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install.R
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install.R
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# File src/library/tools/R/install.R
# Part of the R package, https://www.R-project.org
#
# Copyright (C) 1995-2019 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
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. Currently it only fixes backslashes;
# more extensive escaping might be a good idea
quote_path <- function(path, quote = "'")
paste0(quote, gsub("\\\\", "\\\\\\\\", path), quote)
on.exit(do_exit_on_error())
WINDOWS <- .Platform$OS.type == "windows"
if (WINDOWS) MAKE <- "make"
else MAKE <- Sys.getenv("MAKE") # FIXME shQuote, default?
rarch <- Sys.getenv("R_ARCH") # unix only
if (WINDOWS && nzchar(.Platform$r_arch))
rarch <- paste0("/", .Platform$r_arch)
test_archs <- rarch
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",
"\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 <https://bugs.R-project.org>.", 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.-]+$", "", pkg_name)
if (pkglock)
lock <- "pkglock"
utils:::unpackPkgZip(pkg, pkg_name, lib, libs_only, lock)
return()
}
setwd(pkg)
## We checked this exists, but not that it is readable
desc <- tryCatch(read.dcf(fd <- file.path(pkg, "DESCRIPTION")),
error = identity)
if(inherits(desc, "error") || !length(desc))
stop(gettextf("error reading file '%s'", fd),
domain = NA, call. = FALSE)
desc <- desc[1L,]
## Let's see if we have a bundle
if (!is.na(desc["Bundle"])) {
stop("this seems to be a bundle -- and they are defunct")
} else {
pkg_name <- desc["Package"]
if (is.na(pkg_name)) errmsg("no 'Package' field in 'DESCRIPTION'")
curPkg <<- pkg_name
}
instdir <- file.path(lib, pkg_name) # = <library>/<pkg>
Sys.setenv(R_PACKAGE_NAME = pkg_name, R_PACKAGE_DIR = instdir)
status <- .Rtest_package_depends_R_version()
if (status) do_exit_on_error()
dir.create(instdir, recursive = TRUE, showWarnings = FALSE)
if (!dir.exists(instdir)) {
message("ERROR: unable to create ", sQuote(instdir), domain = NA)
do_exit_on_error()
}
if (!is_subdir(instdir, lib)) {
message("ERROR: ", sQuote(pkg_name), " is not a legal package name",
domain = NA)
do_exit_on_error()
}
## Make sure we do not attempt installing to srcdir.
owd <- setwd(instdir)
if (owd == getwd()) pkgerrmsg("cannot install to srcdir", pkg_name)
setwd(owd)
## Figure out whether this is a source or binary package.
is_source_package <- is.na(desc["Built"])
if (is_source_package) {
## Find out if any C++ standard is requested in DESCRIPTION file
sys_requires <- desc["SystemRequirements"]
if (!is.na(sys_requires)) {
sys_requires <- unlist(strsplit(sys_requires, ","))
if(any(grepl("^[[:space:]]*C[+][+]17[[:space:]]*$",
sys_requires, ignore.case=TRUE))) {
Sys.setenv("R_PKG_CXX_STD"="CXX17")
on.exit(Sys.unsetenv("R_PKG_CXX_STD"))
}
else if(any(grepl("^[[:space:]]*C[+][+]14[[:space:]]*$",
sys_requires, ignore.case=TRUE))) {
Sys.setenv("R_PKG_CXX_STD"="CXX14")
on.exit(Sys.unsetenv("R_PKG_CXX_STD"))
}
else if(any(grepl("^[[:space:]]*C[+][+]11[[:space:]]*$",
sys_requires, ignore.case=TRUE))) {
Sys.setenv("R_PKG_CXX_STD"="CXX11")
on.exit(Sys.unsetenv("R_PKG_CXX_STD"))
}
else if(any(grepl("^[[:space:]]*C[+][+]98[[:space:]]*$",
sys_requires, ignore.case=TRUE))) {
Sys.setenv("R_PKG_CXX_STD"="CXX98")
on.exit(Sys.unsetenv("R_PKG_CXX_STD"))
}
}
}
if (!is_first_package) cat("\n")
if (is_source_package)
do_install_source(pkg_name, instdir, pkg, desc)
else
do_install_binary(pkg_name, instdir, desc)
## Add read permission to all, write permission to owner
## If group-write permissions were requested, set them
.Call(C_dirchmod, instdir, group.writable)
is_first_package <<- FALSE
if (tar_up) { # Unix only
starsmsg(stars, "creating tarball")
version <- desc["Version"]
filename <- if (!grepl("darwin", R.version$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.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.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)
}
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")) {
message(gettextf("generating debug symbols (%s)", "dSYM"),
domain = NA)
dylib <- Sys.glob(paste0(dest, "/*", SHLIB_EXT))
for (file in dylib) system(paste0("dsymutil ", file))
}
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)
{
args <- c(shargs, "-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'.
are_shared <- sapply(slibs,
function(l) grepl("(shared|dynamically linked)",
system(paste("file", l), intern = TRUE)))
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
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", 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, 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
cmd <- paste("elfedit -e \"dyn:value -dynndx -s",
idxs[i], paths[i], "\"", l)
message(cmd)
ret <- suppressWarnings(system(cmd, intern = FALSE))
if (ret == 0)
message("NOTE: fixed path ", old_paths[i])
}
out <- suppressWarnings(
system(paste("elfedit -re dyn:value", 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", 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, final_instdir, oldid,
fixed = TRUE)
cmd <- paste("install_name_tool -id", newid, 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 ",
oldid)
}
## change paths to other libraries
out <- suppressWarnings(
system(paste("otool -L", l), intern = TRUE))
paths <- grep("\\(compatibility", out, value = TRUE)
paths <- gsub("^[ \t]*(.*) \\(compatibility.*", "\\1",
paths)
old_paths <- paths
# "@loader_path/.."
paths <- gsub(instdir, 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",
old_paths[i], paths[i], 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 ", old_paths[i])
}
out <- suppressWarnings(
system(paste("otool -L", 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", l), intern = TRUE))
out <- grep("(^[ \t]*cmd )|(^[ \t]*path )", out,
value = TRUE)
rpidx <- grep("cmd LC_RPATH$", out)
if (length(rpidx)) {
paths <- gsub("^[ \t]*path ", "", out[rpidx+1])
paths <- gsub("(.*) \\(offset .*", "\\1", paths)
old_paths <- paths
# "@loader_path/.."
paths <- gsub(instdir, final_instdir, paths,
fixed = TRUE)
changed <- paths != old_paths
paths <- paths[changed]
old_paths <- old_paths[changed]
for(i in seq_along(paths)) {
hardcoded_paths <- TRUE
cmd <- paste("install_name_tool -rpath",
old_paths[i], paths[i], l)
message(cmd)
ret <- suppressWarnings(system(cmd))
if (ret == 0)
message("NOTE: fixed rpath ", old_paths[i])
}
}
## check no hard-coded paths are left
out <- suppressWarnings(
system(paste("otool -l", l), intern = TRUE))
out <- out[-1L] # first line is l (includes instdir)
if (any(grepl(instdir, out, fixed = TRUE)))
failed_fix <- TRUE
}
} else if (have_patchelf) {
## probably Linux
for(l in slibs) {
# fix rpath
rpath <- suppressWarnings(
system(paste("patchelf --print-rpath", l),
intern = TRUE))
old_rpath <- rpath
# "\\$ORIGIN/.."
rpath <- gsub(instdir, final_instdir, rpath,
fixed = TRUE)
if (length(rpath) && nzchar(rpath) && old_rpath != rpath) {
hardcoded_paths <- TRUE
cmd <- paste("patchelf", "--set-rpath", rpath, l)
message(cmd)
ret <- suppressWarnings(system(cmd))
if (ret == 0)
message("NOTE: fixed rpath ", old_rpath)
rpath <- suppressWarnings(
system(paste("patchelf --print-rpath", 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", 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, 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",
old_paths[i], paths[i], l)
message(cmd)
ret <- suppressWarnings(system(cmd))
if (ret == 0)
message("NOTE: fixed library path ", old_paths[i])
}
out <- suppressWarnings(
system(paste("readelf -d", 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", 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, final_instdir, rpath, fixed = TRUE)
if (length(rpath) && nzchar(rpath) && old_rpath != rpath) {
hardcoded_paths <- TRUE
cmd <- paste("chrpath", "-r", rpath, l)
message(cmd)
ret <- suppressWarnings(system(cmd))
if (ret == 0)
message("NOTE: fixed rpath ", old_rpath)
out <- suppressWarnings(
system(paste("chrpath", 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 $ORIGIN
for(l in slibs) {
out <- suppressWarnings(
system(paste("readelf -d", l), intern = TRUE))
out <- grep("^[ \t]*0x", out, value = TRUE)
if (any(grepl(instdir, out, fixed = TRUE))) {
## give path relative to installation dir
ll <- sub(file.path(instdir, ""), "", l, fixed = TRUE)
errmsg("absolute paths in ",
sQuote(ll),
" include the temporary installation directory:",
" please report to the package maintainer",
" and use ", sQuote("--no-staged-install"))
}
}
}
}
## Make the destination directories available to the developer's
## installation scripts (e.g. configure)
Sys.setenv(R_LIBRARY_DIR = lib)
if (nzchar(lib0)) {
## FIXME: is this needed?
## set R_LIBS to include the current installation directory
rlibs <- Sys.getenv("R_LIBS")
rlibs <- if (nzchar(rlibs)) paste(lib, rlibs, sep = .Platform$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"))
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)
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 (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
starsmsg(stars, "using non-staged installation")
}
if (preclean) run_clean()
if (use_configure) {
if (WINDOWS) {
if (file.exists("configure.win")) {
res <- system("sh ./configure.win")
if (res) pkgerrmsg("configuration failed", pkg_name)
} else if (file.exists("configure"))