/
build.R
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/
build.R
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# File src/library/tools/R/build.R
# Part of the R package, http://www.R-project.org
#
# 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
# http://www.r-project.org/Licenses/
#### R based engine for R CMD build
## R developers can use this to debug the function by running it
## directly as tools:::.build_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 build.
### emulation of Perl Logfile.pm
newLog <- function(filename = "")
{
con <- if(nzchar(filename)) file(filename, "wt") else 0L
Log <- new.env(parent = emptyenv())
Log$con <- con
Log$filename <- filename
Log$stars <- "*"
Log$warnings <- 0L
Log$notes <- 0L
Log
}
closeLog <- function(Log) if (Log$con > 2L) close(Log$con)
printLog <- function(Log, ...)
{
quotes <- function(x) gsub("'([^']*)'", sQuote("\\1"), x)
args <- lapply(list(...), quotes)
do.call(cat, c(args, sep = ""))
if (Log$con > 0L) do.call(cat, c(args, sep = "", file=Log$con))
}
printLog0 <- function(Log, ...)
{
cat(..., sep = "")
if (Log$con > 0L) cat(..., file = Log$con, sep = "")
}
## unused
## setStars <- function(Log, stars) {Log$stars <- stars; Log}
checkingLog <- function(Log, ...)
printLog(Log, Log$stars, " checking ", ..., " ...")
creatingLog <- function(Log, text)
printLog(Log, Log$stars, " creating ", text, " ...")
messageLog <- function(Log, ...)
printLog(Log, Log$stars, " ", ..., "\n")
resultLog <- function(Log, text)
printLog(Log, " ", text, "\n")
errorLog <- function(Log, ...)
{
resultLog(Log, "ERROR")
text <- paste0(...)
if (length(text) && nzchar(text)) printLog(Log, ..., "\n")
}
## <NOTE>
## Perhaps the arguments to errorLog(), warningLog() and noteLog()
## should be synchronized?
## </NOTE>
warningLog <- function(Log, text = "")
{
resultLog(Log, "WARNING")
if(nzchar(text)) printLog(Log, text, "\n")
Log$warnings <- Log$warnings + 1L
}
noteLog <- function(Log, text = "")
{
resultLog(Log, "NOTE")
if(nzchar(text)) printLog(Log, text, "\n")
Log$notes <- Log$notes + 1L
}
summaryLog <- function(Log)
{
if((Log$warnings > 0L) || (Log$notes > 0L)) {
if(Log$warnings > 1L)
printLog(Log,
sprintf("WARNING: There were %d warnings.\n",
Log$warnings))
else if(Log$warnings == 1L)
printLog(Log,
sprintf("WARNING: There was 1 warning.\n"))
if(Log$notes > 1L)
printLog(Log,
sprintf("NOTE: There were %d notes.\n",
Log$notes))
else if(Log$notes == 1L)
printLog(Log,
sprintf("NOTE: There was 1 note.\n"))
printLog(Log,
sprintf("See\n %s\nfor details.\n", sQuote(Log$filename)))
}
}
writeDefaultNamespace <-
function(filename, desc = file.path(dirname(filename), "DESCRIPTION"))
{
pkgInfo <- .split_description(.read_description(desc))
pkgs <- unique(c(names(pkgInfo$Imports), names(pkgInfo$Depends)))
pkgs <- pkgs[pkgs != "base"]
writeLines(c("# Default NAMESPACE created by R",
"# Remove the previous line if you edit this file",
"",
"# Export all names",
"exportPattern(\".\")",
if (length(pkgs))
c("",
"# Import all packages listed as Imports or Depends",
"import(",
paste(" ", pkgs, collapse=",\n"),
")")),
filename)
}
### formerly Perl R::Utils::get_exclude_patterns
## Return list of file patterns excluded by R CMD build and check.
## Kept here so that we ensure that the lists are in sync, but not exported.
## Has Unix-style '/' path separators hard-coded, but that is what dir() uses.
get_exclude_patterns <- function()
c("^\\.Rbuildignore$",
"(^|/)\\.DS_Store$",
"^\\.(RData|Rhistory)$",
"~$", "\\.bak$", "\\.swp$",
"(^|/)\\.#[^/]*$", "(^|/)#[^/]*#$",
## Outdated ...
"^TITLE$", "^data/00Index$",
"^inst/doc/00Index\\.dcf$",
## Autoconf
"^config\\.(cache|log|status)$",
"^autom4te\\.cache$",
## Windows dependency files
"^src/.*\\.d$", "^src/Makedeps$",
## IRIX, of some vintage
"^src/so_locations$",
## Sweave detrius
"^inst/doc/Rplots\\.(ps|pdf)$"
)
### based on Perl build script
.build_packages <- function(args = NULL)
{
## this requires on Windows sh make
WINDOWS <- .Platform$OS.type == "windows"
Sys.umask("022") # Perl version did not have this.
writeLinesNL <- function(text, file)
{
## a version that uses NL line endings everywhere
con <- file(file, "wb")
on.exit(close(con))
writeLines(text, con)
}
## This version of shell_with_capture merges stdout and stderr
## Used to install package and build vignettes.
shell_with_capture <- function (command, args) {
outfile <- tempfile("xshell")
on.exit(unlink(outfile))
status <- system2(command, args, outfile, outfile)
list(status = status, stdout = readLines(outfile, warn = FALSE))
}
## Run silently
Ssystem <- function(command, args = character(), ...)
system2(command, args, stdout = NULL, stderr = NULL, ...)
dir.exists <- function(x) !is.na(isdir <- file.info(x)$isdir) & isdir
do_exit <- function(status = 1L) q("no", status = status, runLast = FALSE)
env_path <- function(...) file.path(..., fsep = .Platform$path.sep)
## Used for BuildVignettes, BuildManual, BuildKeepEmpty,
## and (character not logical) BuildResaveData
parse_description_field <-
function(desc, field, default = TRUE, logical = TRUE)
{
tmp <- desc[field]
if (is.na(tmp)) default
else if(logical)
switch(tmp,
"yes"=, "Yes" =, "true" =, "True" =, "TRUE" = TRUE,
"no" =, "No" =, "false" =, "False" =, "FALSE" = FALSE,
default)
else tmp
}
Usage <- function() {
cat("Usage: R CMD build [options] pkgdirs",
"",
"Build R packages from package sources in the directories specified by",
sQuote("pkgdirs"),
"",
"Options:",
" -h, --help print short help message and exit",
" -v, --version print version info and exit",
"",
" --force force removal of INDEX file",
" --keep-empty-dirs do not remove empty dirs",
" --no-vignettes do not rebuild package vignettes",
" --no-manual do not build the PDF manual even if \\Sexprs are present",
" --resave-data= re-save data files as compactly as possible:",
' "no", "best", "gzip" (default)',
" --resave-data same as --resave-data=best",
" --no-resave-data same as --resave-data=no",
" --compact-vignettes= try to compact PDF files under inst/doc:",
' "no" (default), "qpdf", "gs", "gs+pdf", "both"',
" --compact-vignettes same as --compact-vignettes=qpdf",
" --md5 add MD5 sums",
"",
"Report bugs at bugs.r-project.org .", sep="\n")
}
add_build_stamp_to_description_file <- function(ldpath) {
db <- .read_description(ldpath)
## this is an optional function, so could fail
user <- Sys.info()["user"]
if(user == "unknown") user <- Sys.getenv("LOGNAME")
db["Packaged"] <-
sprintf("%s; %s",
format(Sys.time(), '', tz = 'UTC', usetz = TRUE),
user)
.write_description(db, ldpath)
}
## <FIXME>
## This should really be combined with
## add_build_stamp_to_description_file().
## Also, the build code reads DESCRIPTION files too often ...
add_expanded_R_fields_to_description_file <- function(ldpath) {
db <- .read_description(ldpath)
fields <- .expand_package_description_db_R_fields(db)
if(length(fields))
.write_description(c(db, fields), ldpath)
}
## </FIXME>
temp_install_pkg <- function(pkgdir, libdir) {
dir.create(libdir, mode = "0755", showWarnings = FALSE)
## assume vignettes only need one arch
if (WINDOWS) {
cmd <- file.path(R.home("bin"), "Rcmd.exe")
args <- c("INSTALL -l", shQuote(libdir),
"--no-multiarch", shQuote(pkgdir))
} else {
cmd <- file.path(R.home("bin"), "R")
args <- c("CMD", "INSTALL -l", shQuote(libdir),
"--no-multiarch", shQuote(pkgdir))
}
res <- shell_with_capture(cmd, args)
if (res$status) {
printLog(Log, " -----------------------------------\n")
printLog(Log, paste(c(res$stdout, ""), collapse="\n"))
printLog(Log, " -----------------------------------\n")
unlink(libdir, recursive = TRUE)
printLog(Log, "ERROR: package installation failed\n")
do_exit(1)
}
TRUE
}
prepare_pkg <- function(pkgdir, desc, Log)
{
owd <- setwd(pkgdir); on.exit(setwd(owd))
pkgname <- basename(pkgdir)
checkingLog(Log, "DESCRIPTION meta-information")
res <- try(.check_package_description("DESCRIPTION"))
if (inherits(res, "try-error")) {
resultLog(Log, "ERROR")
messageLog(Log, "running '.check_package_description' failed")
} else {
if (any(sapply(res, length))) {
resultLog(Log, "ERROR")
print(res) # FIXME print to Log?
do_exit(1L)
} else resultLog(Log, "OK")
}
cleanup_pkg(pkgdir, Log)
libdir <- tempfile("Rinst")
pkgInstalled <- build_Rd_db(pkgdir, libdir, desc)
if (file.exists("INDEX")) update_Rd_index("INDEX", "man", Log)
doc_dir <- file.path("inst", "doc")
if ("makefile" %in% dir(doc_dir)) { # avoid case-insensitive match
messageLog(Log, "renaming 'inst/doc/makefile' to 'inst/doc/Makefile'")
file.rename(file.path(doc_dir, "makefile"),
file.path(doc_dir, "Makefile"))
}
if (vignettes &&
parse_description_field(desc, "BuildVignettes", TRUE)) {
## Look for vignette sources
vigns <- pkgVignettes(dir = '.')
if (!is.null(vigns) && length(vigns$docs)) {
if (!pkgInstalled) {
messageLog(Log,
"installing the package to re-build vignettes")
pkgInstalled <- temp_install_pkg(pkgdir, libdir)
}
## Good to do this in a separate process: it might die
creatingLog(Log, "vignettes")
R_LIBS <- Sys.getenv("R_LIBS", NA_character_)
if (!is.na(R_LIBS)) {
on.exit(Sys.setenv(R_LIBS = R_LIBS), add=TRUE)
Sys.setenv(R_LIBS = env_path(libdir, R_LIBS))
} else {
on.exit(Sys.unsetenv("R_LIBS"), add=TRUE)
Sys.setenv(R_LIBS = libdir)
}
cmd <- file.path(R.home("bin"), "Rscript")
args <- c("--vanilla",
"--default-packages=", # some vignettes assume methods
"-e", shQuote("tools::buildVignettes(dir = '.')"))
## since so many people use 'R CMD' in Makefiles,
oPATH <- Sys.getenv("PATH")
Sys.setenv(PATH = paste(R.home("bin"), oPATH,
sep = .Platform$path.sep))
res <- shell_with_capture(cmd, args)
Sys.setenv(PATH = oPATH)
if (res$status) {
resultLog(Log, "ERROR")
printLog(Log, paste(c(res$stdout, ""), collapse="\n"))
do_exit(1L)
} else {
## Do any of the .R files which will be generated
## exist in inst/doc? If so the latter should be removed.
sources <- basename(list_files_with_exts(doc_dir, "R"))
if (length(sources)) {
vf <- basename(list_files_with_type(doc_dir, "vignette"))
new_sources <- sub("\\.[RrSs](nw|tex)$", ".R", vf)
dups <- sources[sources %in% new_sources]
if(length(dups)) {
warningLog(Log)
printLog(Log,
paste(c(" Unused files in inst/doc which are pointless or misleading",
" as they will be re-created from the vignettes on installation:",
paste(" ", dups),
" have been removed", ""),
collapse = "\n"))
unlink(file.path(doc_dir, dups))
} else resultLog(Log, "OK")
} else resultLog(Log, "OK")
}
## We may need to install them.
if (basename(vigns$dir) == "vignettes") {
## inst may not yet exist
dir.create(doc_dir, recursive = TRUE, showWarnings = FALSE)
pdfs <- sub("\\.[RrSs](nw|tex)$", ".pdf", vigns$docs)
file.copy(c(vigns$docs, pdfs), doc_dir)
unlink(pdfs)
extras_file <- file.path("vignettes", ".install_extras")
if (file.exists(extras_file)) {
extras <- readLines(extras_file, warn = FALSE)
if(length(extras)) {
allfiles <- dir("vignettes", all.files = TRUE,
full.names = TRUE, recursive = TRUE,
include.dirs = TRUE)
inst <- rep(FALSE, length(allfiles))
for (e in extras)
inst <- inst | grepl(e, allfiles, perl = TRUE,
ignore.case = WINDOWS)
file.copy(allfiles[inst], doc_dir, recursive = TRUE)
}
}
}
}
}
if (compact_vignettes != "no" &&
length(pdfs <- dir(doc_dir, pattern = "\\.pdf", recursive = TRUE,
full.names = TRUE))) {
messageLog(Log, "compacting vignettes and other PDF files")
if(compact_vignettes %in% c("gs", "gs+pdf", "both")) {
gs_cmd <- find_gs_cmd(Sys.getenv("R_GSCMD", ""))
gs_quality <- "ebook"
} else {
gs_cmd <- ""
gs_quality <- "none"
}
qpdf <-
ifelse(compact_vignettes %in% c("qpdf", "gs+pdf", "both"),
Sys.which(Sys.getenv("R_QPDF", "qpdf")), "")
res <- compactPDF(pdfs, qpdf = qpdf,
gs_cmd = gs_cmd, gs_quality = gs_quality)
res <- format(res, diff = 1e5)
if(length(res))
printLog(Log, paste(" ", format(res), collapse = "\n"), "\n")
}
if (pkgInstalled) {
unlink(libdir, recursive = TRUE)
## And finally, clean up again.
cleanup_pkg(pkgdir, Log)
}
}
cleanup_pkg <- function(pkgdir, Log)
{
owd <- setwd(pkgdir); on.exit(setwd(owd))
pkgname <- basename(pkgdir)
if (dir.exists("src")) {
setwd("src")
messageLog(Log, "cleaning src")
if (WINDOWS) {
if (file.exists("Makefile.win")) {
Ssystem(Sys.getenv("MAKE", "make"), "-f Makefile.win clean")
} else {
if (file.exists("Makevars.win")) {
makefiles <- paste()
makefiles <- paste("-f",
shQuote(file.path(R.home("share"), "make", "clean.mk")),
"-f Makevars.win")
Ssystem(Sys.getenv("MAKE", "make"),
c(makefiles, "clean"))
}
## Also cleanup possible Unix leftovers ...
unlink(c(Sys.glob(c("*.o", "*.sl", "*.so", "*.dylib")),
paste0(pkgname, c(".a", ".dll", ".def"))))
if (dir.exists(".libs")) unlink(".libs", recursive = TRUE)
if (dir.exists("_libs")) unlink("_libs", recursive = TRUE)
}
} else {
makefiles <- paste("-f",
shQuote(file.path(R.home("etc"),
Sys.getenv("R_ARCH"),
"Makeconf")))
if (file.exists("Makefile")) {
makefiles <- paste(makefiles, "-f", "Makefile")
Ssystem(Sys.getenv("MAKE", "make"), c(makefiles, "clean"))
} else {
if (file.exists("Makevars")) {
## ensure we do have a 'clean' target.
makefiles <- paste(makefiles, "-f",
shQuote(file.path(R.home("share"), "make", "clean.mk")),
"-f Makevars")
Ssystem(Sys.getenv("MAKE", "make"),
c(makefiles, "clean"))
}
## Also cleanup possible Windows leftovers ...
unlink(c(Sys.glob(c("*.o", "*.sl", "*.so", "*.dylib")),
paste0(pkgname, c(".a", ".dll", ".def"))))
if (dir.exists(".libs")) unlink(".libs", recursive = TRUE)
if (dir.exists("_libs")) unlink("_libs", recursive = TRUE)
}
}
}
setwd(owd)
## It is not clear that we want to do this: INSTALL should do so.
## Also, certain environment variables should be set according
## to 'Writing R Extensions', but were not in Perl version (nor
## was cleanup.win used).
if (WINDOWS) {
if (file.exists("cleanup.win")) {
Sys.setenv(R_PACKAGE_NAME = pkgname)
Sys.setenv(R_PACKAGE_DIR = pkgdir)
Sys.setenv(R_LIBRARY_DIR = dirname(pkgdir))
messageLog(Log, "running 'cleanup.win'")
Ssystem("sh", "./cleanup.win")
}
} else if (file_test("-x", "cleanup")) {
Sys.setenv(R_PACKAGE_NAME = pkgname)
Sys.setenv(R_PACKAGE_DIR = pkgdir)
Sys.setenv(R_LIBRARY_DIR = dirname(pkgdir))
messageLog(Log, "running 'cleanup'")
Ssystem("./cleanup")
}
}
update_Rd_index <- function(oldindex, Rd_files, Log)
{
newindex <- tempfile()
res <- try(Rdindex(Rd_files, newindex))
if (inherits(res, "try-error")) {
errorLog(Log, "computing Rd index failed")
do_exit(1L)
}
checkingLog(Log, "whether ", sQuote(oldindex), " is up-to-date")
if (file.exists(oldindex)) {
ol <- readLines(oldindex, warn = FALSE) # e.g. BaM had missing final NL
nl <- readLines(newindex)
if (!identical(ol, nl)) {
resultLog(Log, "NO")
if (force) {
messageLog(Log, "removing ", sQuote(oldindex),
" as '--force' was given")
unlink(oldindex)
} else {
messageLog(Log, "use '--force' to remove ",
"the existing ", sQuote(oldindex))
unlink(newindex)
}
} else {
resultLog(Log, "OK")
unlink(newindex)
}
} else {
resultLog(Log, "NO")
messageLog(Log, "creating new ", sQuote(oldindex))
file.rename(newindex, oldindex)
}
}
build_Rd_db <- function(pkgdir, libdir, desc) {
db <- .build_Rd_db(pkgdir, stages=NULL, os=c("unix", "windows"), step=1)
if (!length(db)) return(FALSE)
# Strip the pkgdir off the names
names(db) <- substring(names(db), nchar(file.path(pkgdir, "man", ""))+1)
containsSexprs <-
which(sapply(db, function(Rd) getDynamicFlags(Rd)["\\Sexpr"]))
if (!length(containsSexprs)) return(FALSE)
messageLog(Log, "installing the package to process help pages")
dir.create(libdir, mode = "0755", showWarnings = FALSE)
savelib <- .libPaths()
.libPaths(c(libdir, savelib))
on.exit(.libPaths(savelib), add = TRUE)
temp_install_pkg(pkgdir, libdir)
containsBuildSexprs <-
which(sapply(db, function(Rd) getDynamicFlags(Rd)["build"]))
if (length(containsBuildSexprs)) {
for (i in containsBuildSexprs)
db[[i]] <- prepare_Rd(db[[i]], stages = "build",
stage2 = FALSE, stage3 = FALSE)
messageLog(Log, "saving partial Rd database")
partial <- db[containsBuildSexprs]
dir.create("build", showWarnings = FALSE)
saveRDS(partial, file.path("build", "partial.rdb"))
}
needRefman <- manual &&
parse_description_field(desc, "BuildManual", TRUE) &&
any(sapply(db, function(Rd) any(getDynamicFlags(Rd)[c("install", "render")])))
if (needRefman) {
messageLog(Log, "building the PDF package manual")
dir.create("build", showWarnings = FALSE)
refman <- file.path(pkgdir, "build",
paste0(basename(pkgdir), ".pdf"))
..Rd2pdf(c("--force", "--no-preview",
paste0("--output=", refman),
pkgdir), quit = FALSE)
}
return(TRUE)
}
## also fixes up missing final NL
fix_nonLF_in_files <- function(pkgname, dirPattern, Log)
{
if(dir.exists(sDir <- file.path(pkgname, "src"))) {
files <- dir(sDir, pattern = dirPattern,
full.names = TRUE, recursive = TRUE)
## FIXME: This "destroys" all timestamps
for (ff in files) {
lines <- readLines(ff, warn = FALSE)
writeLinesNL(lines, ff)
}
}
}
fix_nonLF_in_source_files <- function(pkgname, Log) {
fix_nonLF_in_files(pkgname, dirPattern = "\\.([cfh]|cc|cpp)$", Log)
}
fix_nonLF_in_make_files <- function(pkgname, Log) {
fix_nonLF_in_files(pkgname,
paste("^",c("Makefile", "Makefile.in", "Makefile.win",
"Makevars", "Makevars.in", "Makevars.win"),
"$", sep=""), Log)
}
find_empty_dirs <- function(d)
{
## dir(recursive = TRUE) did not include directories, so
## we needed to do this recursively
files <- dir(d, all.files = TRUE, full.names = TRUE)
isdir <- file.info(files)$isdir
for (dd in files[isdir]) {
if (grepl("/\\.+$", dd)) next
find_empty_dirs(dd)
}
## allow per-package override
keep_empty1 <- parse_description_field(desc, "BuildKeepEmpty",
keep_empty)
if (!keep_empty1) # might have removed a dir
files <- dir(d, all.files = TRUE, full.names = TRUE)
if (length(files) <= 2L) { # always has ., ..
if (keep_empty1) {
printLog(Log, "WARNING: directory ", sQuote(d), " is empty\n")
} else {
unlink(d, recursive = TRUE)
printLog(Log, "Removed empty directory ", sQuote(d), "\n")
}
}
}
fixup_R_dep <- function(pkgname, ver="2.10")
{
desc <- .read_description(file.path(pkgname, "DESCRIPTION"))
Rdeps <- .split_description(desc)$Rdepends2
for(dep in Rdeps) {
if(dep$op != '>=') next
if(dep$version >= package_version(ver)) return()
}
on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")))
Sys.setlocale("LC_CTYPE", "C")
flatten <- function(x) {
if(length(x) == 3L)
paste0(x$name, " (", x$op, " ", x$version, ")")
else x[[1L]]
}
deps <- desc["Depends"]
desc["Depends"] <- if(!is.na(deps)) {
deps <- .split_dependencies(deps)
deps <- deps[names(deps) != "R"] # could be more than one
paste(c(sprintf("R (>= %s)", ver), sapply(deps, flatten)),
collapse = ", ")
} else sprintf("R (>= %s)", ver)
.write_description(desc, file.path(pkgname, "DESCRIPTION"))
printLog(Log,
" NB: this package now depends on R (>= ", ver, ")\n")
}
resave_data_rda <- function(pkgname, resave_data)
{
if (resave_data == "no") return()
ddir <- file.path(pkgname, "data")
if(resave_data == "best") {
files <- Sys.glob(c(file.path(ddir, "*.rda"),
file.path(ddir, "*.RData"),
file.path(pkgname, "R", "sysdata.rda")))
messageLog(Log, "re-saving image files")
resaveRdaFiles(files)
rdas <- checkRdaFiles(files)
if(any(rdas$compress %in% c("bzip2", "xz")))
fixup_R_dep(pkgname, "2.10")
} else {
rdas <- checkRdaFiles(ddir)
if(nrow(rdas)) {
update <- with(rdas, ASCII | compress == "none" | version < 2)
if(any(update)) {
messageLog(Log, "re-saving image files")
resaveRdaFiles(row.names(rdas)[update], "gzip")
}
}
if(file.exists(f <- file.path(pkgname, "R", "sysdata.rda"))) {
rdas <- checkRdaFiles(f)
update <- with(rdas, ASCII | compress == "none" | version < 2)
if(any(update)) {
messageLog(Log, "re-saving sysdata.rda")
resaveRdaFiles(f, "gzip")
}
}
}
}
resave_data_others <- function(pkgname, resave_data)
{
if (resave_data == "no") return()
ddir <- file.path(pkgname, "data")
dataFiles <- grep("\\.(rda|RData)$",
list_files_with_type(ddir, "data"),
invert = TRUE, value = TRUE)
if (!length(dataFiles)) return()
Rs <- grep("\\.[Rr]$", dataFiles, value = TRUE)
if (length(Rs)) { # these might use .txt etc
messageLog(Log, "re-saving .R files as .rda")
## ensure utils is visible
library("utils")
lapply(Rs, function(x){
envir <- new.env(hash = TRUE)
sys.source(x, chdir = TRUE, envir = envir)
save(list = ls(envir, all.names = TRUE),
file = sub("\\.[Rr]$", ".rda", x),
compress = TRUE, compression_level = 9,
envir = envir)
unlink(x)
})
printLog(Log,
" NB: *.R converted to .rda: other files may need to be removed\n")
}
tabs <- grep("\\.(CSV|csv|TXT|tab|txt)$", dataFiles, value = TRUE)
if (length(tabs)) {
messageLog(Log, "re-saving tabular files")
if (resave_data == "gzip") {
lapply(tabs, function(nm) {
## DiceDesign/data/greenwood.table.txt is missing NL
x <- readLines(nm, warn = FALSE)
con <- gzfile(paste(nm, "gz", sep = "."), "wb")
writeLines(x, con)
close(con)
unlink(nm)
})
} else {
OK <- TRUE
lapply(tabs, function(nm) {
x <- readLines(nm, warn = FALSE)
nm3 <- paste(nm, c("gz", "bz2", "xz"), sep = ".")
con <- gzfile(nm3[1L], "wb", compression=9); writeLines(x, con); close(con)
con <- bzfile(nm3[2L], "wb", compression=9); writeLines(x, con); close(con)
con <- xzfile(nm3[3L], "wb", compression=9); writeLines(x, con); close(con)
sizes <- file.info(nm3)$size * c(0.9, 1, 1)
ind <- which.min(sizes)
if(ind > 1) OK <<- FALSE
unlink(c(nm, nm3[-ind]))
})
if (!OK) fixup_R_dep(pkgname, "2.10")
}
}
}
force <- FALSE
vignettes <- TRUE
manual <- TRUE # Install the manual if Rds contain \Sexprs
with_md5 <- FALSE
INSTALL_opts <- character()
pkgs <- character()
options(showErrorCalls = FALSE, warn = 1)
## read in ~/.R/build.Renviron[.rarch]
rarch <- .Platform$r_arch
if (nzchar(rarch) &&
file.exists(Renv <- paste("~/.R/build.Renviron", rarch, sep = ".")))
readRenviron(Renv)
else if (file.exists(Renv <- "~/.R/build.Renviron")) readRenviron(Renv)
## Configurable variables.
compact_vignettes <- Sys.getenv("_R_BUILD_COMPACT_VIGNETTES_", "no")
resave_data <- Sys.getenv("_R_BUILD_RESAVE_DATA_", "gzip")
keep_empty <-
config_val_to_logical(Sys.getenv("_R_BUILD_KEEP_EMPTY_DIRS_", "FALSE"))
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]
}
while(length(args)) {
a <- args[1L]
if (a %in% c("-h", "--help")) {
Usage()
do_exit(0L)
}
else if (a %in% c("-v", "--version")) {
cat("R add-on package builder: ",
R.version[["major"]], ".", R.version[["minor"]],
" (r", R.version[["svn rev"]], ")\n", sep = "")
cat("",
"Copyright (C) 1997-2011 The R Core Development Team.",
"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(0L)
} else if (a == "--force") {
force <- TRUE
} else if (a == "--keep-empty-dirs") {
keep_empty <- TRUE
} else if (a == "--no-vignettes") {
vignettes <- FALSE
} else if (a == "--resave-data") {
resave_data <- "best"
} else if (a == "--no-resave-data") {
resave_data <- "no"
} else if (substr(a, 1, 14) == "--resave-data=") {
resave_data <- substr(a, 15, 1000)
} else if (a == "--no-manual") {
manual <- FALSE
} else if (substr(a, 1, 20) == "--compact-vignettes=") {
compact_vignettes <- substr(a, 21, 1000)
} else if (a == "--compact-vignettes") {
compact_vignettes <- "qpdf"
} else if (a == "--md5") {
with_md5 <- TRUE
} else if (substr(a, 1, 1) == "-") {
message("Warning: unknown option ", sQuote(a))
} else pkgs <- c(pkgs, a)
args <- args[-1L]
}
if(!compact_vignettes %in% c("no", "qpdf", "gs", "gs+pdf", "both")) {
warning('invalid value for --compact-vignettes, assuming "qpdf"')
compact_vignettes <-"qpdf"
}
Sys.unsetenv("R_DEFAULT_PACKAGES")
startdir <- getwd()
if (is.null(startdir))
stop("current working directory cannot be ascertained")
R_platform <- Sys.getenv("R_PLATFORM", "unknown-binary")
libdir <- tempfile("Rinst")
if (WINDOWS) {
## Some people have *assumed* that R_HOME uses / in Makefiles
## Spaces in paths might still cause trouble.
rhome <- chartr("\\", "/", R.home())
Sys.setenv(R_HOME = rhome)
}
for(pkg in pkgs) {
Log <- newLog() # if not stdin; on.exit(closeLog(Log))
## remove any trailing /, for Windows' sake
pkg <- sub("/$", "", pkg)
## 'Older versions used $pkg as absolute or relative to $startdir.
## This does not easily work if $pkg is a symbolic link.
## Hence, we now convert to absolute paths.'
setwd(startdir)
res <- try(setwd(pkg), silent = TRUE)
if (inherits(res, "try-error")) {
errorLog(Log, "cannot change to directory ", sQuote(pkg))
do_exit(1L)
}
pkgdir <- getwd()
pkgname <- basename(pkgdir)
checkingLog(Log, "for file ", sQuote(file.path(pkg, "DESCRIPTION")))
f <- file.path(pkgdir, "DESCRIPTION")
if (file.exists(f)) {
desc <- try(read.dcf(f))
if (inherits(desc, "try-error") || !length(desc)) {
resultLog(Log, "EXISTS but not correct format")
do_exit(1L)
}
desc <- desc[1L, ]
resultLog(Log, "OK")
} else {
resultLog(Log, "NO")
do_exit(1L)
}
intname <- desc["Package"]
## make a copy, cd to parent of copy
setwd(dirname(pkgdir))
filename <- paste0(intname, "_", desc["Version"], ".tar")
filepath <- file.path(startdir, filename)
Tdir <- tempfile("Rbuild")
dir.create(Tdir, mode = "0755")
if (WINDOWS) {
## This preserves read-only for files, but not dates
if (!file.copy(pkgname, Tdir, recursive = TRUE)) {
errorLog(Log, "copying to build directory failed")
do_exit(1L)
}
} else {
## This should preserve dates and permissions (subject to
## umask, if that is consulted which it seems it usually is not).
## Permissions are increased later.
cp_sw <- if(Sys.info()[["sysname"]] == "Linux") ## << need GNU cp
## unfortunately, '-pr' does not dereference sym.links
"-Lr --preserve=timestamps" else "-pr"
if (system(paste("cp", cp_sw, shQuote(pkgname), shQuote(Tdir)))) {
errorLog(Log, "copying to build directory failed")
do_exit(1L)
}
}
setwd(Tdir)
## Now correct the package name (PR#9266)
if (pkgname != intname) {
if (!file.rename(pkgname, intname)) {
message("Error: cannot rename directory to ", sQuote(intname))
do_exit(1L)
}
pkgname <- intname
}
## prepare the copy
messageLog(Log, "preparing ", sQuote(pkgname), ":")
prepare_pkg(normalizePath(pkgname, "/"), desc, Log);
owd <- setwd(pkgname)
## remove exclude files
allfiles <- dir(".", all.files = TRUE, recursive = TRUE,
full.names = TRUE, include.dirs = TRUE)
allfiles <- substring(allfiles, 3L) # drop './'
bases <- basename(allfiles)
exclude <- rep(FALSE, length(allfiles))
ignore <- get_exclude_patterns()
## handle .Rbuildignore:
## 'These patterns should be Perl regexps, one per line,
## to be matched against the file names relative to
## the top-level source directory.'
ignore_file <- file.path(pkgdir, ".Rbuildignore")
if (file.exists(ignore_file))
ignore <- c(ignore, readLines(ignore_file, warn = FALSE))
for(e in ignore[nzchar(ignore)])
exclude <- exclude | grepl(e, allfiles, perl = TRUE,
ignore.case = WINDOWS)
isdir <- file_test("-d", allfiles)
## old (pre-2.10.0) dirnames
exclude <- exclude | (isdir & (bases %in%
c("check", "chm", .vc_dir_names)))
exclude <- exclude | (isdir & grepl("([Oo]ld|\\.Rcheck)$", bases))
## FIXME: GNU make uses GNUmakefile (note capitalization)
exclude <- exclude | bases %in% c("Read-and-delete-me", "GNUMakefile")
## Mac resource forks
exclude <- exclude | grepl("^\\._", bases)
## Windows DLL resource file
exclude <- exclude | (bases == paste0("src/", pkgname, "_res.rc"))
unlink(allfiles[exclude], recursive = TRUE, force = TRUE)
setwd(owd)
## Fix up man, R, demo inst/doc directories
res <- .check_package_subdirs(pkgname, TRUE)
if (any(sapply(res, length))) {
messageLog(Log, "excluding invalid files")
print(res) # FIXME print to Log?
}
setwd(Tdir)
## Fix permissions for all files to be at least 644, and dirs 755
## Not restricted by umask.
if (!WINDOWS) .Internal(dirchmod(pkgname))
## Add build stamp to the DESCRIPTION file.
add_build_stamp_to_description_file(file.path(pkgname,
"DESCRIPTION"))
## Add expanded R fields to the DESCRIPTION file.
add_expanded_R_fields_to_description_file(file.path(pkgname,
"DESCRIPTION"))
messageLog(Log,
"checking for LF line-endings in source and make files")
fix_nonLF_in_source_files(pkgname, Log)
fix_nonLF_in_make_files(pkgname, Log)
messageLog(Log, "checking for empty or unneeded directories");
find_empty_dirs(pkgname)
for(dir in c("Meta", "R-ex", "chtml", "help", "html", "latex")) {
d <- file.path(pkgname, dir)
if (dir.exists(d)) {
msg <- paste("WARNING: Removing directory",
sQuote(d),
"which should only occur",
"in an installed package")
printLog(Log, paste(strwrap(msg, indent = 0L, exdent = 2L),
collapse = "\n"), "\n")
unlink(d, recursive=TRUE)
}
}
## remove subarch build directories
unlink(file.path(pkgname,
c("src-i386", "src-x64", "src-x86_64", "src-ppc")),
recursive = TRUE)
## work on 'data' directory if present
if(file_test("-d", file.path(pkgname, "data")) ||
file_test("-f", file.path(pkgname, "R", "sysdata.rda"))) {
messageLog(Log, "looking to see if a 'data/datalist' file should be added")
## in some cases data() needs the package installed as
## there are links to the package's namespace
tryCatch(add_datalist(pkgname),
error = function(e)
printLog(Log, " unable to create a 'datalist' file: may need the package to be installed\n"))
## allow per-package override
resave_data1 <- parse_description_field(desc, "BuildResaveData",
resave_data, FALSE)
resave_data_others(pkgname, resave_data1)
resave_data_rda(pkgname, resave_data1)
}
## add NAMESPACE if the author didn't write one
if(!file.exists(namespace <- file.path(pkgname, "NAMESPACE")) ) {