#! @PERL@
#-*- perl -*-

# Copyright (C) 2000-2002 R Development Core Team
#
# 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, 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 via WWW at
# http://www.gnu.org/copyleft/gpl.html.	 You can also obtain it by
# writing to the Free Software Foundation, Inc., 59 Temple Place,
# Suite 330, Boston, MA  02111-1307  USA.

# Send any bug reports to r-bugs@r-project.org

## <FIXME>
## This is not portable: has system().
## </FIXME>

use Cwd;
use File::Basename;
use File::Copy;
use File::Find;
use File::Path;
use Getopt::Long;
use R::Dcf;
use R::Logfile;
use R::Rdtools;
use R::Utils;
use R::Vars;
use Text::DelimMatch;
use Text::Wrap;

## don't buffer output
$| = 1;

my $revision = ' $Revision: 1.96 $ ';
my $version;
my $name;
$revision =~ / ([\d\.]*) /;
$version = $1;
($name = $0) =~ s|.*/||;

## Options
my $opt_clean = 1;
my $opt_examples = 1;
my $opt_tests = 1;
my $opt_latex = 1;
my $opt_use_gct = 0;
my $opt_codoc = 1;
my $opt_perms = 1;
my $opt_install = 1;
my $opt_vignettes = 1;

my $WINDOWS = ($R::Vars::OSTYPE eq "windows");

R::Vars::error("R_HOME", "R_CMD", "R_EXE");

my @knownoptions = ("help|h", "version|v", "outdir|o:s", "library|l:s",
		    "no-clean", "no-examples", "no-tests", "no-latex",
		    "use-gct" => \$opt_use_gct, "no-codoc", "no-perms",
		    "no-install", "no-vignettes");
GetOptions (@knownoptions) or usage();

R_version("R add-on package checker", $version) if $opt_version;
usage() if $opt_help;

$opt_clean = 0 if $opt_no_clean;
$opt_examples = 0 if $opt_no_examples;
$opt_tests = 0 if $opt_no_tests;
$opt_latex = 0 if $opt_no_latex;
$opt_codoc = 0 if $opt_no_codoc;
$opt_perms = 0 if $opt_no_perms;
$opt_install = 0 if $opt_no_install;
$opt_vignettes = 0 if $opt_no_vignettes;

my $startdir = cwd();
$opt_outdir = $startdir unless $opt_outdir;
chdir($opt_outdir)
    or die "Error: cannot change to directory '$opt_outdir'\n";
my $outdir = cwd();
chdir($startdir);

my $R_LIBS = $ENV{'R_LIBS'};
my $library;
if($opt_library) {
    chdir($opt_library)
	or die "Error: cannot change to directory '$opt_library'\n";
    $library = cwd();
    $ENV{'R_LIBS'} = env_path($library, $R_LIBS);

    chdir($startdir);
}

my $R_opts = "--vanilla";

if($opt_latex) {
    my $log = new R::Logfile();
    $log->checking("for working latex");
    open(TEXFILE,
	 "> " . &file_path(${R::Vars::TMPDIR}, "Rtextest$$.tex"))
      or die "Error: cannot write to Rtextest$$.tex\n";
    print TEXFILE "\\documentclass\{article\}\\begin\{document\}" .
	"test\\end\{document\}\n";
    close TEXFILE;
    chdir($R::Vars::TMPDIR);
    if(R_system("${R::Vars::LATEX} Rtextest$$ > Rtextest$$.out")) {
	$log->result("NO");
	$HAVE_LATEX = 0;
    } else {
	$log->result("OK");
	$HAVE_LATEX = 1;
    }
    unlink(<Rtextest$$.*>);
    chdir($startdir);
    $log->close();
}
## get the valid keywords for later ...
my %standard_keywords = ();
open(KEYWORDS,
     "< " . &file_path(${R::Vars::R_HOME}, "doc", "KEYWORDS.db"))
  or die "Error: cannot open 'KEYWORDS.db'";
while(<KEYWORDS>) {
    if(/^.*\|([^:]*):.*/) {
	$standard_keywords{$1} = 1;
    }
}
close KEYWORDS;

## this is the main loop over all packages to be checked
$#ARGV >= 0 or die "Error: no packages were specified";
foreach my $pkg (@ARGV) {
    ## $pkg should be the path to the package (bundle) root source
    ## directory, either absolute or relative to $startdir.
    ## $pkgdir is the corresponding absolute path.
    ## $pkgname is the name of the package (bundle).
    chdir($startdir);
    $pkg =~ s/\/$//;
    (-d $pkg) or die "Error: package dir '$pkg' does not exist";
    chdir($pkg)
	or die "Error: cannot change to directory '$pkg'\n";
    my $pkgdir = cwd();
    my $pkgname = basename($pkgdir);
    chdir($startdir);

    my $pkgoutdir = &file_path($outdir, "$pkgname.Rcheck");
    rmtree($pkgoutdir) if ($opt_clean && (-d $pkgoutdir)) ;
    if(! -d $pkgoutdir) {
	if(! mkdir($pkgoutdir, 0755)) {
	    die("Error: cannot create directory '$pkgoutdir'\n");
	    exit(1);
	}
    }

    $log = new R::Logfile(&file_path($pkgoutdir, "00check.log"));
    $log->message("using log directory '$pkgoutdir'");

    if(! $opt_library) {
	$library = $pkgoutdir;
	$ENV{'R_LIBS'} = env_path($library, $R_LIBS);
    }

    my $description;
    my $is_base_pkg = 0;
    ## Package sources from the R distribution are special.  They have a
    ## `DESCRIPTION.in' file (instead of `DESCRIPTION'), with Version
    ## field containing `@VERSION@' for substitution by configure.  We
    ## test for such packages by looking for `DESCRIPTION.in' with
    ## Priority `base', and skip the installation test for such
    ## packages.
    if(-r &file_path($pkgdir, "DESCRIPTION.in")) {
	$description =
	  new R::Dcf(&file_path($pkgdir, "DESCRIPTION.in"));
	if($description->{"Priority"} eq "base") {
	    $log->message("looks like '${pkgname}' is a base package");
	    $log->message("skipping installation test");
	    $is_base_pkg = 1;
	}
    }

    if(!$is_base_pkg) {
	if($opt_install) {
	    print("\n");
	    if(system("${R::Vars::R_CMD} INSTALL -l $library $pkgdir")) {
		$log->error();
		$log->print("Installation failed.\n");
		exit(1);
	    }
	    print("\n");
	}

	$log->checking(join("",
			    ("for file '",
			     &file_path($pkgname, "DESCRIPTION"),
			     "'")));
	if(-r &file_path($pkgdir, "DESCRIPTION")) {
	    $description =
	      new R::Dcf(&file_path($pkgdir, "DESCRIPTION"));
	    $log->result("OK");
	}
	else {
	    $log->result("NO");
	    exit(1);
	}
    }

    my $is_bundle = 0;
    if($description->{"Contains"}) {
	$log->message("looks like '${pkgname}' is a package bundle");
	$is_bundle = 1;
	my @bundlepkgs = split(/\s+/, $description->{"Contains"});
	foreach my $ppkg (@bundlepkgs) {
	    $log->message("checking '$ppkg' in bundle '$pkgname'");
	    $log->setstars("**");
	    chdir($startdir);
	    check_pkg(&file_path($pkgdir, $ppkg), $pkgoutdir, $startdir,
		      $library, $is_bundle, $description, $log,
		      $is_base_pkg);
	    $log->setstars("*");
	}
    }
    else {
	$is_bundle = 0;
	chdir($startdir);
	check_pkg($pkgdir, $pkgoutdir, $startdir, $library,
		  $is_bundle, $description, $log, $is_base_pkg);
    }

    if($log->{"warnings"}) {
	print("\n") ;
	$log->summary();
    }
    $log->close();
    print("\n");
}

#**********************************************************

sub check_pkg {

    my ($pkg, $pkgoutdir, $startdir, $library,
	$in_bundle, $description, $log, $is_base_pkg) = @_;
    my ($pkgdir, $pkgname);

    ## $pkg is the argument we received from the main loop.
    ## $pkgdir is the corresponding absolute path,
    ## $pkgname the name of the package.
    ## Note that we need to do repeat the checking from the main loop in
    ## the case of package bundles (and we could check for this).
    $log->checking("package directory");
    chdir($startdir);
    $pkg =~ s/\/$//;
    if(-d $pkg) {
	chdir($pkg)
	  or die "Error: cannot change to directory '$pkg'\n";
	$pkgdir = cwd();
	$pkgname = basename($pkgdir);
    }
    else {
	$log->error("Error: package dir '$pkg' does not exist");
	exit(1);
    }
    $log->result("OK");

    chdir($pkgdir);

    ## Check for sufficient file permissions (Unix only).

    ## This is a bit controversial, and hence has an option `--no-perms'
    ## to turn this off.  In fact, the code below does a bit too much.
    ## What would really be needed is the following:
    ## * All dirs or files must be at least 555 or 444, respectively.
    ## * Everything that gets installed must be writeable.  This
    ##   includes DESCRIPTION COPYING INDEX TITLE data/* demo/* exec/*
    ##   and inst/*.
    ## * All directories used for building `objects' must be at least
    ##   755.  This includes `.' and src.
    ## Given time, the above could be implemented.

    if($opt_perms && ($R::Vars::OSTYPE eq "unix")) {
	$log->checking("for sufficient/correct file permissions");
	my @badfiles = ();
	my @excludepatterns = R::Utils::get_exclude_patterns();
	if(-f "./.Rbuildignore") {
	    open(RBUILDIGNORE, "./.Rbuildignore");
	    while(<RBUILDIGNORE>) {
		chop;
		push(@excludepatterns, $_) if $_;
	    }
	    close(RBUILDIGNORE);
	}

	## Phase A.  Directories at least 755, files at least 644.
	sub findWrongPermsA {
	    my $filename = $File::Find::name;
	    $filename =~ s/^[^\/]*\///;
	    foreach my $p (@excludepatterns) {
		return 0 if($filename =~ /$p/);
	    }
	    if(-d $_ && (((stat $_)[2] & 00755) < oct("755"))) {
		push @badfiles, $File::Find::name;
	    }
	    if(-f $_ && (((stat $_)[2] & 00644) < oct("644"))) {
		push @badfiles, $File::Find::name;
	    }
	}
        find(\&findWrongPermsA, ".");
        if($#badfiles >= 0) {
	    $log->error();
	    $log->print("Found the following files with " .
			"insufficient permissions:\n");
	    $log->print("  " . join("\n  ", @badfiles) . "\n");
	    $log->print(wrap("", "",
			     ("Permissions should be at least 755",
			      "for directories and 644 for files.\n")));
	    $log->print("Please fix permissions and try again.\n");
	    exit(1);
	}

	## Phase B.  Text files (as determined by their extensions)
	## should really be mode 644.
	@badfiles = ();
	my @textfile_patterns =
	  ("\\.[RSdqr]\$",	# R source code
	   "\\.[Rr]d\$",	# Rd files
	   "\\.([Ccfh]|cc|cpp)\$",
				# C/C++/FORTRAN sources and headers
	   "^(DESCRIPTION|INDEX|README|TITLE)\$");
	sub findWrongPermsB {
	    my $filename = $File::Find::name;
	    $filename =~ s/^[^\/]*\///;
	    foreach my $p (@excludepatterns) {
		return 0 if($filename =~ /$p/);
	    }
	    if(-f $_ && (((stat $_)[2] & 00777) != oct("644"))) {
		foreach my $p (@textfile_patterns) {
		    if($filename =~ /$p/) {
			push @badfiles, $File::Find::name;
			last;
		    }
		}
	    }
	}
	find(\&findWrongPermsB, ".");
	if($#badfiles >= 0) {
	    $log->warning();
	    $log->print("Found the following text files with " .
			"incorrect permissions:\n");
	    $log->print("  " . join("\n  ", @badfiles) . "\n");
	    $log->print(wrap("", "",
			     ("Permissions for text files",
			      "(including R, Rd, and C/C++/FORTRAN",
			      "sources) should be exactly 644.\n")));
	    $log->print("Please fix permissions.\n");
	}
	else {
	    $log->result("OK");
	}
    }

    if($in_bundle) {		# join DESCRIPTION and DESCRIPTION.in
        if(-r "DESCRIPTION.in") {
	    $log->checking("for file 'DESCRIPTION.in'");
	    my $description_in = new R::Dcf("DESCRIPTION.in");
	    foreach my $key (keys(%$description)) {
		$description_in->{$key} = $description->{$key};
	    }
	    ## from now on use $description_in instead of $description
	    ## in this subroutine
	    $description = $description_in;
	    $log->result("OK");
	    $log->message("joining DESCRIPTION and DESCRIPTION.in");
	}
	else {
	    $log->result("NO");
	    exit(1);
	}
    }

    ## Check mandatory entries in DESCRIPTION:
    ##   Package, Version, License, Description, Title, Author,
    ##   Maintainer.

    my @msg_DESCRIPTION
      = ("See the information on DESCRIPTION files",
	 "in section 'Creating R packages'",
	 "of the 'Writing R Extensions' manual.\n");

    $log->checking("DESCRIPTION Package field");
    if(! $description->{"Package"}) {
	$log->error();
	$log->print("No DESCRIPTION Package field found.\n");
	$log->print(wrap("", "", @msg_DESCRIPTION));
        exit(1);
    }
    my $tmp = $description->{"Package"};
    if($description->{"Package"} ne $pkgname) {
	$log->error();
	$log->print("DESCRIPTION Package field differs from dir name.\n");
	exit(1);
    }
    $log->result("OK");

    $log->checking("DESCRIPTION Version field");
    if(! $description->{"Version"}) {
	$log->error();
	$log->print("No DESCRIPTION Version field found.\n");
	$log->print(wrap("", "", @msg_DESCRIPTION));
	exit(1);
    }
    if(($description->{"Version"} =~ /[^\d\.\-]/) && !$is_base_pkg) {
	## Package sources from the R distribution have `@VERSION@' in
	## their `DESCRIPTION.in' files ...
	$log->error();
	$log->print("Version may only contain digits, '.' and '-'.\n");
	$log->print(wrap("", "", @msg_DESCRIPTION));
	exit(1);
    }
    $log->result("OK");

    foreach my $field (qw(License Description Title Author)) {
	$log->checking("DESCRIPTION $field field");
	if(! $description->{$field}) {
	    $log->error();
	    $log->print("No DESCRIPTION $field field found.\n");
	    $log->print(wrap("", "", @msg_DESCRIPTION));
	    exit(1);
	}
	$log->result("OK");
    }

    $log->checking("DESCRIPTION Maintainer field");
    if(!$description->{"Maintainer"}) {
	$log->error();
	$log->print("No DESCRIPTION Maintainer field found.\n");
	$log->print(wrap("", "", @msg_DESCRIPTION));
	exit(1);
    }
    elsif($description->{"Maintainer"} !~ /^[^<>]*<[^<>]+> *$/) {
	$log->error();
	$log->print("Malformed Maintainer field.\n");
	$log->print(wrap("", "", @msg_DESCRIPTION));
	exit(1);
    }
    else {
	$log->result("OK");
    }

    if($description->{"Depends"}) {
	$log->checking("DESCRIPTION Depends field");
	my @dependencies = split(/\,/, $description->{"Depends"});
	my $any = 0;
	foreach my $dep (@dependencies) {
	    $dep =~ /^\s*(\w+)(\s*\(([^) ]+)\s+([^) ]+)\))?\s*$/;
	    ## The entry is malformed if there is no match, or there is
	    ## a match but the dep_op is different from `<=' or `>', or
	    ## the dep_version does not only consist of digits, `.' or
	    ## `-'.
	    if(!($1) || ($2 && (!(($3 eq "<=") || ($3 eq ">="))
				|| ($4 =~ /[^\d\.\-]/)))) {
		$any++;
		break;
	    }
	}
	if($any == 0) {
	    $log->result("OK")
	}
	else {
	    $log->error();
	    $log->print("Malformed Depends field.\n");
	    $log->print(wrap("", "", @msg_DESCRIPTION));
	    exit(1);
	}
    }

    ## Check R code for syntax errors.

    if(!$is_base_pkg && -d "R") {
	$log->checking("R files for syntax errors");
	my @Rfiles = &list_files_with_exts("R", "[RrSsq]");
	my $Rcmd = "Rfiles <- c(\"";
	$Rcmd .= join("\", \"", @Rfiles) . "\")\n";
	$Rcmd .= "for(f in Rfiles)\n";
	$Rcmd .= "if(inherits(try(parse(f)), \"try-error\")) stop(f)\n";
        my @out = R_runR($Rcmd, "${R_opts} --quiet");
	@out = grep(/^Error:/, @out);
	if($#out >= 0) {
	    my $Rfile = $out[0];
	    $Rfile =~ s/^Error: *//;
	    $log->error();
	    $log->print("Syntax error in file " . $Rfile . "\n");
	    exit(1);
	}
	else {
	    $log->result("OK");
	}
    }

    ## Check usage of library.dynam (if any).

    if(!$is_base_pkg && -d "R") {
	$log->checking("R files for library.dynam");
	my @Rfiles;
	if($opt_install) {
	    ## Only need to check the installed file (if installed).
	    @Rfiles = (&file_path($library, $pkgname, "R", $pkgname));
	}
	else {
	    ## Otherwise (if the package was not installed), we need to
	    ## check all R code files.
	    @Rfiles = &list_files_with_exts("R", "[RrSsq]");
	}
	my $any = 0;
	my $ext;
	foreach my $Rfile (@Rfiles) {
	    last if $any;
	    open(RFILE, "< $Rfile")
	      or die "Error: cannot open file '$Rfile' for reading";
	    while(<RFILE>) {
		if(/library.dynam\(\"(.*?)\"/o) {
		    my $arg = $1;
		    if($arg =~ /\.(so|sl|dll)$/) {
			$ext = $1;
			$any++;
			last;
		    }
		}
	    }
	    close(RFILE);
	}
	if($any == 0) {
	    $log->result("OK");
	}
	else {
	    $log->error();
	    $log->print("library.dynam() used with extension '.$ext'\n");
	    $log->print(wrap("", "",
			     ("The system-specific extension for",
			      "shared libraries should not be added.\n")));
	    $log->print("See ?library.dynam\n");
	    exit(1);
	}
    }

    ## Check whether methods have all arguments of the corresponding
    ## generic.

    if(-d "R") {
	$log->checking("generic/method consistency");

	my $Rcmd = "library(tools)\n";
	if($opt_install && ($R::Vars::OSTYPE eq "unix")) {
	    $Rcmd .= "checkMethods(package = \"${pkgname}\")\n";
	}
        else {
	    $Rcmd .= "checkMethods(dir = \"${pkgdir}\")\n";
	}

        my @out = R_runR($Rcmd, "${R_opts} --quiet");
	@out = grep(!/^\>/, @out);
	if($#out>=0) {
	    $log->warning();
	    $log->print(join("\n", @out) . "\n");
	}
	else {
	    $log->result("OK");
	}
    }

    ## Check whether assignment functions have their final argument
    ## named `value'.

    if(-d "R") {
	$log->checking("for assignment functions with final arg not " .
		       "named 'value'");
	my $Rcmd = "library(tools)\n";
	if($opt_install && ($R::Vars::OSTYPE eq "unix")) {
	    $Rcmd .= "checkAssignFuns(package = \"${pkgname}\")\n";
	}
	else {
	    $Rcmd .= "checkAssignFuns(dir = \"${pkgdir}\")\n";
	}

        my @out = R_runR($Rcmd, "${R_opts} --quiet");
        @out = grep(!/^\>/, @out);
	if($#out>=0) {
            ## <FIXME>
            ## Change back from warning() to error() and exit when we
            ## have output from loading packages under control.
	    $log->warning();
	    $log->print(join("\n", @out) . "\n");
	    ## exit(1);
            ## </FIXME>
	}
	else {
	    $log->result("OK");
	}
    }

    ## Check R documentation files.

    if(-d "man") {
	$log->checking("Rd files");
	my @rdfiles = &list_files_with_exts("man", "[Rr]d");
	my $manOSdir = &file_path("man", $R::Vars::OSTYPE);
	if(-d $manOSdir) {
	    @rdfiles = (@rdfiles,
			&list_files_with_exts($manOSdir, "[Rr]d"));
	}
	my @badfiles = grep(/</, @rdfiles);
	if($#badfiles >= 0) {
	    $log->error();
	    $log->print("Cannot handle Rd file names containing '<'.\n" .
			"These are not legal file names on all R " .
			"platforms.\n" .
			"Please rename the following files and " .
			"try again:\n");
	    $log->print("  " . join("\n  ", @badfiles) . "\n");
	    exit(1);
	}

	@rdfiles = sort(@rdfiles);
	my $file;
	my @mandatoryTags = qw(name alias title description keyword);
	my @uniqueTags = qw(name title description usage arguments
			    format details value references source
			    seealso examples note author synopsis);
	my @badbraces;
	my %badmandatory;
	my %badunique;
	my %badkeywords;

	## create hash allTags with all tags found in mandatory Tags and
	## uniqueTags
	my %allTags;
	foreach my $tag (@mandatoryTags, @uniqueTags) {
	    $allTags{$tag}++;
	}

	foreach my $rdfile (@rdfiles) {
	    open(RDFILE, "< $rdfile")
	      or die "Error: cannot open '$rdfile' for reading\n";

	    my %keywords;
	    my %tagcount;
	    while(<RDFILE>) {
		my $line = $_;
		foreach my $tag (keys %allTags) {
		    if($line =~ /^\s*\\$tag/) {
			$tagcount{$tag}++;
		    }
		}
                if($line =~ /^\s*\\keyword{\s*([^}]*[^}\s])\s*}.*/) {
                    $keywords{$1} = 1;
                }
	    }
	    close RDFILE;

	    foreach my $tag (@mandatoryTags) {
		push(@{$badmandatory{$tag}}, $rdfile)
		    unless $tagcount{$tag}>0;
	    }
	    foreach my $tag (@uniqueTags) {
		push(@{$badunique{$tag}}, $rdfile)
		    unless $tagcount{$tag}<=1;
	    }
            foreach my $key (keys(%keywords)) {
                push(@{$badkeywords{$rdfile}}, $key)
                    unless $standard_keywords{$key};
            }

	    ## Check for unbalanced braces.
	    my $text = "";
	    ## Read the Rd file via Rdpp, and get rid of the \alias
	    ## entries as these may have unbalanced braces (Paren.Rd).
	    my @lines = split(/\n/, &Rdpp($rdfile, $R::Vars::OSTYPE));
	    foreach my $line (@lines) {
		$text .= "\n$line" unless ($line =~ /^\\alias/);
	    }
	    $text .= "\n";
	    my $delimcurly = new Text::DelimMatch;
	    $delimcurly->delim("\{", "\}");
	    $delimcurly->escape("\\");
	    $text =~ s/([^\\])%.*\n/$1\n/g; # ???
	    ## Now loop through matching pairs of braces.
	    while($delimcurly->match($text)) {
		$text = $delimcurly->post_matched;
	    }
	    ## Get rid of trailing comments.
	    $text =~ s/^%.*\n/\n/gs;
	    $text =~ s/\n%.*\n/\n/gs;
	    ## Anything left in $text means unbalanced.
	    if(!($text =~ /^\s*$/)) {
		push(@badbraces, $rdfile);
	    }

	}

	my $any = 0;

	if($#badbraces >= 0) {
	    $log->error();
	    $log->print("Rd files with unbalanced braces:\n");
	    $log->print("  " . join("\n  ", @badbraces) . "\n");
	    $log->print(wrap("", "",
			     ("Unbalanced braces are Rd syntax",
			      "errors, and result in incorrect",
			      "documentation.\n")));
	    exit(1);
	}

	my @msg_writing_Rd
	  = ("See chapter 'Writing R documentation'",
	     "in manual 'Writing R Extensions'.\n");

	my $any_missing_mandatory_tag = 0;
	foreach my $tag (@mandatoryTags) {
	    if(exists $badmandatory{$tag}) {
		$log->warning("") unless $any;
		$any++;
		$any_missing_mandatory_tag++;
		$log->print("Rd files without '${tag}':\n");
		$log->print("  " .
			    join("\n  ", @{$badmandatory{$tag}}) .
			    "\n");
	    }
	}
	if($any_missing_mandatory_tag) {
	    $log->print("These tags are required in an Rd file.\n");
	    $log->print(wrap("", "", @msg_writing_Rd));
	}

	my $any_duplicate_unique_tag = 0;
	foreach my $tag (@uniqueTags) {
	    if(exists $badunique{$tag}) {
		$log->warning("") unless $any;
		$any++;
		$any_duplicate_unique_tag++;
		$log->print("Rd files with duplicate '${tag}':\n");
		$log->print("  " .
			    join("\n  ", @{$badunique{$tag}}) .
			    "\n");
	    }
	}
	if($any_duplicate_unique_tag) {
	    $log->print("These tags must be unique in an Rd file.\n");
	    $log->print(wrap("", "", @msg_writing_Rd));
	}

        if(keys(%badkeywords)) {
	    $log->warning("") unless $any;
	    $any++;
	    $log->print("Rd files with non-standard keywords:\n");
            foreach my $file (keys(%badkeywords)) {
                $log->print(wrap("  ", "    ",
				   ("'$file':",
				    @{$badkeywords{$file}},
				    "\n")));
            }
	    $log->print(wrap("", "",
			     ("Each '\\keyword' entry should specify",
			      "one of the standard keywords",
			      "(as listed in file 'KEYWORDS.db'",
			      "in the 'doc' subdirectory",
			      "of the R home directory).\n")));
	    $log->print(wrap("", "", @msg_writing_Rd));
        }

	$log->result("OK") unless $any;
    }

    ## Check for undocumented objects.

    if(((-d "R") || (-d "data")) && -d "man") {
	$log->checking("for undocumented objects");

	my $Rcmd = "library(tools)\n";
	if($opt_install && ($R::Vars::OSTYPE eq "unix")) {
	    $Rcmd .= "undoc(package = \"${pkgname}\")\n";
	}
	else {
	    $Rcmd .= "undoc(dir = \"${pkgdir}\")\n";
	}

        my @out = R_runR($Rcmd, "${R_opts} --quiet");
	my @err = grep(/^Error/, @out);
	@out = grep(!/^\>/, @out);
	if($#err<0) {
	    if($#out>=0) {
		$log->warning();
                $log->print(join("\n", @out) . "\n");
	    }
	    else {
		$log->result("OK");
	    }
	}
	else {
	    $log->error();
	    $log->print(join("\n", @err) . "\n");
	    exit(1);
	}
    }

    ## Check for code/documentation mismatches.

    if($opt_codoc && ((-d "R") || (-d "data")) && -d "man") {
	$log->checking("for code/documentation mismatches");

	my $Rcmd = "library(tools)\n";
	if($opt_install && ($R::Vars::OSTYPE eq "unix")) {
	    $Rcmd .= "codoc(package = \"${pkgname}\")\n";
	}
	else {
	    $Rcmd .= "codoc(dir = \"${pkgdir}\")\n";
	}
        my @out = R_runR($Rcmd, "${R_opts} --quiet");

	## <FIXME>
	## With the current heuristics codoc() may throw an error even
	## though the documentation is valid.  Change this when we know
	## what must be valid R code, similar to the above for undoc().
	@out = grep(!/^\>/, @out);
	if($#out>=0) {
	    $log->warning();
	    $log->print(join("\n", @out) . "\n");
	}
	else {
	    $log->result("OK");
	}
	## </FIXME>
    }

    ## Check whether all arguments shown in \usage are documented in
    ## \arguments.

    if(-d "man") {
	$log->checking("for undocumented arguments in \\usage");

	my $Rcmd = "library(tools)\n";
	if($opt_install && ($R::Vars::OSTYPE eq "unix")) {
	    $Rcmd .= "checkDocArgs(package = \"${pkgname}\")\n";
	}
	else {
	    $Rcmd .= "checkDocArgs(dir = \"${pkgdir}\")\n";
	}

        my @out = R_runR($Rcmd, "${R_opts} --quiet");
	@out = grep(!/^\>/, @out);
	if($#out>=0) {
	    $log->warning();
	    $log->print(join("\n", @out) . "\n");
	}
	else {
	    $log->result("OK");
	}
    }

    ## Check C sources/headers for CRLF line endings.

    if(-d "src") {
	$log->checking("for CRLF line endings in C sources/headers");
	my @srcfiles = &list_files_with_exts("src", "[ch]");
	my @badfiles = ();
	foreach my $file (@srcfiles) {
	    open(SRCFILE, "< $file")
	      or die "Error: cannot open '$file' for reading\n";
            binmode(SRCFILE);	# for Windows
	    while(<SRCFILE>) {
		chop;
		if($_ =~ /\r$/) {
		    push(@badfiles, $file);
		    last;
		}
	    }
	    close(SRCFILE);
	}
	if($#badfiles >= 0) {
	    $log->warning();
	    $log->print("Found the following C sources/headers with " .
			"CRLF line endings:\n");
	    $log->print("  " . join("\n  ", @badfiles) . "\n");
	    $log->print("ISO C requires CR line endings.\n");
	}
	else {
	    $log->result("OK");
	}
    }

    chdir($pkgoutdir);

    ## Run the examples.

    if($opt_examples && -d &file_path($library, $pkgname, "R-ex")) {
	$log->creating("${pkgname}-Ex.R");
	my $Rexdir = &file_path($library, $pkgname, "R-ex");
        my $iszipped = 0;
	my $cmd;

        if(-e &file_path($Rexdir, "Rex.zip")) {
            $iszipped = 1;
	    my $UNZIP = &R_getenv("R_UNZIPCMD", "unzip -q");
            system(join(" ",
			("$UNZIP",
			 &file_path($Rexdir, Rex.zip),
			 " -d $Rexdir")));
        }
        if($WINDOWS) {
            ## avoid Rcmd as line may be too long after expansion.
            $cmd = "perl ${R::Vars::R_HOME}/bin/massage-Examples ".
  		     "${pkgname} ${library}/${pkgname}/R-ex/*.R ".
  		     "> ${pkgname}-Ex.R";
        } else {
	    $cmd = join(" ",
			("${R::Vars::R_CMD} perl",
			 &file_path(${R::Vars::R_HOME}, "share", "perl",
				    "massage-Examples.pl"),
			 "${pkgname} ${Rexdir} > ${pkgname}-Ex.R"));
        }

 	if(R_system($cmd)) {
  	    $log->error();
  	    exit(1);
        }
        if($iszipped) {
            unlink(&list_files_with_exts($Rexdir, "R"));
        }

	$log->result("OK");
	$log->checking("examples");

	if($opt_use_gct) {
            $cmd = "(echo 'gctorture(TRUE)'; cat ${pkgname}-Ex.R) " .
	      "| ${R::Vars::R_EXE} ${R_opts} > ${pkgname}-Ex.Rout";
	}
	else {
            $cmd = "${R::Vars::R_EXE} ${R_opts} " .
	      "< ${pkgname}-Ex.R > ${pkgname}-Ex.Rout";
	}
	if(R_system($cmd)) {
	    $log->error();
	    $log->print("Running examples failed.\n");
	    exit(1);
	}
	$log->result("OK");
    }

    ## Run the package-specific tests.

    if($opt_install && $opt_tests && (-d &file_path($pkgdir, "tests"))) {
        $log->checking("tests");
        my $testsrcdir = &file_path($pkgdir, "tests");
        my $testdir = &file_path($pkgoutdir, "tests");
        if(! -d $testdir) {
            if(! mkdir($testdir, 0755)) {
	        die "Error: cannot create directory $testdir\n";
	        exit(1);
	    }
        }
        chdir($testdir);
	foreach my $file (&list_files($testsrcdir)) {
	    copy($file, basename($file));
	}
        my $makefiles = "-f " . &file_path(${R::Vars::R_HOME},
					   "share", "make",
					   "tests.mk");
        if($WINDOWS) {
            $makefiles = "-f ${R::Vars::R_HOME}/share/make/wintests.mk";}
        my $makevars = "";
        if($WINDOWS && (-r "$testsrcdir/Makefile.win")) {
            $makefiles .= " -f $testsrcdir/Makefile.win";
        }
        elsif(-r &file_path($testsrcdir, "Makefile")) {
            $makefiles .= " -f " . &file_path($testsrcdir, "Makefile");
        }
        if($WINDOWS && (-r "$testsrcdir/Makevars.win")) {
            $makevars = " -f $testsrcdir/Makevars.win";
        }
        elsif(-r &file_path($testsrcdir, "Makevars")) {
            $makevars = " -f " . &file_path($testsrcdir, "Makevars");
        }
        else {
            open MAKEVARS, "> Makevars";
            print MAKEVARS "makevars = -f Makevars\n";
            print MAKEVARS "srcdir = $testsrcdir\n";
            ## at least windows does not pass env correctly to make
            print MAKEVARS "R_LIBS = $ENV{'R_LIBS'}\n";
            print MAKEVARS "VPATH = \$(srcdir)\n\n";
            print MAKEVARS "test-src-1 =";
	    foreach my $file (&list_files_with_exts($testdir, "R")) {
                print MAKEVARS "\\\n " . basename($file);
            }
            print MAKEVARS "\n";
            print MAKEVARS "test-src-auto =";
	    foreach my $file (&list_files_with_exts($testdir, "Rin")) {
                $file =~ s/Rin$/R/;
                print MAKEVARS "\\\n " . basename($file);
            }
            print MAKEVARS "\n";
	    print MAKEVARS "USE_GCT = $opt_use_gct\n";
            close MAKEVARS;
            $makevars = " -f Makevars";
        }
        print "\n";
        if(system("$R::Vars::MAKE $makefiles $makevars")) {
            $log->error();
            exit(1);
        }
        chdir($pkgoutdir);
        $log->result("OK");
    }

    chdir($pkgoutdir);

    if($opt_vignettes && (-d &file_path($pkgdir, "inst", "doc"))) {
	$log->checking(join("",
			    ("Sweave files in '",
			     &file_path("inst", "doc"),
			     "'")));


	my $Rcmd = "library(tools)\n";
	if($opt_install && ($R::Vars::OSTYPE eq "unix")) {
	    $Rcmd .= "checkVignettes(package=\"${pkgname}\", " .
                     "lib.loc = \"$pkgoutdir\", " .
                     "workdir=\"src\")\n";
	}
	else {
	    $Rcmd .= "checkVignettes(dir = \"${pkgdir}\")\n";
	}

        my @out = R_runR($Rcmd, "${R_opts} --quiet");
	@out = grep(!/^\>/, @out);
	if($#out>=0) {
	    $log->warning();
	    $log->print(join("\n", @out) . "\n");
	}
	else {
	    $log->result("OK");
	}
    }

    ## Run LaTeX on the manual.

    if($opt_latex) {
	if(-d &file_path($library, $pkgname, "latex")) {
	    $ENV{'TEXINPUTS'} =
	      env_path(&file_path($R::Vars::R_HOME, "share", "texmf"),
		       $ENV{'TEXINPUTS'});
	    $log->creating("${pkgname}-manual.tex");
	    open MANUAL, "> ${pkgname}-manual.tex";
	    print MANUAL "\\documentclass\{article\}\n" .
	      "\\usepackage[ae,hyper]\{Rd\}\n\\begin\{document\}\n";
	    my @texfiles =
	      &list_files_with_exts(&file_path($library, $pkgname,
					       "latex"),
				    "tex");
	    foreach my $file (@texfiles) {
		open(FILE, "< $file")
		  or die("Error: cannot open file '$file' for reading");
		while(<FILE>) {
		    print MANUAL $_;
		}
		close FILE;
	    }
	    print MANUAL "\\end\{document\}\n";
	    close MANUAL;
	    $log->result("OK");
	    if($HAVE_LATEX) {
		$log->checking("${pkgname}-manual.tex");
		print "\n";
		if(R_system("${R::Vars::LATEX} ${pkgname}-manual")) {
		    $log->error();
		    exit(1);
		}
		$log->result("OK");
	    }
	}
	else {
	    if($HAVE_LATEX) {
		$log->checking("DVI version of manual");
		my $Rd2dvi_opts = "--no-preview -o ${pkgname}-manual.dvi";
		## <FIXME>
		## Surely there is a better way?
		$Rd2dvi_opts .= ">/dev/null 2>&1"
		  if($R::Vars::OSTYPE eq "unix");
		## </FIXME>
		if(R_system("${R::Vars::R_CMD} Rd2dvi " .
			    "${Rd2dvi_opts} $pkgdir")) {
		    $log->error();
		    $log->print("Could not create DVI version.\n");
		    $log->print("This typically indicates Rd problems.\n");
		    exit(1);
		}
		$log->result("OK");
	    }
	}
    }
}

#**********************************************************

sub usage {
    print STDERR <<END;
Usage: R CMD $name [options] pkgdirs

Check R packages from package sources in the directories specified by
pkgdirs.  A variety of diagnostic checks on directory structure, index
and control files are performed.  The package is installed into the log
directory (which includes the translation of all Rd files into several
formats), and the Rd files are tested by LaTeX (if available).  All
examples and tests provided by the package are tested if they run
successfully.

Options:
  -h, --help            print short help message and exit
  -v, --version         print version info and exit
  -l, --library=LIB     library directory used for test installation
                        of packages (default is outdir)
  -o, --outdir=DIR      directory used for logfiles, R output, etc.
                        (default is 'pkg.Rcheck' in current directory,
			where 'pkg' is the name of the package checked)
      --no-clean        do not clean outdir before using it
      --no-perms        do not check sufficient/correct file permissions
      --no-codoc        do not check for code/documentation mismatches
      --no-examples     do not run the examples in the Rd files
      --no-install      skip installation and associated tests
      --no-tests        do not run code in tests subdirectory
      --no-vignettes    do not check vignettes in Sweave format
      --no-latex        do not run LaTeX on help files
      --use-gct         use 'gctorture(TRUE)' when running examples/tests

By default, all test sections are turned on.

Email bug reports to <r-bugs\@r-project.org>.
END
    exit 0;
}