# File src/library/tools/R/install.R # Part of the R package, https://www.R-project.org # # Copyright (C) 1995-2022 The R Core Team # # NB: also copyright dates in Usages. # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # https://www.R-project.org/Licenses/ #### R based engine for R CMD INSTALL SHLIB Rprof #### ##' @param args ## R developers can use this to debug the function by running it ## directly as tools:::.install_packages(args), where the args should ## be what commandArgs(TRUE) would return, that is a character vector ## of (space-delimited) terms that would be passed to R CMD INSTALL. E.g. ## if(FALSE) { tools:::.install_packages(c("--preclean", "--no-multiarch", "tree")) ## or status <- tryCatch( tools:::.install_packages(c("--no-clean-on-error", "--no-multiarch", "tree"), no.q = TRUE) , error = function(e) as.numeric(sub(".* exit status *", "", conditionMessage(e)))) ## or debugonce(tools:::.install_packages) tools:::.install_packages(c("-c", "--debug", "--no-clean-on-error", "--no-multiarch", "tree")) ## and then (after about 40 x [Enter]) when do_install is defined: debug(do_install) ## and 'c' } ##' @return ... .install_packages <- function(args = NULL, no.q = interactive(), warnOption = 1) { ## calls system() on Windows for ## sh (configure.win/cleanup.win) make zip ## global variables curPkg <- character() # list of packages in current pkg lockdir <- "" is_first_package <- TRUE stars <- "*" user.tmpdir <- Sys.getenv("PKG_BUILD_DIR") keep.tmpdir <- nzchar(user.tmpdir) ## Need these here in case of an early error, e.g. missing etc/Makeconf tmpdir <- "" clean_on_error <- TRUE R_runR_deps_only <- function(cmd, deps_only_env, multiarch = FALSE, ...) { deps_only <- config_val_to_logical(Sys.getenv("_R_CHECK_INSTALL_DEPENDS_", "FALSE")) env <- if (deps_only) deps_only_env else "" ## needed for some packages (AnnotationDbi) that install other ## packages during their tests (otherwise system profile fails ## because it cannot find the tests startup file) env <- paste(env, "R_TESTS=") opts <- "--no-save --no-restore --no-echo" if (deps_only) { opts <- paste(opts, "--no-init-file --no-site-file") if (!multiarch) ## do not use --no-environ with multiarch, because Renviron ## may include architecture-specific settings that may differ ## from settings of the host process architecture opts <- paste(opts, "--no-environ") } R_runR(cmd = cmd, Ropts = opts, env = env, ...) } do_exit <- if(no.q) function(status) stop(".install_packages() exit status ", status) else function(status) q("no", status = status, runLast = FALSE) do_exit_on_error <- function(status = 1L) { ## If we are not yet processing a package, we will not have ## set curPkg if(clean_on_error && length(curPkg)) { pkgdir <- file.path(lib, curPkg) if (nzchar(pkgdir) && dir.exists(pkgdir) && is_subdir(pkgdir, lib)) { starsmsg(stars, "removing ", sQuote(pkgdir)) unlink(pkgdir, recursive = TRUE) } if (nzchar(lockdir) && dir.exists(lp <- file.path(lockdir, curPkg)) && is_subdir(lp, lockdir)) { starsmsg(stars, "restoring previous ", sQuote(pkgdir)) if (WINDOWS) { file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) unlink(lp, recursive = TRUE) } else { ## some shells require that they be run in a known dir setwd(startdir) if(system(paste("mv -f", shQuote(lp), shQuote(pkgdir)))) message(" restoration failed\n") } } } do_cleanup() do_exit(status=status) } do_cleanup <- function() { if(!keep.tmpdir && nzchar(tmpdir)) do_cleanup_tmpdir() if (!is_first_package) { ## Only need to do this in case we successfully installed ## at least one package if (lib == .Library && "html" %in% build_help_types) utils::make.packages.html(.Library, docdir = R.home("doc")) } if (nzchar(lockdir)) unlink(lockdir, recursive = TRUE) } do_cleanup_tmpdir <- function() { ## Solaris will not remove any directory in the current path setwd(startdir) if (!keep.tmpdir && dir.exists(tmpdir)) unlink(tmpdir, recursive=TRUE) } # This produces a (by default single) quoted string for use in a # command sent to another R process. quote_path <- function(path, quote = "'") { path <- gsub("\\", "\\\\", path, fixed = TRUE) path <- gsub(quote, paste0("\\", quote), path, fixed = TRUE) paste0(quote, path, quote) } # Escape backslashes in a replacement string for gsub etc. # To be used when the replacement is a path name which may include # backslashes, e.g. with UNC paths on Windows. quote_replacement <- function(r) paste0(gsub("\\", "\\\\", r, fixed=TRUE)) on.exit(do_exit_on_error()) WINDOWS <- .Platform$OS.type == "windows" cross <- Sys.getenv("R_CROSS_BUILD") have_cross <- nzchar(cross) if(have_cross && !cross %in% c("i386", "x64")) stop("invalid value ", sQuote(cross), " for R_CROSS_BUILD") if (have_cross) { WINDOWS <- TRUE Sys.setenv(R_OSTYPE = "windows") } if (WINDOWS) MAKE <- "make" else MAKE <- Sys.getenv("MAKE") # FIXME shQuote, default? rarch <- Sys.getenv("R_ARCH") # unix only if (WINDOWS && nzchar(.Platform$r_arch)) rarch <- paste0("/", .Platform$r_arch) cross <- Sys.getenv("R_CROSS_BUILD") if(have_cross && !cross %in% c("i386", "x64")) stop("invalid value ", sQuote(cross), " for R_CROSS_BUILD") test_archs <- rarch if (have_cross) { WINDOWS <- TRUE r_arch <- paste0("/", cross) test_archs <- c() } SHLIB_EXT <- if (WINDOWS) ".dll" else { ## can we do better? mconf <- file.path(R.home(), paste0("etc", rarch), "Makeconf") ## PCRE needed for Debian arm* platforms sub(".*= ", "", grep("^SHLIB_EXT", readLines(mconf), value = TRUE, perl = TRUE)) } if(getOption("warn") < warnOption) { op <- options(warn = warnOption) on.exit(options(op), add = TRUE) } invisible(Sys.setlocale("LC_COLLATE", "C")) # discard output if (WINDOWS) { rhome <- chartr("\\", "/", R.home()) ## These might be needed for configure.win and Make{file,vars}.win ## Some people have *assumed* that R_HOME uses / Sys.setenv(R_HOME = rhome) if (nzchar(rarch)) Sys.setenv(R_ARCH = rarch, R_ARCH_BIN = rarch) } Usage <- function() { cat("Usage: R CMD INSTALL [options] pkgs", "", "Install the add-on packages specified by pkgs. The elements of pkgs can", "be relative or absolute paths to directories with the package", "sources, or to gzipped package 'tar' archives. The library tree", "to install to can be specified via '--library'. By default, packages are", "installed in the library tree rooted at the first directory in", ".libPaths() for an R session run in the current environment.", "", "Options:", " -h, --help print short help message and exit", " -v, --version print INSTALL version info and exit", " -c, --clean remove files created during installation", " --preclean remove files created during a previous run", " -d, --debug turn on debugging messages", if(WINDOWS) " and build a debug DLL", " -l, --library=LIB install packages to library tree LIB", " --no-configure do not use the package's configure script", " --no-docs do not install HTML, LaTeX or examples help", " --html build HTML help", " --no-html do not build HTML help", " --latex install LaTeX help", " --example install R code for help examples", " --fake do minimal install for testing purposes", " --no-lock install on top of any existing installation", " without using a lock directory", " --lock use a per-library lock directory (default)", " --pkglock use a per-package lock directory", " (default for a single package)", " --build build binaries of the installed package(s)", " --install-tests install package-specific tests (if any)", " --no-R, --no-libs, --no-data, --no-help, --no-demo, --no-exec,", " --no-inst", " suppress installation of the specified part of the", " package for testing or other special purposes", " --no-multiarch build only the main architecture", " --libs-only only install the libs directory", " --data-compress= none, gzip (default), bzip2 or xz compression", " to be used for lazy-loading of data", " --resave-data re-save data files as compactly as possible", " --compact-docs re-compress PDF files under inst/doc", " --with-keep.source", " --without-keep.source", " use (or not) 'keep.source' for R code", " --with-keep.parse.data", " --without-keep.parse.data", " use (or not) 'keep.parse.data' for R code", " --byte-compile byte-compile R code", " --no-byte-compile do not byte-compile R code", " --staged-install install to a temporary directory and then move", " to the target directory (default)", " --no-staged-install install directly to the target directory", " --no-test-load skip test of loading installed package", " --no-clean-on-error do not remove installed package on error", " --merge-multiarch multi-arch by merging (from a single tarball only)", " --use-vanilla do not read any Renviron or Rprofile files", " --use-LTO use Link-Time Optimization", " --no-use-LTO do not use Link-Time Optimization", "\nfor Unix", " --configure-args=ARGS", " set arguments for the configure scripts (if any)", " --configure-vars=VARS", " set variables for the configure scripts (if any)", " --strip strip shared object(s)", " --strip-lib strip static/dynamic libraries under lib/", " --dsym (macOS only) generate dSYM directory", " --built-timestamp=STAMP", " set timestamp for Built: entry in DESCRIPTION", "\nand on Windows only", " --force-biarch attempt to build both architectures", " even if there is a non-empty configure.win", " --compile-both compile both architectures on 32-bit Windows", "", "Which of --html or --no-html is the default depends on the build of R:", paste0("for this one it is ", if(static_html) "--html" else "--no-html", "."), "", "Report bugs at .", sep = "\n") } ## Check whether dir is a subdirectory of parent, ## to protect against malicious package names like ".." below ## Assumes that both directories exist is_subdir <- function(dir, parent) { rl <- Sys.readlink(dir) ## symbolic link (on POSIX, not Windows) is ok: (!is.na(rl) && nzchar(rl)) || normalizePath(parent) == normalizePath(file.path(dir, "..")) } fullpath <- function(dir) { owd <- setwd(dir) full <- getwd() setwd(owd) full } ## used for LazyData, KeepSource, ByteCompile, Biarch, StagedInstall parse_description_field <- function(desc, field, default) str_parse_logic(desc[field], default = default, otherwise = quote( errmsg("invalid value of ", field, " field in DESCRIPTION"))) starsmsg <- function(stars, ...) message(stars, " ", ..., domain = NA) errmsg <- function(...) { message("ERROR: ", ..., domain = NA) do_exit_on_error() } pkgerrmsg <- function(msg, pkg) errmsg(msg, " for package ", sQuote(pkg)) ## 'pkg' is the absolute path to package sources. do_install <- function(pkg) { if (WINDOWS && endsWith(pkg, ".zip")) { pkg_name <- basename(pkg) pkg_name <- sub("\\.zip$", "", pkg_name) pkg_name <- sub("_[0-9.-]+$", "", pkg_name) reuse_lockdir <- lock && !pkglock if (pkglock) lock <- "pkglock" utils:::unpackPkgZip(pkg, pkg_name, lib, libs_only, lock, reuse_lockdir = reuse_lockdir) return() } setwd(pkg) ## We checked this exists, but not that it is readable desc <- tryCatch(read.dcf(fd <- file.path(pkg, "DESCRIPTION")), error = identity) if(inherits(desc, "error") || !length(desc)) stop(gettextf("error reading file '%s'", fd), domain = NA, call. = FALSE) desc <- desc[1L,] ## Let's see if we have a bundle if (!is.na(desc["Bundle"])) { stop("this seems to be a bundle -- and they are defunct") } else { pkg_name <- desc["Package"] if (is.na(pkg_name)) errmsg("no 'Package' field in 'DESCRIPTION'") curPkg <<- pkg_name } instdir <- file.path(lib, pkg_name) # = / Sys.setenv(R_PACKAGE_NAME = pkg_name, R_PACKAGE_DIR = instdir) status <- .Rtest_package_depends_R_version() if (status) do_exit_on_error() dir.create(instdir, recursive = TRUE, showWarnings = FALSE) if (!dir.exists(instdir)) { # This allows a package to be installed if a broken symbolic # link (or a regular file) is place (PR#18262) unlink(instdir, recursive = FALSE) dir.create(instdir, recursive = TRUE, showWarnings = FALSE) } if (!dir.exists(instdir)) { message("ERROR: unable to create ", sQuote(instdir), domain = NA) do_exit_on_error() } if (!is_subdir(instdir, lib)) { message("ERROR: ", sQuote(pkg_name), " is not a legal package name", domain = NA) do_exit_on_error() } ## Make sure we do not attempt installing to srcdir. owd <- setwd(instdir) if (owd == getwd()) pkgerrmsg("cannot install to srcdir", pkg_name) setwd(owd) ## Figure out whether this is a source or binary package. is_source_package <- is.na(desc["Built"]) if (is_source_package) { ## Find out if any C++ standard is requested in DESCRIPTION file sys_requires <- desc["SystemRequirements"] if (!is.na(sys_requires)) { sys_requires <- unlist(strsplit(sys_requires, ",")) for (i in cxx_standards) { pattern <- paste0("^[[:space:]]*C[+][+]",i,"[[:space:]]*$") if(any(grepl(pattern, sys_requires, ignore.case=TRUE))) { Sys.setenv("R_PKG_CXX_STD"=i) on.exit(Sys.unsetenv("R_PKG_CXX_STD")) break } } } } if (!is_first_package) cat("\n") if (is_source_package) do_install_source(pkg_name, instdir, pkg, desc) else do_install_binary(pkg_name, instdir, desc) ## Add read permission to all, write permission to owner ## If group-write permissions were requested, set them .Call(C_dirchmod, instdir, group.writable) is_first_package <<- FALSE if (tar_up) { # Unix only starsmsg(stars, "creating tarball") version <- desc["Version"] filename <- if (!grepl("darwin", R.version$os)) { paste0(pkg_name, "_", version, "_R_", Sys.getenv("R_PLATFORM"), ".tar.gz") } else { paste0(pkg_name, "_", version,".tgz") } filepath <- file.path(startdir, filename) owd <- setwd(lib) res <- utils::tar(filepath, curPkg, compression = "gzip", compression_level = 9L, tar = Sys.getenv("R_INSTALL_TAR")) if (res) errmsg(sprintf("packaging into %s failed", sQuote(filename))) message("packaged installation of ", sQuote(pkg_name), " as ", sQuote(filename), domain = NA) setwd(owd) } if (zip_up) { # Windows only starsmsg(stars, "MD5 sums") .installMD5sums(instdir) ## we could use utils::zip() here. ZIP <- "zip" # Windows only version <- desc["Version"] filename <- paste0(pkg_name, "_", version, ".zip") filepath <- shQuote(file.path(startdir, filename)) ## system(paste("rm -f", filepath)) unlink(filepath) owd <- setwd(lib) res <- system(paste(shQuote(ZIP), "-r9Xq", filepath, paste(curPkg, collapse = " "))) setwd(owd) if (res) message("running 'zip' failed", domain = NA) else message("packaged installation of ", sQuote(pkg_name), " as ", filename, domain = NA) } if (Sys.getenv("_R_INSTALL_NO_DONE_") != "yes") { ## message("", domain = NA) # ensure next starts on a new line, for R CMD check starsmsg(stars, "DONE (", pkg_name, ")") } curPkg <<- character() } ## Unix only do_install_binary <- function(pkg, instdir, desc) { starsmsg(stars, "installing *binary* package ", sQuote(pkg), " ...") if (file.exists(file.path(instdir, "DESCRIPTION"))) { if (nzchar(lockdir)) system(paste("mv -f", shQuote(instdir), shQuote(file.path(lockdir, pkg)))) dir.create(instdir, recursive = TRUE, showWarnings = FALSE) } TAR <- Sys.getenv("TAR", 'tar') res <- system(paste("cp -R .", shQuote(instdir), "|| (", TAR, "cd - .| (cd", shQuote(instdir), "&&", TAR, "-xf -))" )) if (res) errmsg("installing binary package failed") if (tar_up) { starsmsg(stars, sQuote(pkg), " was already a binary package and will not be rebuilt") tar_up <- FALSE } } ## to be run from package source directory run_clean <- function() { if (dir.exists("src") && length(dir("src", all.files = TRUE) > 2L)) { if (WINDOWS) archs <- c("i386", "x64") else { wd2 <- setwd(file.path(R.home("bin"), "exec")) archs <- Sys.glob("*") setwd(wd2) } if(length(archs)) for(arch in archs) { ss <- paste0("src-", arch) ## it seems fixing permissions is sometimes needed .Call(C_dirchmod, ss, group.writable) unlink(ss, recursive = TRUE) } owd <- setwd("src") if (WINDOWS) { if (file.exists("Makefile.ucrt")) system(paste(MAKE, "-f Makefile.ucrt clean")) else if (file.exists("Makefile.win")) system(paste(MAKE, "-f Makefile.win clean")) else unlink(c("Makedeps", Sys.glob("*_res.rc"), Sys.glob("*.[do]"))) # system("rm -f *_res.rc *.o *.d Makedeps") } else { if (file.exists("Makefile")) system(paste(MAKE, "clean")) else ## we will be using SHLIB --preclean unlink(Sys.glob(paste0("*", SHLIB_EXT))) } setwd(owd) } if (WINDOWS) { if (file.exists("cleanup.ucrt")) system("sh ./cleanup.ucrt") else if (file.exists("cleanup.win")) system("sh ./cleanup.win") } else if (file_test("-x", "cleanup")) system("./cleanup") else if (file.exists("cleanup")) warning("'cleanup' exists but is not executable -- see the 'R Installation and Administration Manual'", call. = FALSE) revert_install_time_patches() } do_install_source <- function(pkg_name, instdir, pkg_dir, desc) { Sys.setenv("R_INSTALL_PKG" = pkg_name) on.exit(Sys.unsetenv("R_INSTALL_PKG")) shlib_install <- function(instdir, arch) { ## install.libs.R allows customization of the libs installation process if (file.exists("install.libs.R")) { message("installing via 'install.libs.R' to ", instdir, domain = NA) ## the following variables are defined to be available, ## and to prevent abuse we don't expose anything else local.env <- local({ SHLIB_EXT <- SHLIB_EXT R_PACKAGE_DIR <- instdir R_PACKAGE_NAME <- pkg_name R_PACKAGE_SOURCE <- pkg_dir R_ARCH <- arch WINDOWS <- WINDOWS environment()}) parent.env(local.env) <- .GlobalEnv source("install.libs.R", local = local.env) return(TRUE) } ## otherwise proceed with the default which is to just copy *${SHLIB_EXT} files <- Sys.glob(paste0("*", SHLIB_EXT)) if (length(files)) { libarch <- if (nzchar(arch)) paste0("libs", arch) else "libs" dest <- file.path(instdir, libarch) message('installing to ', dest, domain = NA) dir.create(dest, recursive = TRUE, showWarnings = FALSE) file.copy(files, dest, overwrite = TRUE) if((do_strip || config_val_to_logical(Sys.getenv("_R_SHLIB_STRIP_", "false"))) && nzchar(strip_cmd <- Sys.getenv("R_STRIP_SHARED_LIB"))) { system(paste(c(strip_cmd, shQuote(file.path(dest, files))), collapse = " ")) } ## not clear if this is still necessary, but sh version did so if (!WINDOWS) Sys.chmod(file.path(dest, files), dmode) ## macOS does not keep debugging symbols in binaries ## anymore so optionally we can create dSYMs. This is ## important since we will blow away .o files so there ## is no way to create it later. if (dsym && startsWith(R.version$os, "darwin")) { starsmsg(stars, gettextf("generating debug symbols (%s)", "dSYM")) dylib <- Sys.glob(paste0(dest, "/*", SHLIB_EXT)) for (d in dylib) system(paste0("dsymutil ", d)) } if(config_val_to_logical(Sys.getenv("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_", "TRUE")) && file_test("-f", "symbols.rds")) { file.copy("symbols.rds", dest) } } } ## This is only called for Makevars[.win], so assume it ## does create a shlib: not so reliably reported on Windows ## Note though that it may not create pkg_name.dll, and ## graph does not. run_shlib <- function(pkg_name, srcs, instdir, arch, use_LTO = NA) { args <- c(shargs, if(isTRUE(use_LTO)) "--use-LTO", if(isFALSE(use_LTO)) "--no-use-LTO", "-o", paste0(pkg_name, SHLIB_EXT), srcs) if (WINDOWS && debug) args <- c(args, "--debug") if (debug) message("about to run ", "R CMD SHLIB ", paste(args, collapse = " "), domain = NA) if (.shlib_internal(args) == 0L) { if(WINDOWS && !file.exists("install.libs.R") && !length(Sys.glob("*.dll"))) { message("no DLL was created") return(TRUE) } shlib_install(instdir, arch) return(FALSE) } else return(TRUE) } ## Patch hardcoded paths in shared objects/dynamic libraries ## so that they can be moved to a different directory. ## Not used on WINDOWS. patch_rpaths <- function() { slibs <- list.files(instdir, recursive = TRUE, all.files = TRUE, full.names = TRUE) slibs <- grep("(\\.sl$)|(\\.so$)|(\\.dylib$)|(\\.dll$)", slibs, value = TRUE) if (!length(slibs)) return() have_file <- nzchar(Sys.which("file")) ## file reports macOS dylibs as 'dynamically linked shared library' if (have_file) { ## RcppParallel has .so files containing ASCII text ## (linker script) which make the tools below produce ## a lot of error messages. However, some docker ## installations do not have "file" utility. ## Solaris' "file" does not use 'shared'. ## ## On macOS, a single "dylib" file can have a shared object ## for multiple architectures, so multiple lines with ## "shared"/"dynamically linked" are_shared <- vapply(slibs, function(l) any(grepl("(shared|dynamically linked)", system(paste("file", shQuote(l)), intern = TRUE))), NA) slibs <- slibs[are_shared] if (!length(slibs)) return() } starsmsg(stars, "checking absolute paths in shared objects and dynamic libraries") uname <- system("uname -a", intern = TRUE) os <- sub(" .*", "", uname) have_chrpath <- nzchar(Sys.which("chrpath")) have_patchelf <- nzchar(Sys.which("patchelf")) have_readelf <- nzchar(Sys.which("readelf")) have_macos_clt <- identical(os, "Darwin") && nzchar(Sys.which("otool")) && nzchar(Sys.which("install_name_tool")) have_solaris_elfedit <- identical(os, "SunOS") && nzchar(Sys.which("elfedit")) hardcoded_paths <- FALSE failed_fix <- FALSE # paths below are protected from the shell, but special # characters/spaces should not be used, because they cannot be # reproduced correctly in the outputs from external tools if (have_solaris_elfedit) { ## Solaris only ## changes both rpath and DT_NEEDED paths for (l in slibs) { out <- suppressWarnings( system(paste("elfedit -re dyn:value", shQuote(l)), intern = TRUE)) out <- grep("^[ \t]*\\[[0-9]+\\]", out, value = TRUE) re <- "^[ \t]*\\[([0-9]+)\\][ \t]+([^ \t]+)[ \t]+([^ \t]+)[ \t]*(.*)" paths <- gsub(re, "\\4", out) idxs <- gsub(re, "\\1", out) old_paths <- paths # "\\$ORIGIN/.." paths <- gsub(instdir, quote_replacement(final_instdir), paths, fixed = TRUE) changed <- paths != old_paths paths <- paths[changed] old_paths <- old_paths[changed] idxs <- idxs[changed] for (i in seq_along(paths)) { hardcoded_paths <- TRUE qp <- gsub('([" \\])', "\\\\\\1", paths[i]) qp <- gsub("'", "\\\\'", qp) cmd <- paste0("elfedit -e \"dyn:value -dynndx -s ", idxs[i], " ", qp, "\" ", shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd, intern = FALSE)) if (ret == 0) message("NOTE: fixed path ", sQuote(old_paths[i])) } out <- suppressWarnings( system(paste("elfedit -re dyn:value", shQuote(l)), intern = TRUE)) out <- grep("^[ \t]*\\[", out, value = TRUE) paths <- gsub(re, "\\4", out) if (any(grepl(instdir, paths, fixed = TRUE))) failed_fix <- TRUE } } else if (have_macos_clt) { ## macOS only for (l in slibs) { ## change identification name of the library out <- suppressWarnings( system(paste("otool -D", shQuote(l)), intern = TRUE)) out <- out[-1L] # first line is l (includes instdir) oldid <- out if (length(oldid) == 1 && grepl(instdir, oldid, fixed = TRUE)) { hardcoded_paths <- TRUE newid <- gsub(instdir, quote_replacement(final_instdir), oldid, fixed = TRUE) cmd <- paste("install_name_tool -id", shQuote(newid), shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd, intern = FALSE)) if (ret == 0) ## NOTE: install_name does not signal an error in ## some cases message("NOTE: fixed library identification name ", sQuote(oldid)) } ## change paths to other libraries out <- suppressWarnings( system(paste("otool -L", shQuote(l)), intern = TRUE)) paths <- grep("\\(compatibility", out, value = TRUE) paths <- gsub("^[ \t]*(.*) \\(compatibility.*", "\\1", paths) old_paths <- paths # "@loader_path/.." paths <- gsub(instdir, quote_replacement(final_instdir), paths, fixed = TRUE) changed <- paths != old_paths paths <- paths[changed] old_paths <- old_paths[changed] for(i in seq_along(paths)) { hardcoded_paths <- TRUE cmd <- paste("install_name_tool -change", shQuote(old_paths[i]), shQuote(paths[i]), shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd, intern = FALSE)) if (ret == 0) ## NOTE: install_name does not signal an error in ## some cases message("NOTE: fixed library path ", sQuote(old_paths[i])) } out <- suppressWarnings( system(paste("otool -L", shQuote(l)), intern = TRUE)) out <- grep("\\(compatibility", out, value = TRUE) if (any(grepl(instdir, out, fixed = TRUE))) failed_fix <- TRUE ## change rpath entries out <- suppressWarnings( system(paste("otool -l", shQuote(l)), intern = TRUE)) out <- grep("(^[ \t]*cmd )|(^[ \t]*path )", out, value = TRUE) rpidx <- grep("cmd LC_RPATH$", out) if (length(rpidx)) { paths <- gsub("^[ \t]*path ", "", out[rpidx+1]) paths <- gsub("(.*) \\(offset .*", "\\1", paths) old_paths <- paths # "@loader_path/.." paths <- gsub(instdir, quote_replacement(final_instdir), paths, fixed = TRUE) changed <- paths != old_paths paths <- paths[changed] old_paths <- old_paths[changed] for(i in seq_along(paths)) { hardcoded_paths <- TRUE cmd <- paste("install_name_tool -rpath", shQuote(old_paths[i]), shQuote(paths[i]), shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd)) if (ret == 0) message("NOTE: fixed rpath ", sQuote(old_paths[i])) } } ## check no hard-coded paths are left out <- suppressWarnings( system(paste("otool -l", shQuote(l)), intern = TRUE)) out <- out[-1L] # first line is l (includes instdir) if (any(grepl(instdir, out, fixed = TRUE))) failed_fix <- TRUE } } else if (have_patchelf) { ## probably Linux for(l in slibs) { # fix rpath rpath <- suppressWarnings( system(paste("patchelf --print-rpath", shQuote(l)), intern = TRUE)) old_rpath <- rpath # "\\$ORIGIN/.." rpath <- gsub(instdir, quote_replacement(final_instdir), rpath, fixed = TRUE) if (length(rpath) && nzchar(rpath) && old_rpath != rpath) { hardcoded_paths <- TRUE cmd <- paste("patchelf", "--set-rpath", shQuote(rpath), shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd)) if (ret == 0) message("NOTE: fixed rpath ", sQuote(old_rpath)) rpath <- suppressWarnings( system(paste("patchelf --print-rpath", shQuote(l)), intern = TRUE)) if (any(grepl(instdir, rpath, fixed = TRUE))) failed_fix <- TRUE } # fix DT_NEEDED if (have_readelf) { out <- suppressWarnings( system(paste("readelf -d", shQuote(l)), intern = TRUE)) re0 <- "0x.*\\(NEEDED\\).*Shared library:" out <- grep(re0, out, value = TRUE) re <- "^[ \t]*0x[0-9]+[ \t]+\\(NEEDED\\)[ \t]+Shared library:[ \t]*\\[(.*)\\]" paths <- gsub(re, "\\1", out) old_paths <- paths # "\\$ORIGIN/.." paths <- gsub(instdir, quote_replacement(final_instdir), paths, fixed = TRUE) changed <- paths != old_paths paths <- paths[changed] old_paths <- old_paths[changed] for(i in seq_along(paths)) { cmd <- paste("patchelf --replace-needed", shQuote(old_paths[i]), shQuote(paths[i]), shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd)) if (ret == 0) message("NOTE: fixed library path ", sQuote(old_paths[i])) } out <- suppressWarnings( system(paste("readelf -d", shQuote(l)), intern = TRUE)) out <- grep(re0, out, value = TRUE) if (any(grepl(instdir, out, fixed = TRUE))) failed_fix <- TRUE } } } else if (have_chrpath) { ## Linux (possibly Solaris, but there elfedit should be ## available, instead); only fixes rpaths, not DT_NEEDED for(l in slibs) { out <- suppressWarnings( system(paste("chrpath", shQuote(l)), intern = TRUE)) # when multiple rpaths are present, there is a single # RUNPATH= line with the paths separated by : rpath <- grep(".*PATH=", out, value=TRUE) rpath <- gsub(".*PATH=", "", rpath) old_rpath <- rpath # "\\$ORIGIN/.." rpath <- gsub(instdir, quote_replacement(final_instdir), rpath, fixed = TRUE) if (length(rpath) && nzchar(rpath) && old_rpath != rpath) { hardcoded_paths <- TRUE cmd <- paste("chrpath", "-r", shQuote(rpath), shQuote(l)) message(cmd) ret <- suppressWarnings(system(cmd)) if (ret == 0) message("NOTE: fixed rpath ", sQuote(old_rpath)) out <- suppressWarnings( system(paste("chrpath", shQuote(l)), intern = TRUE)) rpath <- grep(".*PATH=", out, value = TRUE) rpath <- gsub(".*PATH=", "", rpath) if (any(grepl(instdir, rpath, fixed = TRUE))) failed_fix <- TRUE } } } if (hardcoded_paths) message("WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths") if (failed_fix) errmsg("some hard-coded temporary paths could not be fixed") if (have_readelf) { ## check again, needed mostly on Linux (chrpath may not be ## available or there may be DT_NEEDED entries with absolute ## paths); ldd is not suitable because it interprets $ORIGIN for(l in slibs) { out <- suppressWarnings( system(paste("readelf -d", shQuote(l)), intern = TRUE)) out <- grep("^[ \t]*0x", out, value = TRUE) if (any(grepl(instdir, out, fixed = TRUE))) { ## give path relative to installation dir ll <- sub(file.path(instdir, ""), "", l, fixed = TRUE) errmsg("absolute paths in ", sQuote(ll), " include the temporary installation directory:", " please report to the package maintainer", " and use ", sQuote("--no-staged-install")) } } } } # patch_rpaths() ## Make the destination directories available to the developer's ## installation scripts (e.g. configure) Sys.setenv(R_LIBRARY_DIR = lib) if (nzchar(lib0)) { ## FIXME: is this needed? ## set R_LIBS to include the current installation directory rlibs <- Sys.getenv("R_LIBS") rlibs <- if (nzchar(rlibs)) paste(lib, rlibs, sep = .Platform$path.sep) else lib Sys.setenv(R_LIBS = rlibs) ## This is needed .libPaths(c(lib, .libPaths())) } Type <- desc["Type"] if (!is.na(Type) && Type == "Frontend") { if (WINDOWS) errmsg("'Frontend' packages are Unix-only") starsmsg(stars, "installing *Frontend* package ", sQuote(pkg_name), " ...") if (preclean) system(paste(MAKE, "clean")) if (use_configure) { if (file_test("-x", "configure")) { res <- system(paste(paste(configure_vars, collapse = " "), "./configure", paste(configure_args, collapse = " "))) if (res) pkgerrmsg("configuration failed", pkg_name) } else if (file.exists("configure")) errmsg("'configure' exists but is not executable -- see the 'R Installation and Administration Manual'") } if (file.exists("Makefile")) if (system(MAKE)) pkgerrmsg("make failed", pkg_name) if (clean) system(paste(MAKE, "clean")) return() } if (!is.na(Type) && Type == "Translation") errmsg("'Translation' packages are defunct") OS_type <- desc["OS_type"] if (WINDOWS) { if ((!is.na(OS_type) && OS_type == "unix") && !fake) errmsg(" Unix-only package") } else { if ((!is.na(OS_type) && OS_type == "windows") && !fake) errmsg(" Windows-only package") } if(group.writable) { ## group-write modes if requested: fmode <- "664" dmode <- "775" } else { fmode <- "644" dmode <- "755" } ## At this point we check that we have the dependencies we need. ## We cannot use installed.packages() as other installs might be ## going on in parallel pkgInfo <- .split_description(.read_description("DESCRIPTION")) R_install_force_depends_imports <- config_val_to_logical(Sys.getenv( "_R_INSTALL_LIBS_ONLY_FORCE_DEPENDS_IMPORTS_", "TRUE")) if (libs_only && isFALSE(R_install_force_depends_imports)) pkgs <- unique(c(names(names(pkgInfo$LinkingTo)))) else pkgs <- unique(c(names(pkgInfo$Depends), names(pkgInfo$Imports), names(pkgInfo$LinkingTo))) if (length(pkgs)) { miss <- character() for (pkg in pkgs) { if(!length(find.package(pkg, quiet = TRUE))) miss <- c(miss, pkg) } if (length(miss) > 1) pkgerrmsg(sprintf("dependencies %s are not available", paste(sQuote(miss), collapse = ", ")), pkg_name) else if (length(miss)) pkgerrmsg(sprintf("dependency %s is not available", sQuote(miss)), pkg_name) } starsmsg(stars, "installing *source* package ", sQuote(pkg_name), " ...") stars <- "**" res <- checkMD5sums(pkg_name, getwd()) if(!is.na(res) && res) { starsmsg(stars, gettextf("package %s successfully unpacked and MD5 sums checked", sQuote(pkg_name))) } if (file.exists(file.path(instdir, "DESCRIPTION"))) { ## Back up a previous version if (nzchar(lockdir)) { if (debug) starsmsg(stars, "backing up earlier installation") if(WINDOWS) { file.copy(instdir, lockdir, recursive = TRUE, copy.date = TRUE) if (more_than_libs) unlink(instdir, recursive = TRUE) } else if (more_than_libs) system(paste("mv -f ", shQuote(instdir), shQuote(file.path(lockdir, pkg_name)))) else file.copy(instdir, lockdir, recursive = TRUE, copy.date = TRUE) } else if (more_than_libs) unlink(instdir, recursive = TRUE) if (more_than_libs && dir.exists(instdir)) # On Windows, a DLL cannot be unlinked if in use errmsg("cannot remove earlier installation, is it in use?") dir.create(instdir, recursive = TRUE, showWarnings = FALSE) } pkg_staged_install <- SI <- parse_description_field(desc, "StagedInstall", default = NA) if (is.na(pkg_staged_install)) pkg_staged_install <- staged_install if (have_cross) pkg_staged_install <- FALSE if (pkg_staged_install && libs_only) { pkg_staged_install <- FALSE message("not using staged install with --libs-only") } if (pkg_staged_install && !lock) { pkg_staged_install <- FALSE message("staged installation is only possible with locking") } if (pkg_staged_install) { starsmsg(stars, "using staged installation") final_instdir <- instdir final_lib <- lib final_rpackagedir <- Sys.getenv("R_PACKAGE_DIR") final_rlibs <- Sys.getenv("R_LIBS") final_libpaths <- .libPaths() instdir <- file.path(lockdir, "00new", pkg_name) Sys.setenv(R_PACKAGE_DIR = instdir) dir.create(instdir, recursive = TRUE, showWarnings = FALSE) lib <- file.path(lockdir, "00new") rlibs <- if (nzchar(final_rlibs)) paste(lib, final_rlibs, sep = .Platform$path.sep) else lib Sys.setenv(R_LIBS = rlibs) .libPaths(c(lib, final_libpaths)) } else { if(isFALSE(SI)) starsmsg(stars, "using non-staged installation via StagedInstall field") else if (Sys.getenv("_R_INSTALL_SUPPRESS_NO_STAGED_MESSAGE_") != "yes") starsmsg(stars, "using non-staged installation") } if (preclean) run_clean() if (WINDOWS) { # Installation-time patching was enabled as a temporary measure # during the transition from MSVCRT to UCRT, when packages with # many reverse dependencies had to be updated to link. # URL or a local directory with patches: ("no" to no patching) it_patches_base <- Sys.getenv("_R_INSTALL_TIME_PATCHES_", "no") # The patches are identified by package name. An index is used # to map the name to a directory with patches for a given # package. There may be multiple patches for a single package, # but that hasn't been used. The patches applied to a package # are copied into directory install_time_patches inside the # package installation (so in library, but also in binary # package build) for reference. # The patches are automatically reverted on cleanup, see # revert_install_time_patches, also during R CMD build (see # build.R). The latter is needed to ensure that unpatched source # package tarball is produced when the package native code is # compiled during R CMD build, e.g. to build vignettes. # This feature is experimental, it may be completely removed in # the future. if (!it_patches_base %in% c("no", "disabled", "false", "FALSE")) { patches_idx <- tryCatch({ idxfile <- file(paste0(it_patches_base, "/", "patches_idx.rds")) patches_idx <- readRDS(idxfile) close(idxfile) patches_idx }, error = function(e) NULL) if (is.null(patches_idx)) message("WARNING: installation-time patches will not be applied, could not get the patches index") else { patches_msg <- FALSE for(p in patches_idx[[pkg_name]]) { if (!patches_msg) { patches_msg <- TRUE starsmsg(stars, "applying installation-time patches") } purl <- paste0(it_patches_base, "/", p) have_patch <- nzchar(Sys.which("patch")) if (!have_patch) stop("patch utility is needed for installation-time patching") dir.create("install_time_patches", recursive=TRUE) fname <- paste0("install_time_patches/", basename(p)) if (grepl("^http", purl)) utils::download.file(purl, destfile = fname, mode = "wb") else file.copy(purl, fname) if (system2("patch", args = c("--dry-run", "-p2", "--binary", "--force"), stdin = fname, stdout = NULL, stderr = NULL) != 0) { ## the patch cannot be applied, check if it might ## be reversed if (system2("patch", args = c("--dry-run", "-R", "-p2", "--binary", "--force"), stdin = fname) == 0) message("NOTE: Skipping installation-time patch ", purl, " which seems to be already applied.\n") else message("WARNING: failed to apply patch ", purl, "\n") } else { if (system2("patch", args = c("-p2", "--binary", "--force"), stdin = fname) != 0) ## should not happen as dry-run succeeded message("WARNING: failed to apply patch ", p, "\n") else message("Applied installation-time patch ", purl, " and saved it as ", fname, " in package installation\n") } } } } } if (use_configure) { if (WINDOWS) { if (file.exists("configure.ucrt")) { res <- system("sh ./configure.ucrt") if (res) pkgerrmsg("configuration failed", pkg_name) } else if (file.exists("configure.win")) { res <- system("sh ./configure.win") if (res) pkgerrmsg("configuration failed", pkg_name) } else if (file.exists("configure")) message("\n", " **********************************************\n", " WARNING: this package has a configure script\n", " It probably needs manual configuration\n", " **********************************************\n\n", domain = NA) } else { ## FIXME: should these be quoted? if (file_test("-x", "configure")) { cmd <- paste(paste(configure_vars, collapse = " "), "./configure", paste(configure_args, collapse = " ")) if (debug) message("configure command: ", sQuote(cmd), domain = NA) ## in case the configure script calls SHLIB (some do) cmd <- paste("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_=false", cmd) res <- system(cmd) if (res) pkgerrmsg("configuration failed", pkg_name) } else if (file.exists("configure")) errmsg("'configure' exists but is not executable -- see the 'R Installation and Administration Manual'") } } if (more_than_libs) { for (f in c("NAMESPACE", "LICENSE", "LICENCE", "NEWS", "NEWS.md")) if (file.exists(f)) { file.copy(f, instdir, TRUE) Sys.chmod(file.path(instdir, f), fmode) } res <- try(.install_package_description('.', instdir, built_stamp)) if (inherits(res, "try-error")) pkgerrmsg("installing package DESCRIPTION failed", pkg_name) if (!file.exists(namespace <- file.path(instdir, "NAMESPACE")) ) { if(dir.exists("R")) errmsg("a 'NAMESPACE' file is required") else writeLines("## package without R code", namespace) } } if (install_libs && dir.exists("src") && length(dir("src", all.files = TRUE)) > 2L) { starsmsg(stars, "libs") if (!file.exists(file.path(R.home("include"), "R.h"))) ## maybe even an error? But installing Fortran-based packages should work warning("R include directory is empty -- perhaps need to install R-devel.rpm or similar", call. = FALSE) has_error <- FALSE linkTo <- pkgInfo$LinkingTo if (!is.null(linkTo)) { lpkgs <- sapply(linkTo, function(x) x[[1L]]) ## we checked that these were all available earlier, ## but be cautious in case this changed. paths <- find.package(lpkgs, quiet = TRUE) bpaths <- basename(paths) if (length(paths)) { ## check any version requirements have_vers <- (lengths(linkTo) > 1L) & lpkgs %in% bpaths for (z in linkTo[have_vers]) { p <- z[[1L]] path <- paths[bpaths %in% p] current <- readRDS(file.path(path, "Meta", "package.rds"))$DESCRIPTION["Version"] target <- as.numeric_version(z$version) if (!do.call(z$op, list(as.numeric_version(current), target))) stop(gettextf("package %s %s was found, but %s %s is required by %s", sQuote(p), current, z$op, target, sQuote(pkgname)), call. = FALSE, domain = NA) } clink_cppflags <- paste(paste0("-I'", paths, "/include'"), collapse = " ") Sys.setenv(CLINK_CPPFLAGS = clink_cppflags) } } else clink_cppflags <- "" libdir <- file.path(instdir, paste0("libs", rarch)) dir.create(libdir, showWarnings = FALSE) if (WINDOWS) { owd <- setwd("src") makefiles <- character() if (!is.na(f <- Sys.getenv("R_MAKEVARS_USER", NA_character_))) { if (file.exists(f)) makefiles <- f } else if (file.exists(f <- path.expand("~/.R/Makevars.ucrt"))) makefiles <- f else if (file.exists(f <- path.expand("~/.R/Makevars.win64"))) makefiles <- f else if (file.exists(f <- path.expand("~/.R/Makevars.win"))) makefiles <- f else if (file.exists(f <- path.expand("~/.R/Makevars"))) makefiles <- f if (file.exists(f <- "Makefile.ucrt") || file.exists(f <- "Makefile.win")) { makefiles <- c(f, makefiles) message(paste0(" running 'src/", f, "' ..."), domain = NA) res <- system(paste("make --no-print-directory", paste("-f", shQuote(makefiles), collapse = " "))) if (res == 0L) shlib_install(instdir, rarch) else has_error <- TRUE } else { ## no src/Makefile.win srcs <- dir(pattern = "\\.([cfmM]|cc|cpp|f90|f95|mm)$", all.files = TRUE) archs <- if(have_cross) cross else if (!force_both && !grepl(" x64 ", utils::win.version())) "i386" else { ## see what is installed ## NB, not R.home("bin") f <- dir(file.path(R.home(), "bin")) f[f %in% c("i386", "x64")] } one_only <- !multiarch has_configure_ucrt <- file.exists("../configure.ucrt") if(!one_only && (has_configure_ucrt || file.exists("../configure.win"))) { ## for now, hardcode some exceptions ## These are packages which have arch-independent ## code in configure.win if(pkg_name %notin% c("AnalyzeFMRI", "CORElearn", "PearsonDS", "PKI", "RGtk2", "RNetCDF", "RODBC", "RSclient", "Rcpp", "Runuran", "SQLiteMap", "XML", "arulesSequences", "cairoDevice", "diversitree", "foreign", "fastICA", "glmnet", "gstat", "igraph", "jpeg", "png", "proj4", "randtoolbox", "rgdal", "rngWELL", "rphast", "rtfbs", "sparsenet", "tcltk2", "tiff", "udunits2")) one_only <- sum(nchar(readLines( if(has_configure_ucrt) "../configure.ucrt" else "../configure.win", warn = FALSE), "bytes")) > 0 if(one_only && !force_biarch) { if(parse_description_field(desc, "Biarch", FALSE)) force_biarch <- TRUE else if (has_configure_ucrt) warning("this package has a non-empty 'configure.ucrt' file,\nso building only the main architecture\n", call. = FALSE, domain = NA) else warning("this package has a non-empty 'configure.win' file,\nso building only the main architecture\n", call. = FALSE, domain = NA) } } if(force_biarch) one_only <- FALSE if(one_only || length(archs) < 2L) has_error <- run_shlib(pkg_name, srcs, instdir, rarch, use_LTO) else { setwd(owd) test_archs <- archs for(arch in archs) { message("", domain = NA) # a blank line starsmsg("***", "arch - ", arch) ss <- paste0("src-", arch) dir.create(ss, showWarnings = FALSE) file.copy(Sys.glob("src/*"), ss, recursive = TRUE) ## avoid read-only files/dir such as nested .svn .Call(C_dirchmod, ss, group.writable) setwd(ss) ra <- paste0("/", arch) Sys.setenv(R_ARCH = ra, R_ARCH_BIN = ra) has_error <- run_shlib(pkg_name, srcs, instdir, ra, use_LTO) setwd(owd) if (has_error) break } } } setwd(owd) } else { # not WINDOWS if (file.exists("src/Makefile")) { arch <- substr(rarch, 2, 1000) starsmsg(stars, "arch - ", arch) owd <- setwd("src") system_makefile <- file.path(R.home(), paste0("etc", rarch), "Makeconf") makefiles <- c(system_makefile, makevars_site(), "Makefile", makevars_user()) res <- system(paste(MAKE, paste("-f", shQuote(makefiles), collapse = " "))) if (res == 0L) shlib_install(instdir, rarch) else has_error <- TRUE setwd(owd) } else { ## no src/Makefile owd <- setwd("src") srcs <- dir(pattern = "\\.([cfmM]|cc|cpp|f90|f95|mm)$", all.files = TRUE) ## This allows Makevars to set OBJECTS or its own targets. allfiles <- if (file.exists("Makevars")) c("Makevars", srcs) else srcs wd2 <- setwd(file.path(R.home("bin"), "exec")) archs <- Sys.glob("*") setwd(wd2) if (length(allfiles)) { use_LTO <- if (!is.na(use_LTO)) use_LTO else parse_description_field(desc, "UseLTO", default = NA) ## if there is an executable configure script we install only the main ## sub-architecture if (!multiarch || length(archs) <= 1 || file_test("-x", "../configure")) { if (nzchar(rarch)) starsmsg("***", "arch - ", substr(rarch, 2, 1000)) has_error <- run_shlib(pkg_name, srcs, instdir, rarch, use_LTO) } else { setwd(owd) test_archs <- archs for(arch in archs) { if (arch == "R") { ## top-level, so one arch without subdirs has_error <- run_shlib(pkg_name, srcs, instdir, "", use_LTO) } else { starsmsg("***", "arch - ", arch) ss <- paste0("src-", arch) dir.create(ss, showWarnings = FALSE) file.copy(Sys.glob("src/*"), ss, recursive = TRUE) setwd(ss) ra <- paste0("/", arch) ## FIXME: do this lower down Sys.setenv(R_ARCH = ra) has_error <- run_shlib(pkg_name, srcs, instdir, ra, use_LTO) Sys.setenv(R_ARCH = rarch) setwd(owd) if (has_error) break } } } } else warning("no source files found", call. = FALSE) } setwd(owd) } if (has_error) pkgerrmsg("compilation failed", pkg_name) ## if we have subarchs, update DESCRIPTION fi <- file.info(Sys.glob(file.path(instdir, "libs", "*"))) dirs <- basename(row.names(fi[fi$isdir %in% TRUE, ])) ## avoid DLLs installed by rogue packages if(WINDOWS) dirs <- dirs[dirs %in% c("i386", "x64")] if (length(dirs)) { descfile <- file.path(instdir, "DESCRIPTION") olddesc <- readLines(descfile, warn = FALSE) olddesc <- filtergrep("^Archs:", olddesc, useBytes = TRUE) newdesc <- c(olddesc, paste("Archs:", paste(dirs, collapse = ", ")) ) writeLines(newdesc, descfile, useBytes = TRUE) saveRDS(.split_description(.read_description(descfile)), file.path(instdir, "Meta", "package.rds")) } } else if (multiarch) { # end of src dir if (WINDOWS) { wd2 <- setwd(file.path(R.home(), "bin")) # not R.home("bin") archs <- Sys.glob("*") setwd(wd2) test_archs <- archs[archs %in% c("i386", "x64")] } else { wd2 <- setwd(file.path(R.home("bin"), "exec")) test_archs <- Sys.glob("*") setwd(wd2) } } if (WINDOWS && "x64" %in% test_archs) { ## we cannot actually test x64 unless this is 64-bit ## Windows, even if it is installed. if (!grepl(" x64 ", utils::win.version())) test_archs <- "i386" } if (have_cross) Sys.unsetenv("R_ARCH") if (WINDOWS && dir.exists("install_time_patches")) file.copy("install_time_patches", instdir, recursive = TRUE) ## R files must start with a letter if (install_R && dir.exists("R") && length(dir("R"))) { starsmsg(stars, "R") dir.create(file.path(instdir, "R"), recursive = TRUE, showWarnings = FALSE) ## This cannot be done in a C locale res <- try(.install_package_code_files(".", instdir)) if (inherits(res, "try-error")) pkgerrmsg("unable to collate and parse R files", pkg_name) if (file.exists(f <- file.path("R", "sysdata.rda"))) { comp <- TRUE ## (We set .libPaths) if(!is.na(lazycompress <- desc["SysDataCompression"])) { comp <- switch(lazycompress, "none" = FALSE, "gzip" = TRUE, "bzip2" = 2L, "xz" = 3L, TRUE) # default to gzip } else if(file.size(f) > 1e6) comp <- 3L # "xz" res <- try(sysdata2LazyLoadDB(f, file.path(instdir, "R"), compress = comp)) if (inherits(res, "try-error")) pkgerrmsg("unable to build sysdata DB", pkg_name) } if (fake) { ## Fix up hook functions so they do not attempt to ## (un)load missing compiled code, initialize ... ## This does stop them being tested at all. if (file.exists("NAMESPACE")) { cat("", '.onLoad <- .onAttach <- function(lib, pkg) NULL', '.onUnload <- function(libpaths) NULL', sep = "\n", file = file.path(instdir, "R", pkg_name), append = TRUE) ## ## Tweak fake installation to provide an 'empty' ## useDynLib() for the time being. Completely ## removing the directive results in checkFF() ## being too aggresive in the case where the ## presence of the directive enables unambiguous ## symbol resolution w/out 'PACKAGE' arguments. ## However, empty directives are not really meant ## to work ... ## encoding issues ... so need useBytes = TRUE ## FIXME: some packages have useDynLib() ## spread over several lines. writeLines(sub("useDynLib.*", 'useDynLib("")', readLines("NAMESPACE", warn = FALSE), perl = TRUE, useBytes = TRUE), file.path(instdir, "NAMESPACE")) ## } else { cat("", '.onLoad <- function (libname, pkgname) NULL', '.onAttach <- function (libname, pkgname) NULL', '.onDetach <- function(libpath) NULL', '.onUnload <- function(libpath) NULL', '.Last.lib <- function(libpath) NULL', sep = "\n", file = file.path(instdir, "R", pkg_name), append = TRUE) } } } # end of R ## data files must not be hidden: data() may ignore them if (install_data && dir.exists("data") && length(dir("data"))) { starsmsg(stars, "data") files <- Sys.glob(file.path("data", "*")) # ignores dotfiles if (length(files)) { is <- file.path(instdir, "data") dir.create(is, recursive = TRUE, showWarnings = FALSE) file.remove(Sys.glob(file.path(instdir, "data", "*"))) file.copy(files, is, TRUE) thislazy <- parse_description_field(desc, "LazyData", default = lazy_data) if (!thislazy && resave_data) { paths <- Sys.glob(c(file.path(is, "*.rda"), file.path(is, "*.RData"))) if (length(paths)) { starsmsg(paste0(stars, "*"), "resaving rda files") resaveRdaFiles(paths, compress = "auto") } } Sys.chmod(Sys.glob(file.path(instdir, "data", "*")), fmode) if (thislazy) { starsmsg(paste0(stars, "*"), "moving datasets to lazyload DB") ## 'it is possible that data in a package will ## make use of the code in the package, so ensure ## the package we have just installed is on the ## library path.' ## (We set .libPaths) lazycompress <- desc["LazyDataCompression"] if(!is.na(lazycompress)) data_compress <- switch(lazycompress, "none" = FALSE, "gzip" = TRUE, "bzip2" = 2L, "xz" = 3L, ## perhaps error? TRUE) # default to gzip res <- try(data2LazyLoadDB(pkg_name, lib, compress = data_compress)) if (inherits(res, "try-error")) pkgerrmsg("lazydata failed", pkg_name) } } else warning("empty 'data' directory", call. = FALSE) } ## demos must start with a letter if (install_demo && dir.exists("demo") && length(dir("demo"))) { starsmsg(stars, "demo") dir.create(file.path(instdir, "demo"), recursive = TRUE, showWarnings = FALSE) file.remove(Sys.glob(file.path(instdir, "demo", "*"))) res <- try(.install_package_demos(".", instdir)) if (inherits(res, "try-error")) pkgerrmsg("ERROR: installing demos failed") Sys.chmod(Sys.glob(file.path(instdir, "demo", "*")), fmode) } ## dotnames are ignored. if (install_exec && dir.exists("exec") && length(dir("exec"))) { starsmsg(stars, "exec") dir.create(file.path(instdir, "exec"), recursive = TRUE, showWarnings = FALSE) file.remove(Sys.glob(file.path(instdir, "exec", "*"))) files <- Sys.glob(file.path("exec", "*")) if (length(files)) { file.copy(files, file.path(instdir, "exec"), TRUE) if (!WINDOWS) Sys.chmod(Sys.glob(file.path(instdir, "exec", "*")), dmode) } } if (install_inst && dir.exists("inst") && length(dir("inst", all.files = TRUE)) > 2L) { starsmsg(stars, "inst") i_dirs <- list.dirs("inst")[-1L] # not inst itself i_dirs <- filtergrep(.vc_dir_names_re, i_dirs) ## This ignores any restrictive permissions in the source ## tree, since the later .Call(C_dirchmod) call will ## fix the permissions. ## handle .Rinstignore: ignore_file <- ".Rinstignore" ignore <- if (file.exists(ignore_file)) { ignore <- readLines(ignore_file, warn = FALSE) ignore[nzchar(ignore)] } else character() for(e in ignore) i_dirs <- filtergrep(e, i_dirs, perl = TRUE, ignore.case = TRUE) lapply(gsub("^inst", quote_replacement(instdir), i_dirs), function(p) dir.create(p, FALSE, TRUE)) # be paranoid i_files <- list.files("inst", all.files = TRUE, full.names = TRUE, recursive = TRUE) i_files <- filtergrep(.vc_dir_names_re, i_files) for(e in ignore) i_files <- filtergrep(e, i_files, perl = TRUE, ignore.case = TRUE) i_files <- i_files %w/o% c("inst/doc/Rplots.pdf", "inst/doc/Rplots.ps") i_files <- filtergrep("inst/doc/.*[.](log|aux|bbl|blg|dvi)$", i_files, perl = TRUE, ignore.case = TRUE) ## Temporary kludge if (!dir.exists("vignettes") && pkgname %notin% c("RCurl")) i_files <- filtergrep("inst/doc/.*[.](png|jpg|jpeg|gif|ps|eps)$", i_files, perl = TRUE, ignore.case = TRUE) i_files <- i_files %w/o% "Makefile" i2_files <- gsub("^inst", quote_replacement(instdir), i_files) file.copy(i_files, i2_files) if (!WINDOWS) { ## make executable if the source file was (for owner) modes <- file.mode(i_files) execs <- as.logical(modes & as.octmode("100")) Sys.chmod(i2_files[execs], dmode) } if (compact_docs) { pdfs <- dir(file.path(instdir, "doc"), pattern="\\.pdf", recursive = TRUE, full.names = TRUE, all.files = TRUE) res <- compactPDF(pdfs, gs_quality = "none") ## print selectively print(res[res$old > 1e5, ]) } } rait <- Sys.getenv("R_ALWAYS_INSTALL_TESTS", "FALSE") install_tests <- install_tests || config_val_to_logical(rait) if (install_tests && dir.exists("tests") && length(dir("tests", all.files = TRUE)) > 2L) { starsmsg(stars, "tests") file.copy("tests", instdir, recursive = TRUE) } ## LazyLoading/Compiling if (install_R && dir.exists("R") && length(dir("R"))) { BC <- if (!is.na(byte_compile)) byte_compile else parse_description_field(desc, "ByteCompile", default = TRUE) rcps <- Sys.getenv("R_COMPILE_PKGS") rcp <- switch(rcps, "TRUE"=, "true"=, "True"=, "yes"=, "Yes"= 1, "FALSE"=,"false"=,"False"=, "no"=, "No" = 0, as.numeric(rcps)) if (!is.na(rcp)) BC <- (rcp > 0) if (BC) { starsmsg(stars, "byte-compile and prepare package for lazy loading") ## need to disable JIT cmd <- c("Sys.setenv(R_ENABLE_JIT = 0L)", "invisible(compiler::enableJIT(0))", "invisible(compiler::compilePKGS(1L))", "compiler::setCompilerOptions(suppressAll = FALSE)", "compiler::setCompilerOptions(suppressUndefined = TRUE)", "compiler::setCompilerOptions(suppressNoSuperAssignVar = TRUE);") } else { starsmsg(stars, "preparing package for lazy loading") cmd <- "" } keep.source <- parse_description_field(desc, "KeepSource", default = keep.source) ## Some people change current directory in their R profile, but ## at least .getRequiredPackages needs to find the DESCRIPTION ## file cmd <- append(cmd, paste0("setwd(", quote_path(getwd()), ")")) ## Something above, e.g. lazydata, might have loaded the namespace cmd <- append(cmd, paste0("if (isNamespaceLoaded(\"",pkg_name, "\"))", " unloadNamespace(\"", pkg_name, "\")")) cmd <- append(cmd, "suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))") if (pkg_staged_install) set.install.dir <- paste0(", set.install.dir = ", quote_path(final_instdir)) else set.install.dir <- "" cmd <- append(cmd, paste0("tools:::makeLazyLoading(\"", pkg_name, "\", ", quote_path(lib), ", ", "keep.source = ", keep.source, ", ", "keep.parse.data = ", keep.parse.data, set.install.dir, ")")) cmd <- paste(cmd, collapse="\n") out <- R_runR_deps_only(cmd, setRlibs(LinkingTo = TRUE, quote = TRUE)) if(length(out)) cat(paste(c(out, ""), collapse = "\n")) if(length(attr(out, "status"))) pkgerrmsg("lazy loading failed", pkg_name) } if (install_help) { starsmsg(stars, "help") if (!dir.exists("man") || !length(list_files_with_type("man", "docs"))) cat("No man pages found in package ", sQuote(pkg_name), "\n") encoding <- desc["Encoding"] if (is.na(encoding)) encoding <- "unknown" res <- try(.install_package_Rd_objects(".", instdir, encoding)) if (inherits(res, "try-error")) pkgerrmsg("installing Rd objects failed", pkg_name) starsmsg(paste0(stars, "*"), "installing help indices") ## always want HTML package index .writePkgIndices(pkg_dir, instdir) if (build_help) { ## This is used as the default outputEncoding for latex outenc <- desc["Encoding"] if (is.na(outenc)) outenc <- "latin1" # or ASCII .convertRdfiles(pkg_dir, instdir, types = build_help_types, outenc = outenc) } if (dir.exists(figdir <- file.path(pkg_dir, "man", "figures"))) { starsmsg(paste0(stars, "*"), "copying figures") dir.create(destdir <- file.path(instdir, "help", "figures")) file.copy(Sys.glob(c(file.path(figdir, "*.png"), file.path(figdir, "*.jpg"), file.path(figdir, "*.jpeg"), file.path(figdir, "*.svg"), file.path(figdir, "*.pdf"))), destdir) } } ## pkg indices: this also tangles the vignettes (if installed) if (install_inst || install_demo || install_help) { starsmsg(stars, "building package indices") cmd <- c("tools:::.install_package_indices(\".\",", quote_path(instdir), ")") cmd <- paste(cmd, collapse="\n") out <- R_runR_deps_only(cmd, setRlibs(LinkingTo = TRUE, quote = TRUE)) if(length(out)) cat(paste(c(out, ""), collapse = "\n")) if (length(attr(out, "status"))) errmsg("installing package indices failed") if(dir.exists("vignettes")) { starsmsg(stars, "installing vignettes") enc <- desc["Encoding"] if (is.na(enc)) enc <- "" if (!fake && file_test("-f", file.path("build", "vignette.rds"))) installer <- .install_package_vignettes3 else ## handle pre-3.0.2 tarballs ## and installation from package sources, ## including by temp_install_pkg() during R CMD build installer <- .install_package_vignettes2 res <- try(installer(".", instdir, enc)) if (inherits(res, "try-error")) errmsg("installing vignettes failed") } } ## Install a dump of the parsed NAMESPACE file ## For a fake install, use the modified NAMESPACE file we installed if (install_R && file.exists("NAMESPACE")) { res <- try(.install_package_namespace_info(if(fake) instdir else ".", instdir)) if (inherits(res, "try-error")) errmsg("installing namespace metadata failed") } if (clean) run_clean() do_test_load <- function(extra_cmd = NULL) { ## Do this in a separate R process, in case it crashes R. ## FIXME: maybe the quoting as 'lib' is not quite good enough ## On a Unix-alike this calls system(input=) ## and that uses a temporary file and redirection. cmd <- paste0("tools:::.test_load_package('", pkg_name, "', ", quote_path(lib), ")") if (!is.null(extra_cmd)) cmd <- paste0(cmd, "\n", extra_cmd) ## R_LIBS was set already, but Rprofile/Renviron may change it tlim <- get_timeout(Sys.getenv("_R_INSTALL_TEST_LOAD_ELAPSED_TIMEOUT_")) if (length(test_archs) > 1L) { msgs <- character() for (arch in test_archs) { starsmsg("***", "arch - ", arch) out <- R_runR_deps_only(cmd, deps_only_env = setRlibs(lib0, self = TRUE, quote = TRUE), arch = arch, timeout = tlim, multiarch = TRUE) if(length(attr(out, "status"))) msgs <- c(msgs, arch) if(length(out)) cat(paste(c(out, ""), collapse = "\n")) } if (length(msgs)) { msg <- paste("loading failed for", paste(sQuote(msgs), collapse = ", ")) errmsg(msg) # does not return } } else { out <- R_runR_deps_only(cmd, deps_only_env = setRlibs(lib0, self = TRUE, quote = TRUE), timeout = tlim) if(length(out)) { cat(paste(c(out, ""), collapse = "\n")) } if(length(attr(out, "status"))) errmsg("loading failed") # does not return } } if (test_load && !have_cross) { if (pkg_staged_install) starsmsg(stars, "testing if installed package can be loaded from temporary location") else starsmsg(stars, "testing if installed package can be loaded") do_test_load() } if (pkg_staged_install) { if (WINDOWS) { unlink(final_instdir, recursive = TRUE) # needed for file.rename if (!file.rename(instdir, final_instdir)) { if (dir.exists(instdir) && !dir.exists(final_instdir)) { message("WARNING: moving package to final location failed, copying instead") ret <- file.copy(instdir, dirname(final_instdir), recursive = TRUE, copy.date = TRUE) if (any(!ret)) errmsg(" copying to final location failed") unlink(instdir, recursive = TRUE) } else errmsg(" moving to final location failed") } } else { patch_rpaths() unlink(final_instdir, recursive = TRUE) # needed for mv on some file systems, even though # according to POSIX mv should work when the target is an # empty directory owd <- setwd(startdir) status <- system(paste("mv -f", shQuote(instdir), shQuote(dirname(final_instdir)))) if (status) errmsg(" moving to final location failed") setwd(owd) } instdir <- final_instdir lib <- final_lib Sys.setenv(R_PACKAGE_DIR = final_rpackagedir) Sys.setenv(R_LIBS = final_rlibs) .libPaths(final_libpaths) if (test_load) { starsmsg(stars, "testing if installed package can be loaded from final location") # The test for hard-coded installation path is done together # with test loading to save time. The test is intentionally # run on a loaded package, to allow for paths to be fixed in # .onLoad and loadNamespace(). serf <- tempfile() cmd <- paste0("f <- base::file(", quote_path(serf), ", \"wb\")") cmd <- append(cmd, paste0("base::invisible(base::suppressWarnings(base::serialize(", "base::as.list(base::getNamespace(\"", pkg_name, "\"), all.names=TRUE), f)))")) cmd <- append(cmd, "base::close(f)") do_test_load(extra_cmd = paste(cmd, collapse = "\n")) starsmsg(stars, "testing if installed package keeps a record of temporary installation path") r <- readBin(serf, "raw", n=file.size(serf)) unlink(serf) if (length(grepRaw("00new", r, fixed = TRUE, all = FALSE, value = FALSE))) errmsg("hard-coded installation path: ", "please report to the package maintainer and use ", sQuote("--no-staged-install")) } } if (do_strip_lib && nzchar(strip_cmd <- Sys.getenv("R_STRIP_STATIC_LIB")) && length(a_s <- Sys.glob(file.path(file.path(lib, curPkg), "lib", "*.a")))) { if(length(a_s) > 1L) starsmsg(stars, "stripping static libraries under lib") else starsmsg(stars, "stripping static library under lib") system(paste(c(strip_cmd, shQuote(a_s)), collapse = " ")) } if (do_strip_lib && nzchar(strip_cmd <- Sys.getenv("R_STRIP_SHARED_LIB")) && length(so_s <- Sys.glob(file.path(file.path(lib, curPkg), "lib", paste0("*", SHLIB_EXT))))) { if(length(so_s) > 1L) starsmsg(stars, "stripping dynamic libraries under lib") else starsmsg(stars, "stripping dynamic library under lib") system(paste(c(strip_cmd, shQuote(so_s)), collapse = " ")) } } ## do_install_source options(showErrorCalls = FALSE) pkgs <- character() if (is.null(args)) { args <- commandArgs(TRUE) ## it seems that splits on spaces, so try harder. args <- paste(args, collapse = " ") args <- strsplit(args,'nextArg', fixed = TRUE)[[1L]][-1L] } args0 <- args startdir <- getwd() if (is.null(startdir)) stop("current working directory cannot be ascertained") lib <- lib0 <- "" clean <- FALSE preclean <- FALSE debug <- FALSE static_html <- nzchar(system.file("html", "mean.html", package="base")) build_html <- static_html build_latex <- FALSE build_example <- FALSE use_configure <- TRUE configure_args <- character() configure_vars <- character() fake <- FALSE ## lazy <- TRUE lazy_data <- FALSE byte_compile <- NA # means take from DESCRIPTION file. staged_install <- NA # means not given by command line argument ## Next is not very useful unless R CMD INSTALL reads a startup file lock <- getOption("install.lock", NA) # set for overall or per-package pkglock <- FALSE # set for per-package locking libs_only <- FALSE tar_up <- zip_up <- FALSE shargs <- character() multiarch <- TRUE force_biarch <- FALSE force_both <- FALSE test_load <- TRUE merge <- FALSE dsym <- nzchar(Sys.getenv("PKG_MAKE_DSYM")) get_user_libPaths <- FALSE data_compress <- TRUE # FALSE (none), TRUE (gzip), 2 (bzip2), 3 (xz) resave_data <- FALSE compact_docs <- FALSE keep.source <- getOption("keep.source.pkgs") keep.parse.data <- getOption("keep.parse.data.pkgs") use_LTO <- NA # means take from DESCRIPTION file. built_stamp <- character() install_libs <- TRUE install_R <- TRUE install_data <- TRUE install_demo <- TRUE install_exec <- TRUE install_inst <- TRUE install_help <- TRUE install_tests <- FALSE do_strip <- do_strip_lib <- FALSE while(length(args)) { a <- args[1L] if (a %in% c("-h", "--help")) { Usage() do_exit(0) } else if (a %in% c("-v", "--version")) { cat("R add-on package installer: ", R.version[["major"]], ".", R.version[["minor"]], " (r", R.version[["svn rev"]], ")\n", sep = "") cat("", .R_copyright_msg(2000), "This is free software; see the GNU General Public License version 2", "or later for copying conditions. There is NO warranty.", sep = "\n") do_exit(0) } else if (a %in% c("-c", "--clean")) { clean <- TRUE shargs <- c(shargs, "--clean") } else if (a == "--preclean") { preclean <- TRUE shargs <- c(shargs, "--preclean") } else if (a %in% c("-d", "--debug")) { debug <- TRUE } else if (a == "--no-configure") { use_configure <- FALSE } else if (a == "--no-docs") { build_html <- build_latex <- build_example <- FALSE } else if (a == "--no-html") { build_html <- FALSE } else if (a == "--html") { build_html <- TRUE } else if (a == "--latex") { build_latex <- TRUE } else if (a == "--example") { build_example <- TRUE } else if (a == "--use-zip-data") { warning("use of '--use-zip-data' is defunct", call. = FALSE, domain = NA) warning("use of '--use-zip-data' is deprecated", call. = FALSE, domain = NA) } else if (a == "--auto-zip") { warning("'--auto-zip' is defunct", call. = FALSE, domain = NA) } else if (a == "-l") { if (length(args) >= 2L) {lib <- args[2L]; args <- args[-1L]} else stop("-l option without value", call. = FALSE) } else if (substr(a, 1, 10) == "--library=") { lib <- substr(a, 11, 1000) } else if (substr(a, 1, 17) == "--configure-args=") { configure_args <- c(configure_args, substr(a, 18, 1000)) } else if (substr(a, 1, 17) == "--configure-vars=") { configure_vars <- c(configure_vars, substr(a, 18, 1000)) } else if (a == "--fake") { fake <- TRUE } else if (a == "--no-lock") { lock <- pkglock <- FALSE } else if (a == "--lock") { lock <- TRUE; pkglock <- FALSE } else if (a == "--pkglock") { lock <- pkglock <- TRUE } else if (a == "--libs-only") { libs_only <- TRUE } else if (a == "--no-multiarch") { multiarch <- FALSE } else if (a == "--force-biarch") { force_biarch <- TRUE } else if (a == "--compile-both") { force_both <- TRUE } else if (a == "--maybe-get-user-libPaths") { get_user_libPaths <- TRUE } else if (a == "--build") { if (WINDOWS) zip_up <- TRUE else tar_up <- TRUE } else if (substr(a, 1, 16) == "--data-compress=") { dc <- substr(a, 17, 1000) dc <- match.arg(dc, c("none", "gzip", "bzip2", "xz")) data_compress <- switch(dc, "none" = FALSE, "gzip" = TRUE, "bzip2" = 2, "xz" = 3) } else if (a == "--resave-data") { resave_data <- TRUE } else if (a == "--install-tests") { install_tests <- TRUE } else if (a == "--no-inst") { install_inst <- FALSE } else if (a == "--no-R") { install_R <- FALSE } else if (a == "--no-libs") { install_libs <- FALSE } else if (a == "--no-data") { install_data <- FALSE } else if (a == "--no-demo") { install_demo <- FALSE } else if (a == "--no-exec") { install_exec <- FALSE } else if (a == "--no-help") { install_help <- FALSE } else if (a == "--no-test-load") { test_load <- FALSE } else if (a == "--no-clean-on-error") { clean_on_error <- FALSE } else if (a == "--merge-multiarch") { merge <- TRUE } else if (a == "--compact-docs") { compact_docs <- TRUE } else if (a == "--with-keep.source") { keep.source <- TRUE } else if (a == "--without-keep.source") { keep.source <- FALSE } else if (a == "--with-keep.parse.data") { keep.parse.data <- TRUE } else if (a == "--without-keep.parse.data") { keep.parse.data <- FALSE } else if (a == "--byte-compile") { byte_compile <- TRUE } else if (a == "--no-byte-compile") { byte_compile <- FALSE } else if (a == "--use-LTO") { use_LTO <- TRUE } else if (a == "--no-use-LTO") { use_LTO <- FALSE } else if (a == "--staged-install") { staged_install <- TRUE } else if (a == "--no-staged-install") { staged_install <- FALSE } else if (a == "--dsym") { dsym <- TRUE } else if (a == "--strip") { do_strip <- TRUE } else if (a == "--strip-lib") { do_strip_lib <- TRUE } else if (substr(a, 1, 18) == "--built-timestamp=") { built_stamp <- substr(a, 19, 1000) } else if (startsWith(a, "-")) { message("Warning: unknown option ", sQuote(a), domain = NA) } else pkgs <- c(pkgs, a) args <- args[-1L] } if (keep.tmpdir) { make_tmpdir <- function(prefix, nchars = 8, ntries = 100) { for(i in 1:ntries) { name <- paste(sample(c(0:9, letters, LETTERS), nchars, replace=TRUE), collapse="") path <- paste(prefix, name, sep = "/") if (dir.create(path, showWarnings = FALSE, recursive = T)) { return(path) } } stop("cannot create unique directory for build") } tmpdir <- make_tmpdir(user.tmpdir) } else { tmpdir <- tempfile("R.INSTALL") if (!dir.create(tmpdir)) stop("cannot create temporary directory") } if (merge) { if (length(pkgs) != 1L || !file_test("-f", pkgs)) stop("ERROR: '--merge-multiarch' applies only to a single tarball", call. = FALSE) if (WINDOWS) { f <- dir(file.path(R.home(), "bin")) archs <- f[f %in% c("i386", "x64")] if (length(archs) > 1L) { args <- args0 %w/o% c("--merge-multiarch", "--build") ## this will report '* DONE (foo)' if it works, which ## R CMD check treats as an indication of success. ## so use a backdoor to suppress it. Sys.setenv("_R_INSTALL_NO_DONE_" = "yes") for (arch in archs) { cmd <- c(shQuote(file.path(R.home(), "bin", arch, "Rcmd.exe")), "INSTALL", shQuote(args), "--no-multiarch") if (arch == "x64") { ## this will suppress stars message "using ## non-staged installation", which could otherwise ## be turned into R CMD check note Sys.setenv("_R_INSTALL_SUPPRESS_NO_STAGED_MESSAGE_" = "yes") cmd <- c(cmd, "--libs-only --no-staged-install", if(zip_up) "--build") Sys.unsetenv("_R_INSTALL_NO_DONE_") } cmd <- paste(cmd, collapse = " ") if (debug) message("about to run ", cmd, domain = NA) message("\n", "install for ", arch, "\n", domain = NA) res <- system(cmd) if (arch == "x64") Sys.unsetenv("_R_INSTALL_SUPPRESS_NO_STAGED_MESSAGE_") if(res) break } } } else { archs <- dir(file.path(R.home("bin"), "exec")) if (length(archs) > 1L) { args <- args0 %w/o% c("--merge-multiarch", "--build") ## this will report '* DONE (foo)' if it works, which ## R CMD check treats as an indication of success. ## so use a backdoor to suppress it. Sys.setenv("_R_INSTALL_NO_DONE_" = "yes") last <- archs[length(archs)] for (arch in archs) { cmd <- c(shQuote(file.path(R.home("bin"), "R")), "--arch", arch, "CMD", "INSTALL", shQuote(args), "--no-multiarch") if (arch != archs[1L]) { ## this will suppress stars message "using ## non-staged installation", which could otherwise ## be turned into R CMD check note Sys.setenv("_R_INSTALL_SUPPRESS_NO_STAGED_MESSAGE_" = "yes") cmd <- c(cmd, "--libs-only --no-staged-install") } if (arch == last) { Sys.unsetenv("_R_INSTALL_NO_DONE_") if(tar_up) cmd <- c(cmd, "--build") } cmd <- paste(cmd, collapse = " ") if (debug) message("about to run ", cmd, domain = NA) message("\n", "install for ", arch, "\n", domain = NA) res <- system(cmd) if (arch != archs[1L]) Sys.unsetenv("_R_INSTALL_SUPPRESS_NO_STAGED_MESSAGE_") if(res) break } } } if (length(archs) > 1L) { if (res) do_exit_on_error() do_cleanup() on.exit() return(invisible()) } message("only one architecture so ignoring '--merge-multiarch'", domain = NA) } ## now unpack tarballs and do some basic checks allpkgs <- character() for(pkg in pkgs) { if (debug) message("processing ", sQuote(pkg), domain = NA) if (file_test("-f", pkg)) { if (WINDOWS && endsWith(pkg, ".zip")) { if (debug) message("a zip file", domain = NA) pkgname <- basename(pkg) pkgname <- sub("\\.zip$", "", pkgname) pkgname <- sub("_[0-9.-]+$", "", pkgname) allpkgs <- c(allpkgs, pkg) next } if (debug) message("a file", domain = NA) of <- dir(tmpdir, full.names = TRUE) ## force the use of internal untar unless over-ridden ## so e.g. .tar.xz works everywhere if (utils::untar(pkg, exdir = tmpdir, tar = Sys.getenv("R_INSTALL_TAR", "internal"))) errmsg("error unpacking tarball") ## Now see what we got nf <- dir(tmpdir, full.names = TRUE) new <- nf %w/o% of if (!length(new)) errmsg("cannot extract package from ", sQuote(pkg)) if (length(new) > 1L) errmsg("extracted multiple files from ", sQuote(pkg)) if (dir.exists(new)) pkgname <- basename(new) else errmsg("cannot extract package from ", sQuote(pkg)) if (file.exists(file.path(tmpdir, pkgname, "DESCRIPTION"))) { allpkgs <- c(allpkgs, file.path(tmpdir, pkgname)) } else errmsg("cannot extract package from ", sQuote(pkg)) } else if (file.exists(file.path(pkg, "DESCRIPTION"))) { if (debug) message("a directory", domain = NA) pkgname <- basename(pkg) allpkgs <- c(allpkgs, fullpath(pkg)) } else { warning("invalid package ", sQuote(pkg), call. = FALSE) next } } if (!length(allpkgs)) stop("ERROR: no packages specified", call.=FALSE) if (!nzchar(lib)) { lib <- if (get_user_libPaths) { ## need .libPaths()[1L] *after* the site- and user-initialization system(paste(shQuote(file.path(R.home("bin"), "Rscript")), "-e 'cat(.libPaths()[1L])'"), intern = TRUE) } else .libPaths()[1L] starsmsg(stars, "installing to library ", sQuote(lib)) } else { lib0 <- lib <- path.expand(lib) ## lib is allowed to be a relative path. ## should be OK below, but be sure. cwd <- tryCatch(setwd(lib), error = function(e) stop(gettextf("ERROR: cannot cd to directory %s", sQuote(lib)), call. = FALSE, domain = NA)) lib <- getwd() setwd(cwd) } ok <- dir.exists(lib) if (ok) { if (WINDOWS) { ## file.access is unreliable on Windows ## the only known reliable way is to try it fn <- file.path(lib, paste0("_test_dir_", Sys.getpid())) unlink(fn, recursive = TRUE) # precaution res <- try(dir.create(fn, showWarnings = FALSE)) if (inherits(res, "try-error") || !res) ok <- FALSE else unlink(fn, recursive = TRUE) } else ok <- file.access(lib, 2L) == 0L } if (!ok) stop("ERROR: no permission to install to directory ", sQuote(lib), call. = FALSE) group.writable <- if(WINDOWS) FALSE else { ## install package group-writable iff in group-writable lib d <- as.octmode("020") (file.mode(lib) & d) == d ## TRUE iff g-bit is "w" } if (libs_only) { install_R <- FALSE install_data <- FALSE install_demo <- FALSE install_exec <- FALSE install_inst <- FALSE install_help <- FALSE } more_than_libs <- !libs_only ## if(!WINDOWS && !more_than_libs) test_load <- FALSE mk_lockdir <- function(lockdir) { if (file.exists(lockdir)) { message("ERROR: failed to lock directory ", sQuote(lib), " for modifying\nTry removing ", sQuote(lockdir), domain = NA) do_cleanup_tmpdir() do_exit(status = 3) } dir.create(lockdir, recursive = TRUE) if (!dir.exists(lockdir)) { message("ERROR: failed to create lock directory ", sQuote(lockdir), domain = NA) do_cleanup_tmpdir() do_exit(status = 3) } if (debug) starsmsg(stars, "created lock directory ", sQuote(lockdir)) } if (is.na(lock)) { lock <- TRUE pkglock <- length(allpkgs) == 1L } if (lock && !pkglock) { lockdir <- file.path(lib, "00LOCK") mk_lockdir(lockdir) } if (is.na(staged_install)) { # environment variable intended as temporary rsi <- Sys.getenv("R_INSTALL_STAGED") rsi <- switch(rsi, "TRUE"=, "true"=, "True"=, "yes"=, "Yes"= 1, "FALSE"=,"false"=,"False"=, "no"=, "No" = 0, as.numeric(rsi)) if (!is.na(rsi)) staged_install <- (rsi > 0) else staged_install <- TRUE } if ((tar_up || zip_up) && fake) stop("building a fake installation is disallowed") if (fake) { use_configure <- FALSE if("--html" %notin% args0) build_html <- FALSE build_latex <- FALSE build_example <- FALSE install_libs <- FALSE install_demo <- FALSE install_exec <- FALSE # install_inst <- FALSE } build_help_types <- character() if (build_html) build_help_types <- c(build_help_types, "html") if (build_latex) build_help_types <- c(build_help_types, "latex") if (build_example) build_help_types <- c(build_help_types, "example") build_help <- length(build_help_types) > 0L if (debug) starsmsg(stars, "build_help_types=", paste(build_help_types, collapse = " ")) if (debug) starsmsg(stars, "DBG: 'R CMD INSTALL' now doing do_install()") for(pkg in allpkgs) { if (pkglock) { lockdir <- file.path(lib, paste0("00LOCK-", basename(pkg))) mk_lockdir(lockdir) } do_install(pkg) } do_cleanup() on.exit() invisible() } ## .install_packages() ## for R CMD SHLIB on all platforms .SHLIB <- function() { status <- .shlib_internal(commandArgs(TRUE)) q("no", status = (status != 0), runLast=FALSE) } ## for .SHLIB and R CMD INSTALL on all platforms .shlib_internal <- function(args) { Usage <- function() cat("Usage: R CMD SHLIB [options] files | linker options", "", "Build a shared object for dynamic loading from the specified source or", "object files (which are automagically made from their sources) or", "linker options. If not given via '--output', the name for the shared", "object is determined from the first source or object file.", "", "Options:", " -h, --help print short help message and exit", " -v, --version print version info and exit", " -o, --output=LIB use LIB as (full) name for the built library", " -c, --clean remove files created during compilation", " --preclean remove files created during a previous run", " -n, --dry-run dry run, showing commands that would be used", # "", # "Unix only:", " --use-LTO use Link-Time Optimization", " --no-use-LTO do not use Link-Time Optimization", "", "Windows only:", " -d, --debug build a debug DLL", "", "Report bugs at .", sep = "\n") ## FIXME shQuote here? p1 <- function(...) paste(..., collapse = " ") WINDOWS <- .Platform$OS.type == "windows" cross <- Sys.getenv("R_CROSS_BUILD") if(nzchar(cross)) { if(!cross %in% c("i386", "x64")) stop("invalid value ", sQuote(cross), " for R_CROSS_BUILD") WINDOWS <- TRUE Sys.setenv(R_ARCH = paste0("/", cross)) } if (!WINDOWS) { mconf <- readLines(file.path(R.home(), paste0("etc", Sys.getenv("R_ARCH")), "Makeconf")) SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE, perl = TRUE)) SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE, perl = TRUE)) MAKE <- Sys.getenv("MAKE") rarch <- Sys.getenv("R_ARCH") } else { rhome <- chartr("\\", "/", R.home()) Sys.setenv(R_HOME = rhome) SHLIB_EXT <- ".dll" SHLIB_LIBADD <- "" MAKE <- "make" ## Formerly for winshlib.mk to pick up Makeconf rarch <- Sys.getenv("R_ARCH", NA_character_) if(is.na(rarch)) { if (nzchar(.Platform$r_arch)) { rarch <- paste0("/", .Platform$r_arch) Sys.setenv(R_ARCH = rarch) } else rarch <- "" } } OBJ_EXT <- ".o" # all currrent compilers, but not some on Windows ## The order of inclusion of Makefiles on a Unix-alike is ## package's src/Makevars ## etc/Makeconf ## site Makevars ## share/make/shlib.mk ## user Makevars ## and similarly elsewhere objs <- character() shlib <- "" site <- Sys.getenv("R_MAKEVARS_SITE", NA_character_) if (is.na(site)) site <- file.path(paste0(R.home("etc"), rarch), "Makevars.site") makefiles <- c(file.path(paste0(R.home("etc"), rarch), "Makeconf"), if(file.exists(site)) site, file.path(R.home("share"), "make", if (WINDOWS) "winshlib.mk" else "shlib.mk")) shlib_libadd <- if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() with_cxx <- FALSE with_f77 <- FALSE with_f9x <- FALSE with_objc <- FALSE use_cxxstd <- NULL use_fc_link <- FALSE use_lto <- NA pkg_libs <- character() clean <- FALSE preclean <- FALSE dry_run <- FALSE debug <- FALSE while(length(args)) { a <- args[1L] if (a %in% c("-h", "--help")) { Usage() return(0L) } else if (a %in% c("-v", "--version")) { cat("R shared object builder: ", R.version[["major"]], ".", R.version[["minor"]], " (r", R.version[["svn rev"]], ")\n", sep = "") cat("", .R_copyright_msg(2000), "This is free software; see the GNU General Public License version 2", "or later for copying conditions. There is NO warranty.", sep = "\n") return(0L) } else if (a %in% c("-n", "--dry-run")) { dry_run <- TRUE } else if (a %in% c("-d", "--debug")) { debug <- TRUE } else if (a %in% c("-c", "--clean")) { clean <- TRUE } else if (a == "--preclean") { preclean <- TRUE } else if (a == "--use-LTO") { use_lto <- TRUE } else if (a == "--no-use-LTO") { use_lto <- FALSE } else if (a == "-o") { if (length(args) >= 2L) {shlib <- args[2L]; args <- args[-1L]} else stop("-o option without value", call. = FALSE) } else if (substr(a, 1, 9) == "--output=") { shlib <- substr(a, 10, 1000) } else { ## a source file or something like -Ldir -lfoo base <- sub("\\.[[:alnum:]]*$", "", a) ext <- sub(paste0(base, "."), "", a, fixed = TRUE) nobj <- "" if (nzchar(ext)) { ## This will not work if there are no source files in ## the top-level directory if (ext %in% c("cc", "cpp")) { with_cxx <- TRUE nobj <- base } else if (ext == "m") { with_objc <- TRUE nobj <- base } else if (ext %in% c("mm", "M")) { ## ObjC++ implies ObjC because we need ObjC runtime ## ObjC++ implies C++ because we use C++ linker with_objc <- with_cxx <- TRUE nobj <- base } else if (ext == "f") { with_f77 <- TRUE nobj <- base } else if (ext %in% c("f90", "f95")) { with_f9x <- TRUE nobj <- base } else if (ext == "c") { nobj <- base } else if (ext == "o") { nobj <- base } if (nzchar(nobj) && !nzchar(shlib)) shlib <- paste0(nobj, SHLIB_EXT) } if (nzchar(nobj)) objs <- c(objs, nobj) else pkg_libs <- c(pkg_libs, a) } args <- args[-1L] } if (length(objs)) objs <- paste0(objs, OBJ_EXT, collapse = " ") if (WINDOWS) { if (!is.na(f <- Sys.getenv("R_MAKEVARS_USER", NA_character_))) { if (file.exists(f)) makefiles <- c(makefiles, f) } else if (rarch == "/x64" && file.exists(f <- path.expand("~/.R/Makevars.ucrt"))) makefiles <- c(makefiles, f) else if (rarch == "/x64" && file.exists(f <- path.expand("~/.R/Makevars.win64"))) makefiles <- c(makefiles, f) else if (file.exists(f <- path.expand("~/.R/Makevars.win"))) makefiles <- c(makefiles, f) else if (file.exists(f <- path.expand("~/.R/Makevars"))) makefiles <- c(makefiles, f) } else { makefiles <- c(makefiles, makevars_user()) } makeobjs <- paste0("OBJECTS=", shQuote(objs)) if (WINDOWS && (file.exists(fn <- "Makevars.ucrt") || file.exists(fn <- "Makevars.win"))) { makefiles <- c(fn, makefiles) lines <- readLines(fn, warn = FALSE) if (length(grep("^OBJECTS *=", lines, perl=TRUE, useBytes = TRUE))) makeobjs <- "" if (length(ll <- grep("^CXX_STD *=", lines, perl = TRUE, value = TRUE, useBytes = TRUE)) == 1) { val <- gsub("^CXX_STD *= *CXX", "", ll) val <- gsub(" +$", "", val) if (val %in% cxx_standards) { use_cxxstd <- val with_cxx <- TRUE } } if (any(grepl("^USE_FC_TO_LINK", lines, perl=TRUE, useBytes = TRUE))) use_fc_link <- TRUE } else if (file.exists("Makevars")) { makefiles <- c("Makevars", makefiles) lines <- readLines("Makevars", warn = FALSE) if (length(grep("^OBJECTS *=", lines, perl = TRUE, useBytes = TRUE))) makeobjs <- "" if (length(ll <- grep("^CXX_STD *=", lines, perl = TRUE, value = TRUE, useBytes = TRUE)) == 1) { val <- gsub("^CXX_STD *= *CXX", "", ll) val <- gsub(" +$", "", val) if (val %in% cxx_standards) { use_cxxstd <- val with_cxx <- TRUE } } if (any(grepl("^USE_FC_TO_LINK", lines, perl=TRUE, useBytes = TRUE))) use_fc_link <- TRUE } if (is.null(use_cxxstd)) { for (i in cxx_standards) { if (nzchar(Sys.getenv(paste0("USE_CXX", i)))) { use_cxxstd <- i break } } } if (is.null(use_cxxstd)) { val <- Sys.getenv("R_PKG_CXX_STD") if (val %in% cxx_standards) { use_cxxstd <- val } } if (with_cxx) { checkCXX <- function(cxxstd) { for (i in rev(seq_along(makefiles))) { lines <- readLines(makefiles[i], warn = FALSE) pattern <- paste0("^CXX", cxxstd, " *= *") ll <- grep(pattern, lines, perl = TRUE, value = TRUE, useBytes = TRUE) for (j in rev(seq_along(ll))) { cxx <- gsub(pattern, "", ll[j]) return(nzchar(cxx)) } } return(FALSE) } if (!is.null(use_cxxstd)) { if (use_cxxstd == "98") { stop("C++98 standard requested but unsupported", call. = FALSE, domain = NA) } if (!checkCXX(use_cxxstd)) { stop(paste0("C++", use_cxxstd, " standard requested but CXX", use_cxxstd, " is not defined"), call. = FALSE, domain = NA) } } } makeargs <- paste0("SHLIB=", shQuote(shlib)) if (with_cxx) { if (!is.null(use_cxxstd)) { cxx_makeargs <- sprintf(c("CXX='$(CXX%s) $(CXX%sSTD)'", "CXXFLAGS='$(CXX%sFLAGS)'", "CXXPICFLAGS='$(CXX%sPICFLAGS)'", "SHLIB_LDFLAGS='$(SHLIB_CXX%sLDFLAGS)'", "SHLIB_LD='$(SHLIB_CXX%sLD)'"), use_cxxstd, use_cxxstd) makeargs <- c(cxx_makeargs, makeargs) } else { makeargs <- c("SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)'", "SHLIB_LD='$(SHLIB_CXXLD)'", makeargs) } } else if (use_fc_link && (with_f77 || with_f9x)) makeargs <- c("SHLIB_LDFLAGS='$(SHLIB_FCLDFLAGS)'", "SHLIB_LD='$(SHLIB_FCLD)'", ## avoid $(LIBINTL) and $(LIBR) "ALL_LIBS='$(PKG_LIBS) $(SHLIB_LIBADD)'", makeargs) if (with_objc) shlib_libadd <- c(shlib_libadd, "$(OBJC_LIBS)") if (with_f77 || with_f9x) { if (use_fc_link) shlib_libadd <- c(shlib_libadd, "$(FCLIBS_XTRA)") else shlib_libadd <- c(shlib_libadd, "$(FLIBS) $(FCLIBS_XTRA)") } if (length(pkg_libs)) makeargs <- c(makeargs, paste0("PKG_LIBS='", p1(pkg_libs), "'")) if (length(shlib_libadd)) makeargs <- c(makeargs, paste0("SHLIB_LIBADD='", p1(shlib_libadd), "'")) if (with_f9x && file.exists("Makevars") && length(grep("^\\s*PKG_FCFLAGS", lines, perl = TRUE, useBytes = TRUE))) makeargs <- c(makeargs, "P_FCFLAGS='$(PKG_FCFLAGS)'") if (WINDOWS && debug) makeargs <- c(makeargs, "DEBUG=T") ## TCLBIN is needed for tkrplot and tcltk2 if (WINDOWS && rarch == "/x64") makeargs <- c(makeargs, "WIN=64 TCLBIN=") build_objects_symbol_tables <- config_val_to_logical(Sys.getenv("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_", "FALSE")) makeargs <- c(makeargs, if(isTRUE(use_lto)) c(paste0("LTO=", shQuote("$(LTO_OPT)")), paste0("LTO_FC=", shQuote("$(LTO_FC_OPT)"))) else if(isFALSE(use_lto)) c("LTO=", "LTO_FC=") ) cmd <- paste(MAKE, p1(paste("-f", shQuote(makefiles))), p1(makeargs), p1(makeobjs)) if (dry_run) { cat("make cmd is\n ", cmd, "\n\nmake would use\n", sep = "") system(paste(cmd, "-n")) res <- 0 } else { if (preclean) system(paste(cmd, "shlib-clean")) res <- system(cmd) if((res == 0L) && build_objects_symbol_tables) { ## Should only do this if the previous one went ok. system(paste(cmd, "symbols.rds")) } if (clean) system(paste(cmd, "shlib-clean")) } res # probably a multiple of 256 } ## called for base packages from src/Makefile[.win] and from ## .install.packages in this file. Really *help* indices. .writePkgIndices <- function(dir, outDir, OS = .Platform$OS.type, html = TRUE) { re <- function(x) { ## sort order for topics, a little tricky ## FALSE sorts before TRUE xx <- rep.int(TRUE, length(x)) xx[grep("-package", x, fixed = TRUE)] <- FALSE order(xx, toupper(x), x) } html_header <- function(pkg, title, version, conn) { cat(paste(HTMLheader(title, Rhome="../../..", up="../../../doc/html/packages.html", css = "R.css"), collapse = "\n"), '

Documentation for package ‘', pkg, '’ version ', version, '

\n\n', sep = "", file = conn) cat('\n\n

Help Pages

\n\n\n', sep ="", file = conn) } firstLetterCategory <- function(x) { x[endsWith(x, "-package")] <- " " x <- toupper(substr(x, 1, 1)) x[x > "Z"] <- "misc" x[x < "A" & x != " "] <- "misc" x } ## This may well already have been done: Rd <- if (file.exists(f <- file.path(outDir, "Meta", "Rd.rds"))) readRDS(f) else { ## Keep this in sync with .install_package_Rd_indices(). ## Rd objects should already have been installed. db <- tryCatch(Rd_db(basename(outDir), lib.loc = dirname(outDir)), error = function(e) NULL) ## If not, we build the Rd db from the sources: if (is.null(db)) db <- Rd_db(dir = dir) Rd <- Rd_contents(db) saveRDS(Rd, file.path(outDir, "Meta", "Rd.rds")) Rd } topics <- Rd$Aliases M <- if (!length(topics)) { list2DF(list(Topic = character(), File = character(), Title = character(), Internal = character())) } else { lens <- lengths(topics) files <- sub("\\.[Rr]d$", "", Rd$File) internal <- (vapply(Rd$Keywords, function(x) match("internal", x, 0L), 0L) > 0L) list2DF(list(Topic = unlist(topics), File = rep.int(files, lens), Title = rep.int(Rd$Title, lens), Internal = rep.int(internal, lens))) } ## FIXME duplicated aliases warning outman <- file.path(outDir, "help") dir.create(outman, showWarnings = FALSE) MM <- M[re(M[, 1L]), 1:2] utils::write.table(MM, file.path(outman, "AnIndex"), quote = FALSE, row.names = FALSE, col.names = FALSE, sep = "\t") a <- structure(MM[, 2L], names=MM[, 1L]) saveRDS(a, file.path(outman, "aliases.rds")) ## have HTML index even if no help pages outman <- file.path(outDir, "html") dir.create(outman, showWarnings = FALSE) outcon <- file(file.path(outman, "00Index.html"), "wt") on.exit(close(outcon)) ## we know we have a valid file by now. desc <- read.dcf(file.path(outDir, "DESCRIPTION"))[1L, ] ## re-encode if necessary if(!is.na(enc <- desc["Encoding"])) { ## should be valid in UTF-8, might be invalid in declared encoding desc <- iconv(desc, enc, "UTF-8", sub = "byte") } ## drop internal entries M <- M[!M[, 4L], ] if (desc["Package"] %in% c("base", "graphics", "stats", "utils")) { for(pass in 1:2) { ## we skip method aliases gen <- gsub("\\.data\\.frame", ".data_frame", M$Topic) gen <- sub("\\.model\\.matrix$", ".modelmatrix", gen) gen <- sub("^(all|as|is|file|Sys|row|na|model)\\.", "\\1_", gen) gen <- sub("^(.*)\\.test", "\\1_test", gen) gen <- sub("([-[:alnum:]]+)\\.[^.]+$", "\\1", gen) last <- nrow(M) nongen <- gen %in% c("ar", "bw", "contr", "dyn", "lm", "qr", "ts", "which", ".Call", ".External", ".Library", ".First", ".Last") nc <- nchar(gen) asg <- (nc > 3) & endsWith(gen, "<-") skip <- (gen == c("", gen[-last])) & (M$File == c("", M$File[-last])) & !nongen skip <- skip | asg ##N <- cbind(M$Topic, gen, c("", gen[-last]), skip) M <- M[!skip, ] } } # Collapse method links into unique (generic, file) pairs M$Topic <- sub("^([^,]*),.*-method$", "\\1-method", M$Topic) M <- M[!duplicated(M[, c("Topic", "File")]),] M <- M[re(M[, 1L]), ] ## encode some entries. htmlize <- function(x, backtick) { x <- gsub("&", "&", x, fixed = TRUE) x <- gsub("<", "<", x, fixed = TRUE) x <- gsub(">", ">", x, fixed = TRUE) if (backtick) { x <- gsub("---", "-", x, fixed = TRUE) x <- gsub("--", "-", x, fixed = TRUE) ## these have been changed in the Rd parser #x <- gsub("``", "“", x, fixed = TRUE) #x <- gsub("''", "”", x, fixed = TRUE) #x <- gsub("\\`([^']+)'", "‘\\1’", x) #x <- gsub("`", "'", x, fixed = TRUE) } x } M$HTopic <- htmlize(M$Topic, FALSE) M$ Title <- htmlize(M$Title, TRUE) ## No need to handle encodings: everything is in UTF-8 html_header(desc["Package"], htmlize(desc["Title"], TRUE), desc["Version"], outcon) use_alpha <- (nrow(M) > 100) if (use_alpha) { first <- firstLetterCategory(M$Topic) nm <- sort(names(table(first))) m <- match(" ", nm, 0L) # -package if (m) nm <- c(" ", nm[-m]) m <- match("misc", nm, 0L) # force last in all locales. if (m) nm <- c(nm[-m], "misc") writeLines(c('

', paste0("", nm, ""), "

\n"), outcon) for (f in nm) { MM <- M[first == f, ] if (f != " ") cat("\n

-- ", f, " --

\n\n", sep = "", file = outcon) writeLines(c('', paste0('\n'), "
', MM$HTopic, '', MM[, 3L],'
"), outcon) } } else if (nrow(M)) { writeLines(c('', paste0('\n'), "
', M$HTopic, '', M[, 3L],'
"), outcon) } else { # no rows writeLines("There are no help pages in this package", outcon) } writeLines('', outcon) file.copy(file.path(R.home("doc"), "html", "R.css"), outman) invisible(NULL) } ### * .convertRdfiles ## possible types are "html", "latex", "example" ## outenc is used as the default output encoding for latex conversion .convertRdfiles <- function(dir, outDir, types = "html", silent = FALSE, outenc = "UTF-8") { showtype <- function(type) { if (!shown) { nc <- nchar(bf) if (nc < 38L) cat(" ", bf, rep.int(" ", 40L - nc), sep = "") else cat(" ", bf, "\n", rep.int(" ", 44L), sep = "") shown <<- TRUE } ## 'example' is always last, so 5+space cat(type, rep.int(" ", max(0L, 6L - nchar(type))), sep = "") } dirname <- c("html", "latex", "R-ex") ext <- c(".html", ".tex", ".R") names(dirname) <- names(ext) <- c("html", "latex", "example") mandir <- file.path(dir, "man") if (!dir.exists(mandir)) return() desc <- readRDS(file.path(outDir, "Meta", "package.rds"))$DESCRIPTION pkg <- desc["Package"] ver <- desc["Version"] for(type in types) dir.create(file.path(outDir, dirname[type]), showWarnings = FALSE) cat(" converting help for package ", sQuote(pkg), "\n", sep = "") ## FIXME: add this lib to lib.loc? if ("html" %in% types) { ## may be slow, so add a message if (!silent) message(" finding HTML links ...", appendLF = FALSE, domain = NA) Links <- findHTMLlinks(outDir, level = 0:1) if (!silent) message(" done") .Links2 <- function() { message("\n finding level-2 HTML links ...", appendLF = FALSE, domain = NA) Links2 <- findHTMLlinks(level = 2) message(" done", domain = NA) Links2 } delayedAssign("Links2", .Links2()) } ## Rd objects may already have been installed. db <- tryCatch(Rd_db(basename(outDir), lib.loc = dirname(outDir)), error = function(e) NULL) ## If not, we build the Rd db from the sources: if (is.null(db)) db <- Rd_db(dir = dir) if (!length(db)) return() .whandler <- function(e) { .messages <<- c(.messages, paste("Rd warning:", conditionMessage(e))) tryInvokeRestart("muffleWarning") } .ehandler <- function(e) { message("", domain = NA) # force newline unlink(ff) stop(conditionMessage(e), domain = NA, call. = FALSE) } .convert <- function(expr) withCallingHandlers(tryCatch(expr, error = .ehandler), warning = .whandler) files <- names(db) # not full file names for(nf in files) { .messages <- character() Rd <- db[[nf]] attr(Rd, "source") <- NULL bf <- sub("\\.[Rr]d$", "", basename(nf)) # e.g. nf = "unix/Signals.Rd" f <- attr(Rd, "Rdfile")# full file name shown <- FALSE if ("html" %in% types) { type <- "html" ff <- file.path(outDir, dirname[type], paste0(bf, ext[type])) if (!file_test("-f", ff) || file_test("-nt", f, ff)) { showtype(type) ## assume prepare_Rd was run when dumping the .rds ## so use defines = NULL for speed .convert(Rd2HTML(Rd, ff, package = c(pkg, ver), defines = NULL, Links = Links, Links2 = Links2)) } } if ("latex" %in% types) { type <- "latex" ff <- file.path(outDir, dirname[type], paste0(bf, ext[type])) if (!file_test("-f", ff) || file_test("-nt", f, ff)) { showtype(type) .convert(Rd2latex(Rd, ff, defines = NULL, outputEncoding = outenc)) } } if ("example" %in% types) { type <- "example" ff <- file.path(outDir, dirname[type], paste0(bf, ext[type])) if (!file_test("-f", ff) || file_test("-nt", f, ff)) { .convert(Rd2ex(Rd, ff, defines = NULL)) if (file_test("-f", ff)) showtype(type) } } if (shown) { cat("\n") if (length(.messages)) writeLines(unique(.messages)) } } ## Now check for files to remove. ## These start with a letter. bfs <- sub("\\.[Rr]d$", "", basename(files)) # those to keep if ("html" %in% types) { type <- "html" have <- list.files(file.path(outDir, dirname[type])) have2 <- sub(".html", "", basename(have), fixed=TRUE) drop <- have[have2 %notin% c(bfs, "00Index", "R.css")] unlink(file.path(outDir, dirname[type], drop)) } if ("latex" %in% types) { type <- "latex" have <- list.files(file.path(outDir, dirname[type])) have2 <- sub(".tex", "", basename(have), fixed=TRUE) drop <- have[have2 %notin% bfs] unlink(file.path(outDir, dirname[type], drop)) } if ("example" %in% types) { type <- "example" have <- list.files(file.path(outDir, dirname[type])) have2 <- sub(".R", "", basename(have), fixed=TRUE) drop <- have[have2 %notin% bfs] unlink(file.path(outDir, dirname[type], drop)) } } ### * .makeDllRes .makeDllRes <- function(name="", version = "0.0") { if (file.exists(f <- "../DESCRIPTION") || file.exists(f <- "../../DESCRIPTION")) { desc <- read.dcf(f)[[1L]] if (!is.na(f <- desc["Package"])) name <- f if (!is.na(f <- desc["Version"])) version <- f } writeLines(c('#include ', '#include "Rversion.h"', '', 'VS_VERSION_INFO VERSIONINFO', 'FILEVERSION R_FILEVERSION', 'PRODUCTVERSION 3,0,0,0', 'FILEFLAGSMASK 0x3L', 'FILEOS VOS__WINDOWS32', 'FILETYPE VFT_APP', 'BEGIN', ' BLOCK "StringFileInfo"', ' BEGIN', ' BLOCK "040904E4"', ' BEGIN')) cat(" VALUE \"FileDescription\", \"DLL for R package `", name,"'\\0\"\n", " VALUE \"FileVersion\", \"", version, "\\0\"\n", sep = "") writeLines(c( ' VALUE "Compiled under R Version", R_MAJOR "." R_MINOR " (" R_YEAR "-" R_MONTH "-" R_DAY ")\\0"', ' VALUE "Project info", "https://www.r-project.org\\0"', ' END', ' END', ' BLOCK "VarFileInfo"', ' BEGIN', ' VALUE "Translation", 0x409, 1252', ' END', 'END')) } ### * makevars_user makevars_user <- function() { m <- character() if(.Platform$OS.type == "windows") { if(!is.na(f <- Sys.getenv("R_MAKEVARS_USER", NA_character_))) { if(file.exists(f)) m <- f } else if((Sys.getenv("R_ARCH") == "/x64") && file.exists(f <- path.expand("~/.R/Makevars.ucrt"))) m <- f else if((Sys.getenv("R_ARCH") == "/x64") && file.exists(f <- path.expand("~/.R/Makevars.win64"))) m <- f else if(file.exists(f <- path.expand("~/.R/Makevars.win"))) m <- f else if(file.exists(f <- path.expand("~/.R/Makevars"))) m <- f } else { if(!is.na(f <- Sys.getenv("R_MAKEVARS_USER", NA_character_))) { if(file.exists(f)) m <- f } else if(file.exists(f <- path.expand(paste0("~/.R/Makevars-", Sys.getenv("R_PLATFORM"))))) m <- f else if(file.exists(f <- path.expand("~/.R/Makevars"))) m <- f } m } revert_install_time_patches <- function() { WINDOWS <- .Platform$OS.type == "windows" if (WINDOWS && dir.exists("install_time_patches")) { patches <- sort(list.files("install_time_patches"), decreasing = TRUE) for(p in patches) { fname <- paste0("install_time_patches/", p) if (system2("patch", args = c("-p2", "--binary", "--force", "--reverse"), stdin = fname) != 0) message("WARNING: failed to revert patch ", p, "\n") else message("Reverted installation-time patch ", p, " in package installation\n") } unlink("install_time_patches", recursive = TRUE) } } ### * makevars_site makevars_site <- function() { m <- character() if(is.na(f <- Sys.getenv("R_MAKEVARS_SITE", NA_character_))) f <- file.path(paste0(R.home("etc"), Sys.getenv("R_ARCH")), "Makevars.site") if(file.exists(f)) m <- f m } cxx_standards <- c("20", "17", "14", "11", "98") ### Local variables: *** ### mode: outline-minor *** ### outline-regexp: "### [*]+" *** ### End: ***