages\nIf it was installed from an RPM, you may need the R-devel RPM")
## }
## cmd0 <- file.path(R.home("bin"), "R")
## args0 <- c("CMD", "INSTALL")
## output <- if (quiet)
## FALSE
## else ""
## env <- character()
## tlim <- Sys.getenv("_R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_")
## tlim <- if (!nzchar(tlim))
## 0
## else tools:::get_timeout(tlim)
## outdir <- getwd()
## if (is.logical(keep_outputs)) {
## if (is.na(keep_outputs))
## keep_outputs <- FALSE
## }
## else if (is.character(keep_outputs) && (length(keep_outputs) ==
## 1L)) {
## if (!dir.exists(keep_outputs) && !dir.create(keep_outputs,
## recursive = TRUE))
## stop(gettextf("unable to create %s", sQuote(keep_outputs)),
## domain = NA)
## outdir <- normalizePath(keep_outputs)
## keep_outputs <- TRUE
## }
## else stop(gettextf("invalid %s argument", sQuote("keep_outputs")),
## domain = NA)
## if (length(libpath <- .R_LIBS())) {
## if (.Platform$OS.type == "windows") {
## oldrlibs <- Sys.getenv("R_LIBS")
## Sys.setenv(R_LIBS = libpath)
## on.exit(Sys.setenv(R_LIBS = oldrlibs))
## }
## else env <- paste0("R_LIBS=", shQuote(libpath))
## }
## if (is.character(clean))
## args0 <- c(args0, clean)
## if (libs_only)
## args0 <- c(args0, "--libs-only")
## if (!missing(INSTALL_opts)) {
## if (!is.list(INSTALL_opts)) {
## args0 <- c(args0, paste(INSTALL_opts, collapse = " "))
## INSTALL_opts <- list()
## }
## }
## else {
## INSTALL_opts <- list()
## }
## if (verbose)
## message(gettextf("system (cmd0): %s", paste(c(cmd0, args0),
## collapse = " ")), domain = NA)
## if (is.null(repos) && missing(contriburl)) {
## update <- cbind(path.expand(pkgs), lib)
## for (i in seq_len(nrow(update))) {
## if (is.na(update[i, 1L]))
## next
## args <- c(args0, get_install_opts(update[i, 1L]),
## "-l", shQuote(update[i, 2L]), getConfigureArgs(update[i,
## 1L]), getConfigureVars(update[i, 1L]), shQuote(update[i,
## 1L]))
## status <- system2(cmd0, args, env = env, stdout = output,
## stderr = output, timeout = tlim)
## if (status > 0L)
## warning(gettextf("installation of package %s had non-zero exit status",
## sQuote(update[i, 1L])), domain = NA)
## else if (verbose) {
## cmd <- paste(c(cmd0, args), collapse = " ")
## message(sprintf("%d): succeeded '%s'", i, cmd),
## domain = NA)
## }
## }
## return(invisible())
## }
## tmpd <- destdir
## nonlocalrepos <- !all(startsWith(contriburl, "file:"))
## if (is.null(destdir) && nonlocalrepos) {
## tmpd <- file.path(tempdir(), "downloaded_packages")
## if (!file.exists(tmpd) && !dir.create(tmpd))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd)), domain = NA)
## }
## av2 <- NULL
## if (is.null(available)) {
## filters <- getOption("available_packages_filters")
## if (!is.null(filters)) {
## available <- available.packages(contriburl = contriburl,
## method = method, ...)
## }
## else {
## f <- setdiff(available_packages_filters_default,
## c("R_version", "duplicates"))
## av2 <- available.packages(contriburl = contriburl,
## filters = f, method = method, ...)
## f <- available_packages_filters_db[["R_version"]]
## f2 <- available_packages_filters_db[["duplicates"]]
## available <- f2(f(av2))
## }
## }
## if (getDeps)
## pkgs <- getDependencies(pkgs, dependencies, available,
## lib, ..., av2 = av2)
## foundpkgs <- download.packages(pkgs, destdir = tmpd, available = available,
## contriburl = contriburl, method = method, type = "source",
## quiet = quiet, ...)
## if (length(foundpkgs)) {
## if (verbose)
## message(gettextf("foundpkgs: %s", paste(foundpkgs,
## collapse = ", ")), domain = NA)
## update <- unique(cbind(pkgs, lib))
## colnames(update) <- c("Package", "LibPath")
## found <- pkgs %in% foundpkgs[, 1L]
## files <- foundpkgs[match(pkgs[found], foundpkgs[, 1L]),
## 2L]
## if (verbose)
## message(gettextf("files: %s", paste(files, collapse = ", \n\t")),
## domain = NA)
## update <- cbind(update[found, , drop = FALSE], file = files)
## if (nrow(update) > 1L) {
## upkgs <- unique(pkgs <- update[, 1L])
## DL <- .make_dependency_list(upkgs, available)
## p0 <- .find_install_order(upkgs, DL)
## update <- update[sort.list(match(pkgs, p0)), ]
## }
## if (Ncpus > 1L && nrow(update) > 1L) {
## tlim_cmd <- character()
## if (tlim > 0) {
## if (.Platform$OS.type == "windows" && !nzchar(Sys.getenv("R_TIMEOUT")) &&
## grepl("\\windows\\system32\\", tolower(Sys.which("timeout")),
## fixed = TRUE)) {
## warning("Windows default 'timeout' command is not usable for parallel installs")
## }
## else if (nzchar(timeout <- Sys.which(Sys.getenv("R_TIMEOUT",
## "timeout")))) {
## tlim_cmd <- c(shQuote(timeout), "-s INT", tlim)
## }
## else warning("timeouts for parallel installs require the 'timeout' command")
## }
## args0 <- c(args0, "--pkglock")
## tmpd2 <- file.path(tempdir(), "make_packages")
## if (!file.exists(tmpd2) && !dir.create(tmpd2))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd2)), domain = NA)
## mfile <- file.path(tmpd2, "Makefile")
## conn <- file(mfile, "wt")
## deps <- paste(paste0(update[, 1L], ".ts"), collapse = " ")
## deps <- strwrap(deps, width = 75, exdent = 2)
## deps <- paste(deps, collapse = " \\\n")
## cat("all: ", deps, "\n", sep = "", file = conn)
## aDL <- .make_dependency_list(upkgs, available, recursive = TRUE)
## for (i in seq_len(nrow(update))) {
## pkg <- update[i, 1L]
## fil <- update[i, 3L]
## args <- c(args0, get_install_opts(fil), "-l",
## shQuote(update[i, 2L]), getConfigureArgs(fil),
## getConfigureVars(fil), shQuote(fil), ">", paste0(pkg,
## ".out"), "2>&1")
## cmd <- paste(c("MAKEFLAGS=", tlim_cmd, shQuote(cmd0),
## args), collapse = " ")
## deps <- aDL[[pkg]]
## deps <- deps[deps %in% upkgs]
## deps <- if (length(deps))
## paste(paste0(deps, ".ts"), collapse = " ")
## else ""
## cat(paste0(pkg, ".ts: ", deps), paste("\t@echo begin installing package",
## sQuote(pkg)), paste0("\t@", cmd, " && touch ",
## pkg, ".ts"), paste0("\t@cat ", pkg, ".out"),
## "", sep = "\n", file = conn)
## }
## close(conn)
## cwd <- setwd(tmpd2)
## on.exit(setwd(cwd))
## status <- system2(Sys.getenv("MAKE", "make"), c("-k -j",
## Ncpus), stdout = output, stderr = output, env = env)
## if (status > 0L) {
## pkgs <- update[, 1L]
## tss <- sub("[.]ts$", "", dir(".", pattern = "[.]ts$"))
## failed <- pkgs[!pkgs %in% tss]
## for (pkg in failed) {
## if (file.exists(outfile <- paste0(pkg, ".out")))
## system2("cat", outfile)
## }
## n <- length(failed)
## if (n == 1L)
## warning(gettextf("installation of package %s failed",
## sQuote(failed)), domain = NA)
## else if (n > 1L) {
## msg <- paste(sQuote(failed), collapse = ", ")
## if (nchar(msg) < 40)
## warning(gettextf("installation of %d packages failed: %s",
## n, msg), domain = NA)
## else warning(gettextf("installation of %d packages failed:\n %s",
## n, msg), domain = NA)
## }
## }
## if (keep_outputs) {
## outfiles <- paste0(update[, 1L], ".out")
## file.copy(outfiles[file.exists(outfiles)], outdir,
## overwrite = TRUE)
## }
## file.copy(Sys.glob(paste0(update[, 1L], "*.zip")),
## cwd)
## file.copy(Sys.glob(paste0(update[, 1L], "*.tgz")),
## cwd)
## file.copy(Sys.glob(paste0(update[, 1L], "*.tar.gz")),
## cwd)
## setwd(cwd)
## on.exit()
## unlink(tmpd2, recursive = TRUE)
## }
## else {
## tmpd2 <- tempfile()
## if (!dir.create(tmpd2))
## stop(gettextf("unable to create temporary directory %s",
## sQuote(tmpd2)), domain = NA)
## outfiles <- file.path(tmpd2, paste0(update[, 1L],
## ".out"))
## for (i in seq_len(nrow(update))) {
## outfile <- if (keep_outputs)
## outfiles[i]
## else output
## fil <- update[i, 3L]
## args <- c(args0, get_install_opts(fil), "-l",
## shQuote(update[i, 2L]), getConfigureArgs(fil),
## getConfigureVars(fil), shQuote(fil))
## status <- system2(cmd0, args, env = env, stdout = outfile,
## stderr = outfile, timeout = tlim)
## if (!quiet && keep_outputs)
## writeLines(readLines(outfile))
## if (status > 0L)
## warning(gettextf("installation of package %s had non-zero exit status",
## sQuote(update[i, 1L])), domain = NA)
## else if (verbose) {
## cmd <- paste(c(cmd0, args), collapse = " ")
## message(sprintf("%d): succeeded '%s'", i, cmd),
## domain = NA)
## }
## }
## if (keep_outputs)
## file.copy(outfiles, outdir, overwrite = TRUE)
## unlink(tmpd2, recursive = TRUE)
## }
## if (!quiet && nonlocalrepos && !is.null(tmpd) && is.null(destdir))
## cat("\n", gettextf("The downloaded source packages are in\n\t%s",
## sQuote(normalizePath(tmpd, mustWork = FALSE))),
## "\n", sep = "", file = stderr())
## libs_used <- unique(update[, 2L])
## if (.Platform$OS.type == "unix" && .Library %in% libs_used) {
## message("Updating HTML index of packages in '.Library'")
## make.packages.html(.Library)
## }
## }
## else if (!is.null(tmpd) && is.null(destdir))
## unlink(tmpd, TRUE)
## invisible()
## }
## <bytecode: 0x1143d7900>
## <environment: namespace:utils>#If i out a hashtag it is a comment
#Calling packages to use in file
library(psych)
library(psychTools)#Call In Sample Data
data(epi.bfi)
summary(epi.bfi)## epiE epiS epiImp epilie
## Min. : 1.00 Min. : 0.000 Min. :0.000 Min. :0.000
## 1st Qu.:11.00 1st Qu.: 6.000 1st Qu.:3.000 1st Qu.:1.000
## Median :14.00 Median : 8.000 Median :4.000 Median :2.000
## Mean :13.33 Mean : 7.584 Mean :4.368 Mean :2.377
## 3rd Qu.:16.00 3rd Qu.: 9.500 3rd Qu.:6.000 3rd Qu.:3.000
## Max. :22.00 Max. :13.000 Max. :9.000 Max. :7.000
## epiNeur bfagree bfcon bfext
## Min. : 0.00 Min. : 74.0 Min. : 53.0 Min. : 8.0
## 1st Qu.: 7.00 1st Qu.:112.0 1st Qu.: 99.0 1st Qu.: 87.5
## Median :10.00 Median :126.0 Median :114.0 Median :104.0
## Mean :10.41 Mean :125.0 Mean :113.3 Mean :102.2
## 3rd Qu.:14.00 3rd Qu.:136.5 3rd Qu.:128.5 3rd Qu.:118.0
## Max. :23.00 Max. :167.0 Max. :178.0 Max. :168.0
## bfneur bfopen bdi traitanx
## Min. : 34.00 Min. : 73.0 Min. : 0.000 Min. :22.00
## 1st Qu.: 70.00 1st Qu.:110.0 1st Qu.: 3.000 1st Qu.:32.00
## Median : 90.00 Median :125.0 Median : 6.000 Median :38.00
## Mean : 87.97 Mean :123.4 Mean : 6.779 Mean :39.01
## 3rd Qu.:104.00 3rd Qu.:136.5 3rd Qu.: 9.000 3rd Qu.:44.00
## Max. :152.00 Max. :173.0 Max. :27.000 Max. :71.00
## stateanx
## Min. :21.00
## 1st Qu.:32.00
## Median :38.00
## Mean :39.85
## 3rd Qu.:46.50
## Max. :79.00#Run The Histogram and Mean
hist(epi.bfi$bdi)
mean(epi.bfi$bdi)## [1] 6.779221Including Plots
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