From 9d6b5f35bbae817f76a5099702e13836e5957d80 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Sat, 17 Sep 2022 08:11:13 -0700 Subject: [PATCH] Import Upstream version 0.24 --- Changes | 94 +++++ MANIFEST | 27 ++ META.yml | 32 ++ Makefile.PL | 41 ++ README | 200 +++++++++ inc/Module/Install.pm | 470 +++++++++++++++++++++ inc/Module/Install/Base.pm | 83 ++++ inc/Module/Install/Can.pm | 81 ++++ inc/Module/Install/External.pm | 66 +++ inc/Module/Install/Fetch.pm | 93 +++++ inc/Module/Install/Makefile.pm | 414 +++++++++++++++++++ inc/Module/Install/Metadata.pm | 722 +++++++++++++++++++++++++++++++++ inc/Module/Install/Win32.pm | 64 +++ inc/Module/Install/WriteAll.pm | 63 +++ lib/Statistics/R.pm | 617 ++++++++++++++++++++++++++++ lib/Statistics/R/Legacy.pm | 188 +++++++++ lib/Statistics/R/Win32.pm | 191 +++++++++ t/00-load.t | 12 + t/01-pod.t | 9 + t/02-legacy.t | 57 +++ t/03-run.t | 80 ++++ t/04-start-stop.t | 46 +++ t/05-shared.t | 53 +++ t/06-get-set.t | 99 +++++ t/07-robust.t | 25 ++ t/08-errors.t | 26 ++ t/data/script.R | 24 ++ 27 files changed, 3877 insertions(+) create mode 100644 Changes create mode 100644 MANIFEST create mode 100644 META.yml create mode 100644 Makefile.PL create mode 100644 README create mode 100644 inc/Module/Install.pm create mode 100644 inc/Module/Install/Base.pm create mode 100644 inc/Module/Install/Can.pm create mode 100644 inc/Module/Install/External.pm create mode 100644 inc/Module/Install/Fetch.pm create mode 100644 inc/Module/Install/Makefile.pm create mode 100644 inc/Module/Install/Metadata.pm create mode 100644 inc/Module/Install/Win32.pm create mode 100644 inc/Module/Install/WriteAll.pm create mode 100644 lib/Statistics/R.pm create mode 100644 lib/Statistics/R/Legacy.pm create mode 100644 lib/Statistics/R/Win32.pm create mode 100644 t/00-load.t create mode 100644 t/01-pod.t create mode 100644 t/02-legacy.t create mode 100644 t/03-run.t create mode 100644 t/04-start-stop.t create mode 100644 t/05-shared.t create mode 100644 t/06-get-set.t create mode 100644 t/07-robust.t create mode 100644 t/08-errors.t create mode 100644 t/data/script.R diff --git a/Changes b/Changes new file mode 100644 index 0000000..5635c25 --- /dev/null +++ b/Changes @@ -0,0 +1,94 @@ +Revision history for Perl extension Statistics::R. + +0.24 2011-11-09 + - Require Text::Balanced >= 0.97 to prevent bad surprises (reported by Ryan Golhar) + +0.23 2011-10-28 + - Arrays of number-containing strings are now handled properly (RT bug + #71988, patch by dheiman) + +0.22 2011-10-09 + - The run() method now accepts an array of strings as input + - New run_from_file() method to read and execute commands from an R file + - Better detection of R errors by using the R exception system (issue + reported by Mike Imelfort) + - Updated error handling mechanism to detect R syntax errors in addition + to R runtime errors + - Tests now work for different locales (issue reported by Knut Behrends) + +0.21 2011-09-04 + - Tweaked the regular expressions that parse the R output stream for added + speed and robustness + +0.20 2011-08-31 + - Refactored the entire R communication bridge to avoid writing and reading + files. All data is now stored in memory and passed by pipes. This fixes + bug RT #11309, #11918, #66190 and #70314 + - Refactored the communications in shared mode + - Put platform-specific code and legacy code in separate modules + +0.10 2011-08-27 + - Refactoring to remove old code doing platform-specific operations. + - Lots of code cleanup + - Removed the now useless r_dir and tmp_dir options of new() + - Fix for change of dir bug (RT #6724). Also fixes missing synopsis file (RT #70307) + - More subtle cleanup procedure (RT #70392) + +0.09 2011-08-23 + - Changes in the new() method: + * it automatically calls start() + * it has the 'shared' option to start a shared bridge + - More portable filenames (RT #70391) + - Added convenience methods: + * run() replaces send() and read() and checks for errors (RT #70361) + * get() fetches the values in an R vector (RT #70361) + * set() assigns values to an R vector + - Fixed a bug in the unlock() method + - Removed the R() and error() methods and renamed some other. These changes + should be transparent and backward compatible + - Maintenance: many more unit tests, synopsis clarification, POD work, script + touchups, small code cleanups, version numbering, better README generation, + Git and bug tracker URLs + +0.08 2011-03-01 + - Pass options in new() to Statistics::R::Bridge constructor (RT #63906) + +0.07 2010-11-08 + - Tidy up SYNOPSIS (RT #62776) + - Fix undef warning on Win32 (RT #62776) + - Fix is_started() method (RT #62776) + +0.06 2010-09-17 + - Fix error() when used as an accessor (RT #61335) + - Silence DESTROY() when R is not found + - Fix "uninitialized value" warning in read_processR() (RT #61414) + +0.05 2010-09-13 + - Major code refactor: + - strict + warnings wherever possible + - Removed some layers of abstraction + - Win32/Linux classes are now simple subs + - Basic syntax tidying + - POD fix, plus pod test + - Skip tests if R is not available + +0.04 2010-08-28 + - Basic code cleanup with the intention of doing major refactoring by-and-by + - Fix the test suite + +0.03 2008-08-16 + - Fixed RT Bug #23948: bug in Statistics::R + - Fixed --gui + - RT Bug #17925: R --slave --vanilla --gui=none is now R --slave --vanilla --gui=X11 + - RT Bug #20515: Fwd: Delivery Status Notification (Failure) + - RT Bug #14324: error message with recent versions of R + We used the patch from barry.moore since it correctly identifies that we probably + don't want the GUI. + - Fixed RT Bug #17956: Win32: log_dir is not in tmp_dir by default as advertised + +0.02 2004-02-23 + - Just minor changes and POD fix. + +0.01 2004-01-29 23:04:46 + - original version; + diff --git a/MANIFEST b/MANIFEST new file mode 100644 index 0000000..0199ad1 --- /dev/null +++ b/MANIFEST @@ -0,0 +1,27 @@ +Changes +inc/Module/Install.pm +inc/Module/Install/Base.pm +inc/Module/Install/Can.pm +inc/Module/Install/External.pm +inc/Module/Install/Fetch.pm +inc/Module/Install/Makefile.pm +inc/Module/Install/Metadata.pm +inc/Module/Install/Win32.pm +inc/Module/Install/WriteAll.pm +lib/Statistics/R.pm +lib/Statistics/R/Legacy.pm +lib/Statistics/R/Win32.pm +Makefile.PL +MANIFEST This list of files +META.yml +README +t/00-load.t +t/01-pod.t +t/02-legacy.t +t/03-run.t +t/04-start-stop.t +t/05-shared.t +t/06-get-set.t +t/07-robust.t +t/08-errors.t +t/data/script.R diff --git a/META.yml b/META.yml new file mode 100644 index 0000000..bbbd233 --- /dev/null +++ b/META.yml @@ -0,0 +1,32 @@ +--- +abstract: 'Perl interface with the R statistical program' +author: + - 'Florent Angly (2011 rewrite)' +build_requires: + ExtUtils::MakeMaker: 6.56 + Test::More: 0.47 +configure_requires: + ExtUtils::MakeMaker: 6.56 +distribution_type: module +dynamic_config: 1 +generated_by: 'Module::Install version 1.04' +license: perl +meta-spec: + url: http://module-build.sourceforge.net/META-spec-v1.4.html + version: 1.4 +name: Statistics-R +no_index: + directory: + - inc + - t +requires: + IPC::Run: 0 + Regexp::Common: 0 + Text::Balanced: 1.97 + perl: 5.6.0 +resources: + bugtracker: http://rt.cpan.org/Dist/Display.html?Name=Statistics-R + homepage: http://search.cpan.org/search?query=statistics%3A%3AR&mode=dist + license: http://dev.perl.org/licenses/ + repository: git@github.com:bricas/statistics-r.git +version: 0.24 diff --git a/Makefile.PL b/Makefile.PL new file mode 100644 index 0000000..4d7adc3 --- /dev/null +++ b/Makefile.PL @@ -0,0 +1,41 @@ +use strict; +use warnings; + +use inc::Module::Install; + +use lib 'lib'; +if ( $^O =~ m/^(?:.*?win32|dos)$/i ) { + require Statistics::R::Win32; +} + + +name 'Statistics-R'; +all_from 'lib/Statistics/R.pm'; + +resources + homepage 'http://search.cpan.org/search?query=statistics%3A%3AR&mode=dist'; + bugtracker 'http://rt.cpan.org/Dist/Display.html?Name=Statistics-R'; + repository 'git@github.com:bricas/statistics-r.git'; + +build_requires 'Test::More' => '0.47'; + +requires 'Text::Balanced' => '1.97'; +requires 'Regexp::Common' => '0'; +requires 'IPC::Run' => '0'; + +requires_external_bin 'R'; + +WriteAll; + +if ( -e 'MANIFEST.SKIP' ) { + generate_readme( 'lib/Statistics/R.pm', 'README' ); +} + + + +sub generate_readme { + my ($in, $out) = @_; + `pod2text $in $out`; + warn "Warning: Could not generate $out.\n$!\n" if $? == -1; + return $?; # exit status +} diff --git a/README b/README new file mode 100644 index 0000000..7d474a3 --- /dev/null +++ b/README @@ -0,0 +1,200 @@ +NAME + Statistics::R - Perl interface with the R statistical program + +DESCRIPTION + *Statistics::R* is a module to controls the R interpreter (R project for + statistical computing: ). It lets you start + R, pass commands to it and retrieve the output. A shared mode allow to + have several instances of *Statistics::R* talk to the same R process. + + The current *Statistics::R* implementation uses pipes (for stdin, stdout + and and stderr) to communicate with R. This implementation should be + more efficient and reliable than that in previous version, which relied + on reading and writing files. As before, this module works on GNU/Linux, + MS Windows and probably many more systems. + +SYNOPSIS + use Statistics::R; + + # Create a communication bridge with R and start R + my $R = Statistics::R->new(); + + # Run simple R commands + my $output_file = "file.ps"; + $R->run(qq`postscript("$output_file" , horizontal=FALSE , width=500 , height=500 , pointsize=1)`); + $R->run(q`plot(c(1, 5, 10), type = "l")`); + $R->run(q`dev.off()`); + + # Pass and retrieve data (scalars or arrays) + my $input_value = 1; + $R->set('x', $input_value); + $R->run(q`y <- x^2`); + my $output_value = $R->get('y'); + print "y = $output_value\n"; + + $R->stop(); + +METHODS + new() + Build a *Statistics::R* bridge object between Perl and R. Available + options are: + + r_bin + Specify the full path to R if it is not automatically found. See + INSTALLATION. + + shared + Start a shared bridge. When using a shared bridge, several + instances of Statistics::R can communicate with the same unique + R instance. Example: + + use Statistics::R; + + my $R1 = Statistics::R->new( shared => 1); + my $R2 = Statistics::R->new( shared => 1); + + $R1->set( 'x', 'pear' ); + my $x = $R2->get( 'x' ); + print "x = $x\n"; + + Do not call the *stop()* method is you still have processes that + need to interact with R. + + run() + First, start() R if it is not yet running. Then, execute R commands + passed as a string and return the output as a string. If your + command fails to run in R, an error message will be displayed. + + Example: + + my $out = $R->run( q`print( 1 + 2 )` ); + + If you intend on runnning many R commands, it may be convenient to + pass an array of commands or put multiple commands in an here-doc: + + # Array of R commands: + my $out1 = $R->run( + q`a <- 2`, + q`b <- 5`, + q`c <- a * b`, + q`print("ok")` + ); + + # Here-doc with multiple R commands: + my $cmds = <run($cmds); + + To run commands from a file, see the run_from_file() method. + + The output you get from run() is the combination of what R would + display on the standard output and the standard error, but the order + may differ. When loading modules, some may write numerous messages + on standard error. You can disable this behavior using the following + R command: + + suppressPackageStartupMessages(library(library_to_load)) + + run_from_file() + Similar to run() but reads the R commands from the specified file. + Internally, this method uses the R source() command to read the + file. + + set() + Set the value of an R variable (scalar or arrayref). Example: + + $R->set( 'x', 'pear' ); + + or + + $R->set( 'y', [1, 2, 3] ); + + get() + Get the value of an R variable (scalar or arrayref). Example: + + my $x = $R->get( 'x' ); # $y is an scalar + + or + + my $y = $R->get( 'y' ); # $x is an arrayref + + start() + Explicitly start R. Most times, you do not need to do that because + the first execution of run() or set() will automatically call + start(). + + stop() + Stop a running instance of R. + + restart() + stop() and start() R. + + bin() + Get or set the path to the R executable. + + is_shared() + Was R started in shared mode? + + is_started() + Is R running? + + pid() + Return the pid of the running R process + +INSTALLATION + Since *Statistics::R* relies on R to work, you need to install R first. + See this page for downloads, . If R is in + your PATH environment variable, then it should be available from a + terminal and be detected automatically by *Statistics::R*. This means + that you don't have to do anything on Linux systems to get + *Statistics::R* working. On Windows systems, in addition to the folders + described in PATH, the usual suspects will be checked for the presence + of the R binary, e.g. C:\Program Files\R. If *Statistics::R* does not + find R installation, your last recourse is to specify its full path when + calling new(): + + my $R = Statistics::R->new( r_bin => $fullpath ); + + You also need to have the following CPAN Perl modules installed: + + Text::Balanced (>= 1.97) + Regexp::Common + IPC::Run + +SEE ALSO + * Statistics::R::Win32 + + * Statistics::R::Legacy + + * The R-project web site: + + * Statistics:: modules for Perl: + + +AUTHORS + Florent Angly (2011 rewrite) + + Graciliano M. P. (original code) + +MAINTAINER + Brian Cassidy + +COPYRIGHT & LICENSE + This program is free software; you can redistribute it and/or modify it + under the same terms as Perl itself. + +BUGS + All complex software has bugs lurking in it, and this program is no + exception. If you find a bug, please report it on the CPAN Tracker of + Statistics::R: + + Bug reports, suggestions and patches are welcome. The Statistics::R code + is developed on Github () and is + under Git revision control. To get the latest revision, run: + + git clone git@github.com:bricas/statistics-r.git + diff --git a/inc/Module/Install.pm b/inc/Module/Install.pm new file mode 100644 index 0000000..c685ca4 --- /dev/null +++ b/inc/Module/Install.pm @@ -0,0 +1,470 @@ +#line 1 +package Module::Install; + +# For any maintainers: +# The load order for Module::Install is a bit magic. +# It goes something like this... +# +# IF ( host has Module::Install installed, creating author mode ) { +# 1. Makefile.PL calls "use inc::Module::Install" +# 2. $INC{inc/Module/Install.pm} set to installed version of inc::Module::Install +# 3. The installed version of inc::Module::Install loads +# 4. inc::Module::Install calls "require Module::Install" +# 5. The ./inc/ version of Module::Install loads +# } ELSE { +# 1. Makefile.PL calls "use inc::Module::Install" +# 2. $INC{inc/Module/Install.pm} set to ./inc/ version of Module::Install +# 3. The ./inc/ version of Module::Install loads +# } + +use 5.005; +use strict 'vars'; +use Cwd (); +use File::Find (); +use File::Path (); + +use vars qw{$VERSION $MAIN}; +BEGIN { + # All Module::Install core packages now require synchronised versions. + # This will be used to ensure we don't accidentally load old or + # different versions of modules. + # This is not enforced yet, but will be some time in the next few + # releases once we can make sure it won't clash with custom + # Module::Install extensions. + $VERSION = '1.04'; + + # Storage for the pseudo-singleton + $MAIN = undef; + + *inc::Module::Install::VERSION = *VERSION; + @inc::Module::Install::ISA = __PACKAGE__; + +} + +sub import { + my $class = shift; + my $self = $class->new(@_); + my $who = $self->_caller; + + #------------------------------------------------------------- + # all of the following checks should be included in import(), + # to allow "eval 'require Module::Install; 1' to test + # installation of Module::Install. (RT #51267) + #------------------------------------------------------------- + + # Whether or not inc::Module::Install is actually loaded, the + # $INC{inc/Module/Install.pm} is what will still get set as long as + # the caller loaded module this in the documented manner. + # If not set, the caller may NOT have loaded the bundled version, and thus + # they may not have a MI version that works with the Makefile.PL. This would + # result in false errors or unexpected behaviour. And we don't want that. + my $file = join( '/', 'inc', split /::/, __PACKAGE__ ) . '.pm'; + unless ( $INC{$file} ) { die <<"END_DIE" } + +Please invoke ${\__PACKAGE__} with: + + use inc::${\__PACKAGE__}; + +not: + + use ${\__PACKAGE__}; + +END_DIE + + # This reportedly fixes a rare Win32 UTC file time issue, but + # as this is a non-cross-platform XS module not in the core, + # we shouldn't really depend on it. See RT #24194 for detail. + # (Also, this module only supports Perl 5.6 and above). + eval "use Win32::UTCFileTime" if $^O eq 'MSWin32' && $] >= 5.006; + + # If the script that is loading Module::Install is from the future, + # then make will detect this and cause it to re-run over and over + # again. This is bad. Rather than taking action to touch it (which + # is unreliable on some platforms and requires write permissions) + # for now we should catch this and refuse to run. + if ( -f $0 ) { + my $s = (stat($0))[9]; + + # If the modification time is only slightly in the future, + # sleep briefly to remove the problem. + my $a = $s - time; + if ( $a > 0 and $a < 5 ) { sleep 5 } + + # Too far in the future, throw an error. + my $t = time; + if ( $s > $t ) { die <<"END_DIE" } + +Your installer $0 has a modification time in the future ($s > $t). + +This is known to create infinite loops in make. + +Please correct this, then run $0 again. + +END_DIE + } + + + # Build.PL was formerly supported, but no longer is due to excessive + # difficulty in implementing every single feature twice. + if ( $0 =~ /Build.PL$/i ) { die <<"END_DIE" } + +Module::Install no longer supports Build.PL. + +It was impossible to maintain duel backends, and has been deprecated. + +Please remove all Build.PL files and only use the Makefile.PL installer. + +END_DIE + + #------------------------------------------------------------- + + # To save some more typing in Module::Install installers, every... + # use inc::Module::Install + # ...also acts as an implicit use strict. + $^H |= strict::bits(qw(refs subs vars)); + + #------------------------------------------------------------- + + unless ( -f $self->{file} ) { + foreach my $key (keys %INC) { + delete $INC{$key} if $key =~ /Module\/Install/; + } + + local $^W; + require "$self->{path}/$self->{dispatch}.pm"; + File::Path::mkpath("$self->{prefix}/$self->{author}"); + $self->{admin} = "$self->{name}::$self->{dispatch}"->new( _top => $self ); + $self->{admin}->init; + @_ = ($class, _self => $self); + goto &{"$self->{name}::import"}; + } + + local $^W; + *{"${who}::AUTOLOAD"} = $self->autoload; + $self->preload; + + # Unregister loader and worker packages so subdirs can use them again + delete $INC{'inc/Module/Install.pm'}; + delete $INC{'Module/Install.pm'}; + + # Save to the singleton + $MAIN = $self; + + return 1; +} + +sub autoload { + my $self = shift; + my $who = $self->_caller; + my $cwd = Cwd::cwd(); + my $sym = "${who}::AUTOLOAD"; + $sym->{$cwd} = sub { + my $pwd = Cwd::cwd(); + if ( my $code = $sym->{$pwd} ) { + # Delegate back to parent dirs + goto &$code unless $cwd eq $pwd; + } + unless ($$sym =~ s/([^:]+)$//) { + # XXX: it looks like we can't retrieve the missing function + # via $$sym (usually $main::AUTOLOAD) in this case. + # I'm still wondering if we should slurp Makefile.PL to + # get some context or not ... + my ($package, $file, $line) = caller; + die <<"EOT"; +Unknown function is found at $file line $line. +Execution of $file aborted due to runtime errors. + +If you're a contributor to a project, you may need to install +some Module::Install extensions from CPAN (or other repository). +If you're a user of a module, please contact the author. +EOT + } + my $method = $1; + if ( uc($method) eq $method ) { + # Do nothing + return; + } elsif ( $method =~ /^_/ and $self->can($method) ) { + # Dispatch to the root M:I class + return $self->$method(@_); + } + + # Dispatch to the appropriate plugin + unshift @_, ( $self, $1 ); + goto &{$self->can('call')}; + }; +} + +sub preload { + my $self = shift; + unless ( $self->{extensions} ) { + $self->load_extensions( + "$self->{prefix}/$self->{path}", $self + ); + } + + my @exts = @{$self->{extensions}}; + unless ( @exts ) { + @exts = $self->{admin}->load_all_extensions; + } + + my %seen; + foreach my $obj ( @exts ) { + while (my ($method, $glob) = each %{ref($obj) . '::'}) { + next unless $obj->can($method); + next if $method =~ /^_/; + next if $method eq uc($method); + $seen{$method}++; + } + } + + my $who = $self->_caller; + foreach my $name ( sort keys %seen ) { + local $^W; + *{"${who}::$name"} = sub { + ${"${who}::AUTOLOAD"} = "${who}::$name"; + goto &{"${who}::AUTOLOAD"}; + }; + } +} + +sub new { + my ($class, %args) = @_; + + delete $INC{'FindBin.pm'}; + { + # to suppress the redefine warning + local $SIG{__WARN__} = sub {}; + require FindBin; + } + + # ignore the prefix on extension modules built from top level. + my $base_path = Cwd::abs_path($FindBin::Bin); + unless ( Cwd::abs_path(Cwd::cwd()) eq $base_path ) { + delete $args{prefix}; + } + return $args{_self} if $args{_self}; + + $args{dispatch} ||= 'Admin'; + $args{prefix} ||= 'inc'; + $args{author} ||= ($^O eq 'VMS' ? '_author' : '.author'); + $args{bundle} ||= 'inc/BUNDLES'; + $args{base} ||= $base_path; + $class =~ s/^\Q$args{prefix}\E:://; + $args{name} ||= $class; + $args{version} ||= $class->VERSION; + unless ( $args{path} ) { + $args{path} = $args{name}; + $args{path} =~ s!::!/!g; + } + $args{file} ||= "$args{base}/$args{prefix}/$args{path}.pm"; + $args{wrote} = 0; + + bless( \%args, $class ); +} + +sub call { + my ($self, $method) = @_; + my $obj = $self->load($method) or return; + splice(@_, 0, 2, $obj); + goto &{$obj->can($method)}; +} + +sub load { + my ($self, $method) = @_; + + $self->load_extensions( + "$self->{prefix}/$self->{path}", $self + ) unless $self->{extensions}; + + foreach my $obj (@{$self->{extensions}}) { + return $obj if $obj->can($method); + } + + my $admin = $self->{admin} or die <<"END_DIE"; +The '$method' method does not exist in the '$self->{prefix}' path! +Please remove the '$self->{prefix}' directory and run $0 again to load it. +END_DIE + + my $obj = $admin->load($method, 1); + push @{$self->{extensions}}, $obj; + + $obj; +} + +sub load_extensions { + my ($self, $path, $top) = @_; + + my $should_reload = 0; + unless ( grep { ! ref $_ and lc $_ eq lc $self->{prefix} } @INC ) { + unshift @INC, $self->{prefix}; + $should_reload = 1; + } + + foreach my $rv ( $self->find_extensions($path) ) { + my ($file, $pkg) = @{$rv}; + next if $self->{pathnames}{$pkg}; + + local $@; + my $new = eval { local $^W; require $file; $pkg->can('new') }; + unless ( $new ) { + warn $@ if $@; + next; + } + $self->{pathnames}{$pkg} = + $should_reload ? delete $INC{$file} : $INC{$file}; + push @{$self->{extensions}}, &{$new}($pkg, _top => $top ); + } + + $self->{extensions} ||= []; +} + +sub find_extensions { + my ($self, $path) = @_; + + my @found; + File::Find::find( sub { + my $file = $File::Find::name; + return unless $file =~ m!^\Q$path\E/(.+)\.pm\Z!is; + my $subpath = $1; + return if lc($subpath) eq lc($self->{dispatch}); + + $file = "$self->{path}/$subpath.pm"; + my $pkg = "$self->{name}::$subpath"; + $pkg =~ s!/!::!g; + + # If we have a mixed-case package name, assume case has been preserved + # correctly. Otherwise, root through the file to locate the case-preserved + # version of the package name. + if ( $subpath eq lc($subpath) || $subpath eq uc($subpath) ) { + my $content = Module::Install::_read($subpath . '.pm'); + my $in_pod = 0; + foreach ( split //, $content ) { + $in_pod = 1 if /^=\w/; + $in_pod = 0 if /^=cut/; + next if ($in_pod || /^=cut/); # skip pod text + next if /^\s*#/; # and comments + if ( m/^\s*package\s+($pkg)\s*;/i ) { + $pkg = $1; + last; + } + } + } + + push @found, [ $file, $pkg ]; + }, $path ) if -d $path; + + @found; +} + + + + + +##################################################################### +# Common Utility Functions + +sub _caller { + my $depth = 0; + my $call = caller($depth); + while ( $call eq __PACKAGE__ ) { + $depth++; + $call = caller($depth); + } + return $call; +} + +# Done in evals to avoid confusing Perl::MinimumVersion +eval( $] >= 5.006 ? <<'END_NEW' : <<'END_OLD' ); die $@ if $@; +sub _read { + local *FH; + open( FH, '<', $_[0] ) or die "open($_[0]): $!"; + my $string = do { local $/; }; + close FH or die "close($_[0]): $!"; + return $string; +} +END_NEW +sub _read { + local *FH; + open( FH, "< $_[0]" ) or die "open($_[0]): $!"; + my $string = do { local $/; }; + close FH or die "close($_[0]): $!"; + return $string; +} +END_OLD + +sub _readperl { + my $string = Module::Install::_read($_[0]); + $string =~ s/(?:\015{1,2}\012|\015|\012)/\n/sg; + $string =~ s/(\n)\n*__(?:DATA|END)__\b.*\z/$1/s; + $string =~ s/\n\n=\w+.+?\n\n=cut\b.+?\n+/\n\n/sg; + return $string; +} + +sub _readpod { + my $string = Module::Install::_read($_[0]); + $string =~ s/(?:\015{1,2}\012|\015|\012)/\n/sg; + return $string if $_[0] =~ /\.pod\z/; + $string =~ s/(^|\n=cut\b.+?\n+)[^=\s].+?\n(\n=\w+|\z)/$1$2/sg; + $string =~ s/\n*=pod\b[^\n]*\n+/\n\n/sg; + $string =~ s/\n*=cut\b[^\n]*\n+/\n\n/sg; + $string =~ s/^\n+//s; + return $string; +} + +# Done in evals to avoid confusing Perl::MinimumVersion +eval( $] >= 5.006 ? <<'END_NEW' : <<'END_OLD' ); die $@ if $@; +sub _write { + local *FH; + open( FH, '>', $_[0] ) or die "open($_[0]): $!"; + foreach ( 1 .. $#_ ) { + print FH $_[$_] or die "print($_[0]): $!"; + } + close FH or die "close($_[0]): $!"; +} +END_NEW +sub _write { + local *FH; + open( FH, "> $_[0]" ) or die "open($_[0]): $!"; + foreach ( 1 .. $#_ ) { + print FH $_[$_] or die "print($_[0]): $!"; + } + close FH or die "close($_[0]): $!"; +} +END_OLD + +# _version is for processing module versions (eg, 1.03_05) not +# Perl versions (eg, 5.8.1). +sub _version ($) { + my $s = shift || 0; + my $d =()= $s =~ /(\.)/g; + if ( $d >= 2 ) { + # Normalise multipart versions + $s =~ s/(\.)(\d{1,3})/sprintf("$1%03d",$2)/eg; + } + $s =~ s/^(\d+)\.?//; + my $l = $1 || 0; + my @v = map { + $_ . '0' x (3 - length $_) + } $s =~ /(\d{1,3})\D?/g; + $l = $l . '.' . join '', @v if @v; + return $l + 0; +} + +sub _cmp ($$) { + _version($_[1]) <=> _version($_[2]); +} + +# Cloned from Params::Util::_CLASS +sub _CLASS ($) { + ( + defined $_[0] + and + ! ref $_[0] + and + $_[0] =~ m/^[^\W\d]\w*(?:::\w+)*\z/s + ) ? $_[0] : undef; +} + +1; + +# Copyright 2008 - 2011 Adam Kennedy. diff --git a/inc/Module/Install/Base.pm b/inc/Module/Install/Base.pm new file mode 100644 index 0000000..b520616 --- /dev/null +++ b/inc/Module/Install/Base.pm @@ -0,0 +1,83 @@ +#line 1 +package Module::Install::Base; + +use strict 'vars'; +use vars qw{$VERSION}; +BEGIN { + $VERSION = '1.04'; +} + +# Suspend handler for "redefined" warnings +BEGIN { + my $w = $SIG{__WARN__}; + $SIG{__WARN__} = sub { $w }; +} + +#line 42 + +sub new { + my $class = shift; + unless ( defined &{"${class}::call"} ) { + *{"${class}::call"} = sub { shift->_top->call(@_) }; + } + unless ( defined &{"${class}::load"} ) { + *{"${class}::load"} = sub { shift->_top->load(@_) }; + } + bless { @_ }, $class; +} + +#line 61 + +sub AUTOLOAD { + local $@; + my $func = eval { shift->_top->autoload } or return; + goto &$func; +} + +#line 75 + +sub _top { + $_[0]->{_top}; +} + +#line 90 + +sub admin { + $_[0]->_top->{admin} + or + Module::Install::Base::FakeAdmin->new; +} + +#line 106 + +sub is_admin { + ! $_[0]->admin->isa('Module::Install::Base::FakeAdmin'); +} + +sub DESTROY {} + +package Module::Install::Base::FakeAdmin; + +use vars qw{$VERSION}; +BEGIN { + $VERSION = $Module::Install::Base::VERSION; +} + +my $fake; + +sub new { + $fake ||= bless(\@_, $_[0]); +} + +sub AUTOLOAD {} + +sub DESTROY {} + +# Restore warning handler +BEGIN { + $SIG{__WARN__} = $SIG{__WARN__}->(); +} + +1; + +#line 159 diff --git a/inc/Module/Install/Can.pm b/inc/Module/Install/Can.pm new file mode 100644 index 0000000..a162ad4 --- /dev/null +++ b/inc/Module/Install/Can.pm @@ -0,0 +1,81 @@ +#line 1 +package Module::Install::Can; + +use strict; +use Config (); +use File::Spec (); +use ExtUtils::MakeMaker (); +use Module::Install::Base (); + +use vars qw{$VERSION @ISA $ISCORE}; +BEGIN { + $VERSION = '1.04'; + @ISA = 'Module::Install::Base'; + $ISCORE = 1; +} + +# check if we can load some module +### Upgrade this to not have to load the module if possible +sub can_use { + my ($self, $mod, $ver) = @_; + $mod =~ s{::|\\}{/}g; + $mod .= '.pm' unless $mod =~ /\.pm$/i; + + my $pkg = $mod; + $pkg =~ s{/}{::}g; + $pkg =~ s{\.pm$}{}i; + + local $@; + eval { require $mod; $pkg->VERSION($ver || 0); 1 }; +} + +# check if we can run some command +sub can_run { + my ($self, $cmd) = @_; + + my $_cmd = $cmd; + return $_cmd if (-x $_cmd or $_cmd = MM->maybe_command($_cmd)); + + for my $dir ((split /$Config::Config{path_sep}/, $ENV{PATH}), '.') { + next if $dir eq ''; + my $abs = File::Spec->catfile($dir, $_[1]); + return $abs if (-x $abs or $abs = MM->maybe_command($abs)); + } + + return; +} + +# can we locate a (the) C compiler +sub can_cc { + my $self = shift; + my @chunks = split(/ /, $Config::Config{cc}) or return; + + # $Config{cc} may contain args; try to find out the program part + while (@chunks) { + return $self->can_run("@chunks") || (pop(@chunks), next); + } + + return; +} + +# Fix Cygwin bug on maybe_command(); +if ( $^O eq 'cygwin' ) { + require ExtUtils::MM_Cygwin; + require ExtUtils::MM_Win32; + if ( ! defined(&ExtUtils::MM_Cygwin::maybe_command) ) { + *ExtUtils::MM_Cygwin::maybe_command = sub { + my ($self, $file) = @_; + if ($file =~ m{^/cygdrive/}i and ExtUtils::MM_Win32->can('maybe_command')) { + ExtUtils::MM_Win32->maybe_command($file); + } else { + ExtUtils::MM_Unix->maybe_command($file); + } + } + } +} + +1; + +__END__ + +#line 156 diff --git a/inc/Module/Install/External.pm b/inc/Module/Install/External.pm new file mode 100644 index 0000000..062563d --- /dev/null +++ b/inc/Module/Install/External.pm @@ -0,0 +1,66 @@ +#line 1 +package Module::Install::External; + +# Provides dependency declarations for external non-Perl things + +use strict; +use Module::Install::Base (); + +use vars qw{$VERSION $ISCORE @ISA}; +BEGIN { + $VERSION = '1.04'; + $ISCORE = 1; + @ISA = qw{Module::Install::Base}; +} + +sub requires_external_cc { + my $self = shift; + + # We need a C compiler, use the can_cc method for this + unless ( $self->can_cc ) { + print "Unresolvable missing external dependency.\n"; + print "This package requires a C compiler.\n"; + print STDERR "NA: Unable to build distribution on this platform.\n"; + exit(0); + } + + # Unlike some of the other modules, while we need to specify a + # C compiler as a dep, it needs to be a build-time dependency. + + 1; +} + +sub requires_external_bin { + my ($self, $bin, $version) = @_; + if ( $version ) { + die "requires_external_bin does not support versions yet"; + } + + # Load the package containing can_run early, + # to avoid breaking the message below. + $self->load('can_run'); + + # Locate the bin + print "Locating bin:$bin..."; + my $found_bin = $self->can_run( $bin ); + if ( $found_bin ) { + print " found at $found_bin.\n"; + } else { + print " missing.\n"; + print "Unresolvable missing external dependency.\n"; + print "Please install '$bin' seperately and try again.\n"; + print STDERR "NA: Unable to build distribution on this platform.\n"; + exit(0); + } + + # Once we have some way to specify external deps, do it here. + # In the mean time, continue as normal. + + 1; +} + +1; + +__END__ + +#line 138 diff --git a/inc/Module/Install/Fetch.pm b/inc/Module/Install/Fetch.pm new file mode 100644 index 0000000..a412576 --- /dev/null +++ b/inc/Module/Install/Fetch.pm @@ -0,0 +1,93 @@ +#line 1 +package Module::Install::Fetch; + +use strict; +use Module::Install::Base (); + +use vars qw{$VERSION @ISA $ISCORE}; +BEGIN { + $VERSION = '1.04'; + @ISA = 'Module::Install::Base'; + $ISCORE = 1; +} + +sub get_file { + my ($self, %args) = @_; + my ($scheme, $host, $path, $file) = + $args{url} =~ m|^(\w+)://([^/]+)(.+)/(.+)| or return; + + if ( $scheme eq 'http' and ! eval { require LWP::Simple; 1 } ) { + $args{url} = $args{ftp_url} + or (warn("LWP support unavailable!\n"), return); + ($scheme, $host, $path, $file) = + $args{url} =~ m|^(\w+)://([^/]+)(.+)/(.+)| or return; + } + + $|++; + print "Fetching '$file' from $host... "; + + unless (eval { require Socket; Socket::inet_aton($host) }) { + warn "'$host' resolve failed!\n"; + return; + } + + return unless $scheme eq 'ftp' or $scheme eq 'http'; + + require Cwd; + my $dir = Cwd::getcwd(); + chdir $args{local_dir} or return if exists $args{local_dir}; + + if (eval { require LWP::Simple; 1 }) { + LWP::Simple::mirror($args{url}, $file); + } + elsif (eval { require Net::FTP; 1 }) { eval { + # use Net::FTP to get past firewall + my $ftp = Net::FTP->new($host, Passive => 1, Timeout => 600); + $ftp->login("anonymous", 'anonymous@example.com'); + $ftp->cwd($path); + $ftp->binary; + $ftp->get($file) or (warn("$!\n"), return); + $ftp->quit; + } } + elsif (my $ftp = $self->can_run('ftp')) { eval { + # no Net::FTP, fallback to ftp.exe + require FileHandle; + my $fh = FileHandle->new; + + local $SIG{CHLD} = 'IGNORE'; + unless ($fh->open("|$ftp -n")) { + warn "Couldn't open ftp: $!\n"; + chdir $dir; return; + } + + my @dialog = split(/\n/, <<"END_FTP"); +open $host +user anonymous anonymous\@example.com +cd $path +binary +get $file $file +quit +END_FTP + foreach (@dialog) { $fh->print("$_\n") } + $fh->close; + } } + else { + warn "No working 'ftp' program available!\n"; + chdir $dir; return; + } + + unless (-f $file) { + warn "Fetching failed: $@\n"; + chdir $dir; return; + } + + return if exists $args{size} and -s $file != $args{size}; + system($args{run}) if exists $args{run}; + unlink($file) if $args{remove}; + + print(((!exists $args{check_for} or -e $args{check_for}) + ? "done!" : "failed! ($!)"), "\n"); + chdir $dir; return !$?; +} + +1; diff --git a/inc/Module/Install/Makefile.pm b/inc/Module/Install/Makefile.pm new file mode 100644 index 0000000..035cef2 --- /dev/null +++ b/inc/Module/Install/Makefile.pm @@ -0,0 +1,414 @@ +#line 1 +package Module::Install::Makefile; + +use strict 'vars'; +use ExtUtils::MakeMaker (); +use Module::Install::Base (); +use Fcntl qw/:flock :seek/; + +use vars qw{$VERSION @ISA $ISCORE}; +BEGIN { + $VERSION = '1.04'; + @ISA = 'Module::Install::Base'; + $ISCORE = 1; +} + +sub Makefile { $_[0] } + +my %seen = (); + +sub prompt { + shift; + + # Infinite loop protection + my @c = caller(); + if ( ++$seen{"$c[1]|$c[2]|$_[0]"} > 3 ) { + die "Caught an potential prompt infinite loop ($c[1]|$c[2]|$_[0])"; + } + + # In automated testing or non-interactive session, always use defaults + if ( ($ENV{AUTOMATED_TESTING} or -! -t STDIN) and ! $ENV{PERL_MM_USE_DEFAULT} ) { + local $ENV{PERL_MM_USE_DEFAULT} = 1; + goto &ExtUtils::MakeMaker::prompt; + } else { + goto &ExtUtils::MakeMaker::prompt; + } +} + +# Store a cleaned up version of the MakeMaker version, +# since we need to behave differently in a variety of +# ways based on the MM version. +my $makemaker = eval $ExtUtils::MakeMaker::VERSION; + +# If we are passed a param, do a "newer than" comparison. +# Otherwise, just return the MakeMaker version. +sub makemaker { + ( @_ < 2 or $makemaker >= eval($_[1]) ) ? $makemaker : 0 +} + +# Ripped from ExtUtils::MakeMaker 6.56, and slightly modified +# as we only need to know here whether the attribute is an array +# or a hash or something else (which may or may not be appendable). +my %makemaker_argtype = ( + C => 'ARRAY', + CONFIG => 'ARRAY', +# CONFIGURE => 'CODE', # ignore + DIR => 'ARRAY', + DL_FUNCS => 'HASH', + DL_VARS => 'ARRAY', + EXCLUDE_EXT => 'ARRAY', + EXE_FILES => 'ARRAY', + FUNCLIST => 'ARRAY', + H => 'ARRAY', + IMPORTS => 'HASH', + INCLUDE_EXT => 'ARRAY', + LIBS => 'ARRAY', # ignore '' + MAN1PODS => 'HASH', + MAN3PODS => 'HASH', + META_ADD => 'HASH', + META_MERGE => 'HASH', + PL_FILES => 'HASH', + PM => 'HASH', + PMLIBDIRS => 'ARRAY', + PMLIBPARENTDIRS => 'ARRAY', + PREREQ_PM => 'HASH', + CONFIGURE_REQUIRES => 'HASH', + SKIP => 'ARRAY', + TYPEMAPS => 'ARRAY', + XS => 'HASH', +# VERSION => ['version',''], # ignore +# _KEEP_AFTER_FLUSH => '', + + clean => 'HASH', + depend => 'HASH', + dist => 'HASH', + dynamic_lib=> 'HASH', + linkext => 'HASH', + macro => 'HASH', + postamble => 'HASH', + realclean => 'HASH', + test => 'HASH', + tool_autosplit => 'HASH', + + # special cases where you can use makemaker_append + CCFLAGS => 'APPENDABLE', + DEFINE => 'APPENDABLE', + INC => 'APPENDABLE', + LDDLFLAGS => 'APPENDABLE', + LDFROM => 'APPENDABLE', +); + +sub makemaker_args { + my ($self, %new_args) = @_; + my $args = ( $self->{makemaker_args} ||= {} ); + foreach my $key (keys %new_args) { + if ($makemaker_argtype{$key}) { + if ($makemaker_argtype{$key} eq 'ARRAY') { + $args->{$key} = [] unless defined $args->{$key}; + unless (ref $args->{$key} eq 'ARRAY') { + $args->{$key} = [$args->{$key}] + } + push @{$args->{$key}}, + ref $new_args{$key} eq 'ARRAY' + ? @{$new_args{$key}} + : $new_args{$key}; + } + elsif ($makemaker_argtype{$key} eq 'HASH') { + $args->{$key} = {} unless defined $args->{$key}; + foreach my $skey (keys %{ $new_args{$key} }) { + $args->{$key}{$skey} = $new_args{$key}{$skey}; + } + } + elsif ($makemaker_argtype{$key} eq 'APPENDABLE') { + $self->makemaker_append($key => $new_args{$key}); + } + } + else { + if (defined $args->{$key}) { + warn qq{MakeMaker attribute "$key" is overriden; use "makemaker_append" to append values\n}; + } + $args->{$key} = $new_args{$key}; + } + } + return $args; +} + +# For mm args that take multiple space-seperated args, +# append an argument to the current list. +sub makemaker_append { + my $self = shift; + my $name = shift; + my $args = $self->makemaker_args; + $args->{$name} = defined $args->{$name} + ? join( ' ', $args->{$name}, @_ ) + : join( ' ', @_ ); +} + +sub build_subdirs { + my $self = shift; + my $subdirs = $self->makemaker_args->{DIR} ||= []; + for my $subdir (@_) { + push @$subdirs, $subdir; + } +} + +sub clean_files { + my $self = shift; + my $clean = $self->makemaker_args->{clean} ||= {}; + %$clean = ( + %$clean, + FILES => join ' ', grep { length $_ } ($clean->{FILES} || (), @_), + ); +} + +sub realclean_files { + my $self = shift; + my $realclean = $self->makemaker_args->{realclean} ||= {}; + %$realclean = ( + %$realclean, + FILES => join ' ', grep { length $_ } ($realclean->{FILES} || (), @_), + ); +} + +sub libs { + my $self = shift; + my $libs = ref $_[0] ? shift : [ shift ]; + $self->makemaker_args( LIBS => $libs ); +} + +sub inc { + my $self = shift; + $self->makemaker_args( INC => shift ); +} + +sub _wanted_t { +} + +sub tests_recursive { + my $self = shift; + my $dir = shift || 't'; + unless ( -d $dir ) { + die "tests_recursive dir '$dir' does not exist"; + } + my %tests = map { $_ => 1 } split / /, ($self->tests || ''); + require File::Find; + File::Find::find( + sub { /\.t$/ and -f $_ and $tests{"$File::Find::dir/*.t"} = 1 }, + $dir + ); + $self->tests( join ' ', sort keys %tests ); +} + +sub write { + my $self = shift; + die "&Makefile->write() takes no arguments\n" if @_; + + # Check the current Perl version + my $perl_version = $self->perl_version; + if ( $perl_version ) { + eval "use $perl_version; 1" + or die "ERROR: perl: Version $] is installed, " + . "but we need version >= $perl_version"; + } + + # Make sure we have a new enough MakeMaker + require ExtUtils::MakeMaker; + + if ( $perl_version and $self->_cmp($perl_version, '5.006') >= 0 ) { + # MakeMaker can complain about module versions that include + # an underscore, even though its own version may contain one! + # Hence the funny regexp to get rid of it. See RT #35800 + # for details. + my ($v) = $ExtUtils::MakeMaker::VERSION =~ /^(\d+\.\d+)/; + $self->build_requires( 'ExtUtils::MakeMaker' => $v ); + $self->configure_requires( 'ExtUtils::MakeMaker' => $v ); + } else { + # Allow legacy-compatibility with 5.005 by depending on the + # most recent EU:MM that supported 5.005. + $self->build_requires( 'ExtUtils::MakeMaker' => 6.36 ); + $self->configure_requires( 'ExtUtils::MakeMaker' => 6.36 ); + } + + # Generate the MakeMaker params + my $args = $self->makemaker_args; + $args->{DISTNAME} = $self->name; + $args->{NAME} = $self->module_name || $self->name; + $args->{NAME} =~ s/-/::/g; + $args->{VERSION} = $self->version or die <<'EOT'; +ERROR: Can't determine distribution version. Please specify it +explicitly via 'version' in Makefile.PL, or set a valid $VERSION +in a module, and provide its file path via 'version_from' (or +'all_from' if you prefer) in Makefile.PL. +EOT + + if ( $self->tests ) { + my @tests = split ' ', $self->tests; + my %seen; + $args->{test} = { + TESTS => (join ' ', grep {!$seen{$_}++} @tests), + }; + } elsif ( $Module::Install::ExtraTests::use_extratests ) { + # Module::Install::ExtraTests doesn't set $self->tests and does its own tests via harness. + # So, just ignore our xt tests here. + } elsif ( -d 'xt' and ($Module::Install::AUTHOR or $ENV{RELEASE_TESTING}) ) { + $args->{test} = { + TESTS => join( ' ', map { "$_/*.t" } grep { -d $_ } qw{ t xt } ), + }; + } + if ( $] >= 5.005 ) { + $args->{ABSTRACT} = $self->abstract; + $args->{AUTHOR} = join ', ', @{$self->author || []}; + } + if ( $self->makemaker(6.10) ) { + $args->{NO_META} = 1; + #$args->{NO_MYMETA} = 1; + } + if ( $self->makemaker(6.17) and $self->sign ) { + $args->{SIGN} = 1; + } + unless ( $self->is_admin ) { + delete $args->{SIGN}; + } + if ( $self->makemaker(6.31) and $self->license ) { + $args->{LICENSE} = $self->license; + } + + my $prereq = ($args->{PREREQ_PM} ||= {}); + %$prereq = ( %$prereq, + map { @$_ } # flatten [module => version] + map { @$_ } + grep $_, + ($self->requires) + ); + + # Remove any reference to perl, PREREQ_PM doesn't support it + delete $args->{PREREQ_PM}->{perl}; + + # Merge both kinds of requires into BUILD_REQUIRES + my $build_prereq = ($args->{BUILD_REQUIRES} ||= {}); + %$build_prereq = ( %$build_prereq, + map { @$_ } # flatten [module => version] + map { @$_ } + grep $_, + ($self->configure_requires, $self->build_requires) + ); + + # Remove any reference to perl, BUILD_REQUIRES doesn't support it + delete $args->{BUILD_REQUIRES}->{perl}; + + # Delete bundled dists from prereq_pm, add it to Makefile DIR + my $subdirs = ($args->{DIR} || []); + if ($self->bundles) { + my %processed; + foreach my $bundle (@{ $self->bundles }) { + my ($mod_name, $dist_dir) = @$bundle; + delete $prereq->{$mod_name}; + $dist_dir = File::Basename::basename($dist_dir); # dir for building this module + if (not exists $processed{$dist_dir}) { + if (-d $dist_dir) { + # List as sub-directory to be processed by make + push @$subdirs, $dist_dir; + } + # Else do nothing: the module is already present on the system + $processed{$dist_dir} = undef; + } + } + } + + unless ( $self->makemaker('6.55_03') ) { + %$prereq = (%$prereq,%$build_prereq); + delete $args->{BUILD_REQUIRES}; + } + + if ( my $perl_version = $self->perl_version ) { + eval "use $perl_version; 1" + or die "ERROR: perl: Version $] is installed, " + . "but we need version >= $perl_version"; + + if ( $self->makemaker(6.48) ) { + $args->{MIN_PERL_VERSION} = $perl_version; + } + } + + if ($self->installdirs) { + warn qq{old INSTALLDIRS (probably set by makemaker_args) is overriden by installdirs\n} if $args->{INSTALLDIRS}; + $args->{INSTALLDIRS} = $self->installdirs; + } + + my %args = map { + ( $_ => $args->{$_} ) } grep {defined($args->{$_} ) + } keys %$args; + + my $user_preop = delete $args{dist}->{PREOP}; + if ( my $preop = $self->admin->preop($user_preop) ) { + foreach my $key ( keys %$preop ) { + $args{dist}->{$key} = $preop->{$key}; + } + } + + my $mm = ExtUtils::MakeMaker::WriteMakefile(%args); + $self->fix_up_makefile($mm->{FIRST_MAKEFILE} || 'Makefile'); +} + +sub fix_up_makefile { + my $self = shift; + my $makefile_name = shift; + my $top_class = ref($self->_top) || ''; + my $top_version = $self->_top->VERSION || ''; + + my $preamble = $self->preamble + ? "# Preamble by $top_class $top_version\n" + . $self->preamble + : ''; + my $postamble = "# Postamble by $top_class $top_version\n" + . ($self->postamble || ''); + + local *MAKEFILE; + open MAKEFILE, "+< $makefile_name" or die "fix_up_makefile: Couldn't open $makefile_name: $!"; + eval { flock MAKEFILE, LOCK_EX }; + my $makefile = do { local $/; }; + + $makefile =~ s/\b(test_harness\(\$\(TEST_VERBOSE\), )/$1'inc', /; + $makefile =~ s/( -I\$\(INST_ARCHLIB\))/ -Iinc$1/g; + $makefile =~ s/( "-I\$\(INST_LIB\)")/ "-Iinc"$1/g; + $makefile =~ s/^(FULLPERL = .*)/$1 "-Iinc"/m; + $makefile =~ s/^(PERL = .*)/$1 "-Iinc"/m; + + # Module::Install will never be used to build the Core Perl + # Sometimes PERL_LIB and PERL_ARCHLIB get written anyway, which breaks + # PREFIX/PERL5LIB, and thus, install_share. Blank them if they exist + $makefile =~ s/^PERL_LIB = .+/PERL_LIB =/m; + #$makefile =~ s/^PERL_ARCHLIB = .+/PERL_ARCHLIB =/m; + + # Perl 5.005 mentions PERL_LIB explicitly, so we have to remove that as well. + $makefile =~ s/(\"?)-I\$\(PERL_LIB\)\1//g; + + # XXX - This is currently unused; not sure if it breaks other MM-users + # $makefile =~ s/^pm_to_blib\s+:\s+/pm_to_blib :: /mg; + + seek MAKEFILE, 0, SEEK_SET; + truncate MAKEFILE, 0; + print MAKEFILE "$preamble$makefile$postamble" or die $!; + close MAKEFILE or die $!; + + 1; +} + +sub preamble { + my ($self, $text) = @_; + $self->{preamble} = $text . $self->{preamble} if defined $text; + $self->{preamble}; +} + +sub postamble { + my ($self, $text) = @_; + $self->{postamble} ||= $self->admin->postamble; + $self->{postamble} .= $text if defined $text; + $self->{postamble} +} + +1; + +__END__ + +#line 540 diff --git a/inc/Module/Install/Metadata.pm b/inc/Module/Install/Metadata.pm new file mode 100644 index 0000000..31c953e --- /dev/null +++ b/inc/Module/Install/Metadata.pm @@ -0,0 +1,722 @@ +#line 1 +package Module::Install::Metadata; + +use strict 'vars'; +use Module::Install::Base (); + +use vars qw{$VERSION @ISA $ISCORE}; +BEGIN { + $VERSION = '1.04'; + @ISA = 'Module::Install::Base'; + $ISCORE = 1; +} + +my @boolean_keys = qw{ + sign +}; + +my @scalar_keys = qw{ + name + module_name + abstract + version + distribution_type + tests + installdirs +}; + +my @tuple_keys = qw{ + configure_requires + build_requires + requires + recommends + bundles + resources +}; + +my @resource_keys = qw{ + homepage + bugtracker + repository +}; + +my @array_keys = qw{ + keywords + author +}; + +*authors = \&author; + +sub Meta { shift } +sub Meta_BooleanKeys { @boolean_keys } +sub Meta_ScalarKeys { @scalar_keys } +sub Meta_TupleKeys { @tuple_keys } +sub Meta_ResourceKeys { @resource_keys } +sub Meta_ArrayKeys { @array_keys } + +foreach my $key ( @boolean_keys ) { + *$key = sub { + my $self = shift; + if ( defined wantarray and not @_ ) { + return $self->{values}->{$key}; + } + $self->{values}->{$key} = ( @_ ? $_[0] : 1 ); + return $self; + }; +} + +foreach my $key ( @scalar_keys ) { + *$key = sub { + my $self = shift; + return $self->{values}->{$key} if defined wantarray and !@_; + $self->{values}->{$key} = shift; + return $self; + }; +} + +foreach my $key ( @array_keys ) { + *$key = sub { + my $self = shift; + return $self->{values}->{$key} if defined wantarray and !@_; + $self->{values}->{$key} ||= []; + push @{$self->{values}->{$key}}, @_; + return $self; + }; +} + +foreach my $key ( @resource_keys ) { + *$key = sub { + my $self = shift; + unless ( @_ ) { + return () unless $self->{values}->{resources}; + return map { $_->[1] } + grep { $_->[0] eq $key } + @{ $self->{values}->{resources} }; + } + return $self->{values}->{resources}->{$key} unless @_; + my $uri = shift or die( + "Did not provide a value to $key()" + ); + $self->resources( $key => $uri ); + return 1; + }; +} + +foreach my $key ( grep { $_ ne "resources" } @tuple_keys) { + *$key = sub { + my $self = shift; + return $self->{values}->{$key} unless @_; + my @added; + while ( @_ ) { + my $module = shift or last; + my $version = shift || 0; + push @added, [ $module, $version ]; + } + push @{ $self->{values}->{$key} }, @added; + return map {@$_} @added; + }; +} + +# Resource handling +my %lc_resource = map { $_ => 1 } qw{ + homepage + license + bugtracker + repository +}; + +sub resources { + my $self = shift; + while ( @_ ) { + my $name = shift or last; + my $value = shift or next; + if ( $name eq lc $name and ! $lc_resource{$name} ) { + die("Unsupported reserved lowercase resource '$name'"); + } + $self->{values}->{resources} ||= []; + push @{ $self->{values}->{resources} }, [ $name, $value ]; + } + $self->{values}->{resources}; +} + +# Aliases for build_requires that will have alternative +# meanings in some future version of META.yml. +sub test_requires { shift->build_requires(@_) } +sub install_requires { shift->build_requires(@_) } + +# Aliases for installdirs options +sub install_as_core { $_[0]->installdirs('perl') } +sub install_as_cpan { $_[0]->installdirs('site') } +sub install_as_site { $_[0]->installdirs('site') } +sub install_as_vendor { $_[0]->installdirs('vendor') } + +sub dynamic_config { + my $self = shift; + my $value = @_ ? shift : 1; + if ( $self->{values}->{dynamic_config} ) { + # Once dynamic we never change to static, for safety + return 0; + } + $self->{values}->{dynamic_config} = $value ? 1 : 0; + return 1; +} + +# Convenience command +sub static_config { + shift->dynamic_config(0); +} + +sub perl_version { + my $self = shift; + return $self->{values}->{perl_version} unless @_; + my $version = shift or die( + "Did not provide a value to perl_version()" + ); + + # Normalize the version + $version = $self->_perl_version($version); + + # We don't support the really old versions + unless ( $version >= 5.005 ) { + die "Module::Install only supports 5.005 or newer (use ExtUtils::MakeMaker)\n"; + } + + $self->{values}->{perl_version} = $version; +} + +sub all_from { + my ( $self, $file ) = @_; + + unless ( defined($file) ) { + my $name = $self->name or die( + "all_from called with no args without setting name() first" + ); + $file = join('/', 'lib', split(/-/, $name)) . '.pm'; + $file =~ s{.*/}{} unless -e $file; + unless ( -e $file ) { + die("all_from cannot find $file from $name"); + } + } + unless ( -f $file ) { + die("The path '$file' does not exist, or is not a file"); + } + + $self->{values}{all_from} = $file; + + # Some methods pull from POD instead of code. + # If there is a matching .pod, use that instead + my $pod = $file; + $pod =~ s/\.pm$/.pod/i; + $pod = $file unless -e $pod; + + # Pull the different values + $self->name_from($file) unless $self->name; + $self->version_from($file) unless $self->version; + $self->perl_version_from($file) unless $self->perl_version; + $self->author_from($pod) unless @{$self->author || []}; + $self->license_from($pod) unless $self->license; + $self->abstract_from($pod) unless $self->abstract; + + return 1; +} + +sub provides { + my $self = shift; + my $provides = ( $self->{values}->{provides} ||= {} ); + %$provides = (%$provides, @_) if @_; + return $provides; +} + +sub auto_provides { + my $self = shift; + return $self unless $self->is_admin; + unless (-e 'MANIFEST') { + warn "Cannot deduce auto_provides without a MANIFEST, skipping\n"; + return $self; + } + # Avoid spurious warnings as we are not checking manifest here. + local $SIG{__WARN__} = sub {1}; + require ExtUtils::Manifest; + local *ExtUtils::Manifest::manicheck = sub { return }; + + require Module::Build; + my $build = Module::Build->new( + dist_name => $self->name, + dist_version => $self->version, + license => $self->license, + ); + $self->provides( %{ $build->find_dist_packages || {} } ); +} + +sub feature { + my $self = shift; + my $name = shift; + my $features = ( $self->{values}->{features} ||= [] ); + my $mods; + + if ( @_ == 1 and ref( $_[0] ) ) { + # The user used ->feature like ->features by passing in the second + # argument as a reference. Accomodate for that. + $mods = $_[0]; + } else { + $mods = \@_; + } + + my $count = 0; + push @$features, ( + $name => [ + map { + ref($_) ? ( ref($_) eq 'HASH' ) ? %$_ : @$_ : $_ + } @$mods + ] + ); + + return @$features; +} + +sub features { + my $self = shift; + while ( my ( $name, $mods ) = splice( @_, 0, 2 ) ) { + $self->feature( $name, @$mods ); + } + return $self->{values}->{features} + ? @{ $self->{values}->{features} } + : (); +} + +sub no_index { + my $self = shift; + my $type = shift; + push @{ $self->{values}->{no_index}->{$type} }, @_ if $type; + return $self->{values}->{no_index}; +} + +sub read { + my $self = shift; + $self->include_deps( 'YAML::Tiny', 0 ); + + require YAML::Tiny; + my $data = YAML::Tiny::LoadFile('META.yml'); + + # Call methods explicitly in case user has already set some values. + while ( my ( $key, $value ) = each %$data ) { + next unless $self->can($key); + if ( ref $value eq 'HASH' ) { + while ( my ( $module, $version ) = each %$value ) { + $self->can($key)->($self, $module => $version ); + } + } else { + $self->can($key)->($self, $value); + } + } + return $self; +} + +sub write { + my $self = shift; + return $self unless $self->is_admin; + $self->admin->write_meta; + return $self; +} + +sub version_from { + require ExtUtils::MM_Unix; + my ( $self, $file ) = @_; + $self->version( ExtUtils::MM_Unix->parse_version($file) ); + + # for version integrity check + $self->makemaker_args( VERSION_FROM => $file ); +} + +sub abstract_from { + require ExtUtils::MM_Unix; + my ( $self, $file ) = @_; + $self->abstract( + bless( + { DISTNAME => $self->name }, + 'ExtUtils::MM_Unix' + )->parse_abstract($file) + ); +} + +# Add both distribution and module name +sub name_from { + my ($self, $file) = @_; + if ( + Module::Install::_read($file) =~ m/ + ^ \s* + package \s* + ([\w:]+) + \s* ; + /ixms + ) { + my ($name, $module_name) = ($1, $1); + $name =~ s{::}{-}g; + $self->name($name); + unless ( $self->module_name ) { + $self->module_name($module_name); + } + } else { + die("Cannot determine name from $file\n"); + } +} + +sub _extract_perl_version { + if ( + $_[0] =~ m/ + ^\s* + (?:use|require) \s* + v? + ([\d_\.]+) + \s* ; + /ixms + ) { + my $perl_version = $1; + $perl_version =~ s{_}{}g; + return $perl_version; + } else { + return; + } +} + +sub perl_version_from { + my $self = shift; + my $perl_version=_extract_perl_version(Module::Install::_read($_[0])); + if ($perl_version) { + $self->perl_version($perl_version); + } else { + warn "Cannot determine perl version info from $_[0]\n"; + return; + } +} + +sub author_from { + my $self = shift; + my $content = Module::Install::_read($_[0]); + if ($content =~ m/ + =head \d \s+ (?:authors?)\b \s* + ([^\n]*) + | + =head \d \s+ (?:licen[cs]e|licensing|copyright|legal)\b \s* + .*? copyright .*? \d\d\d[\d.]+ \s* (?:\bby\b)? \s* + ([^\n]*) + /ixms) { + my $author = $1 || $2; + + # XXX: ugly but should work anyway... + if (eval "require Pod::Escapes; 1") { + # Pod::Escapes has a mapping table. + # It's in core of perl >= 5.9.3, and should be installed + # as one of the Pod::Simple's prereqs, which is a prereq + # of Pod::Text 3.x (see also below). + $author =~ s{ E<( (\d+) | ([A-Za-z]+) )> } + { + defined $2 + ? chr($2) + : defined $Pod::Escapes::Name2character_number{$1} + ? chr($Pod::Escapes::Name2character_number{$1}) + : do { + warn "Unknown escape: E<$1>"; + "E<$1>"; + }; + }gex; + } + elsif (eval "require Pod::Text; 1" && $Pod::Text::VERSION < 3) { + # Pod::Text < 3.0 has yet another mapping table, + # though the table name of 2.x and 1.x are different. + # (1.x is in core of Perl < 5.6, 2.x is in core of + # Perl < 5.9.3) + my $mapping = ($Pod::Text::VERSION < 2) + ? \%Pod::Text::HTML_Escapes + : \%Pod::Text::ESCAPES; + $author =~ s{ E<( (\d+) | ([A-Za-z]+) )> } + { + defined $2 + ? chr($2) + : defined $mapping->{$1} + ? $mapping->{$1} + : do { + warn "Unknown escape: E<$1>"; + "E<$1>"; + }; + }gex; + } + else { + $author =~ s{E}{<}g; + $author =~ s{E}{>}g; + } + $self->author($author); + } else { + warn "Cannot determine author info from $_[0]\n"; + } +} + +#Stolen from M::B +my %license_urls = ( + perl => 'http://dev.perl.org/licenses/', + apache => 'http://apache.org/licenses/LICENSE-2.0', + apache_1_1 => 'http://apache.org/licenses/LICENSE-1.1', + artistic => 'http://opensource.org/licenses/artistic-license.php', + artistic_2 => 'http://opensource.org/licenses/artistic-license-2.0.php', + lgpl => 'http://opensource.org/licenses/lgpl-license.php', + lgpl2 => 'http://opensource.org/licenses/lgpl-2.1.php', + lgpl3 => 'http://opensource.org/licenses/lgpl-3.0.html', + bsd => 'http://opensource.org/licenses/bsd-license.php', + gpl => 'http://opensource.org/licenses/gpl-license.php', + gpl2 => 'http://opensource.org/licenses/gpl-2.0.php', + gpl3 => 'http://opensource.org/licenses/gpl-3.0.html', + mit => 'http://opensource.org/licenses/mit-license.php', + mozilla => 'http://opensource.org/licenses/mozilla1.1.php', + open_source => undef, + unrestricted => undef, + restrictive => undef, + unknown => undef, +); + +sub license { + my $self = shift; + return $self->{values}->{license} unless @_; + my $license = shift or die( + 'Did not provide a value to license()' + ); + $license = __extract_license($license) || lc $license; + $self->{values}->{license} = $license; + + # Automatically fill in license URLs + if ( $license_urls{$license} ) { + $self->resources( license => $license_urls{$license} ); + } + + return 1; +} + +sub _extract_license { + my $pod = shift; + my $matched; + return __extract_license( + ($matched) = $pod =~ m/ + (=head \d \s+ L(?i:ICEN[CS]E|ICENSING)\b.*?) + (=head \d.*|=cut.*|)\z + /xms + ) || __extract_license( + ($matched) = $pod =~ m/ + (=head \d \s+ (?:C(?i:OPYRIGHTS?)|L(?i:EGAL))\b.*?) + (=head \d.*|=cut.*|)\z + /xms + ); +} + +sub __extract_license { + my $license_text = shift or return; + my @phrases = ( + '(?:under )?the same (?:terms|license) as (?:perl|the perl (?:\d )?programming language)' => 'perl', 1, + '(?:under )?the terms of (?:perl|the perl programming language) itself' => 'perl', 1, + 'Artistic and GPL' => 'perl', 1, + 'GNU general public license' => 'gpl', 1, + 'GNU public license' => 'gpl', 1, + 'GNU lesser general public license' => 'lgpl', 1, + 'GNU lesser public license' => 'lgpl', 1, + 'GNU library general public license' => 'lgpl', 1, + 'GNU library public license' => 'lgpl', 1, + 'GNU Free Documentation license' => 'unrestricted', 1, + 'GNU Affero General Public License' => 'open_source', 1, + '(?:Free)?BSD license' => 'bsd', 1, + 'Artistic license 2\.0' => 'artistic_2', 1, + 'Artistic license' => 'artistic', 1, + 'Apache (?:Software )?license' => 'apache', 1, + 'GPL' => 'gpl', 1, + 'LGPL' => 'lgpl', 1, + 'BSD' => 'bsd', 1, + 'Artistic' => 'artistic', 1, + 'MIT' => 'mit', 1, + 'Mozilla Public License' => 'mozilla', 1, + 'Q Public License' => 'open_source', 1, + 'OpenSSL License' => 'unrestricted', 1, + 'SSLeay License' => 'unrestricted', 1, + 'zlib License' => 'open_source', 1, + 'proprietary' => 'proprietary', 0, + ); + while ( my ($pattern, $license, $osi) = splice(@phrases, 0, 3) ) { + $pattern =~ s#\s+#\\s+#gs; + if ( $license_text =~ /\b$pattern\b/i ) { + return $license; + } + } + return ''; +} + +sub license_from { + my $self = shift; + if (my $license=_extract_license(Module::Install::_read($_[0]))) { + $self->license($license); + } else { + warn "Cannot determine license info from $_[0]\n"; + return 'unknown'; + } +} + +sub _extract_bugtracker { + my @links = $_[0] =~ m#L<( + https?\Q://rt.cpan.org/\E[^>]+| + https?\Q://github.com/\E[\w_]+/[\w_]+/issues| + https?\Q://code.google.com/p/\E[\w_\-]+/issues/list + )>#gx; + my %links; + @links{@links}=(); + @links=keys %links; + return @links; +} + +sub bugtracker_from { + my $self = shift; + my $content = Module::Install::_read($_[0]); + my @links = _extract_bugtracker($content); + unless ( @links ) { + warn "Cannot determine bugtracker info from $_[0]\n"; + return 0; + } + if ( @links > 1 ) { + warn "Found more than one bugtracker link in $_[0]\n"; + return 0; + } + + # Set the bugtracker + bugtracker( $links[0] ); + return 1; +} + +sub requires_from { + my $self = shift; + my $content = Module::Install::_readperl($_[0]); + my @requires = $content =~ m/^use\s+([^\W\d]\w*(?:::\w+)*)\s+(v?[\d\.]+)/mg; + while ( @requires ) { + my $module = shift @requires; + my $version = shift @requires; + $self->requires( $module => $version ); + } +} + +sub test_requires_from { + my $self = shift; + my $content = Module::Install::_readperl($_[0]); + my @requires = $content =~ m/^use\s+([^\W\d]\w*(?:::\w+)*)\s+([\d\.]+)/mg; + while ( @requires ) { + my $module = shift @requires; + my $version = shift @requires; + $self->test_requires( $module => $version ); + } +} + +# Convert triple-part versions (eg, 5.6.1 or 5.8.9) to +# numbers (eg, 5.006001 or 5.008009). +# Also, convert double-part versions (eg, 5.8) +sub _perl_version { + my $v = $_[-1]; + $v =~ s/^([1-9])\.([1-9]\d?\d?)$/sprintf("%d.%03d",$1,$2)/e; + $v =~ s/^([1-9])\.([1-9]\d?\d?)\.(0|[1-9]\d?\d?)$/sprintf("%d.%03d%03d",$1,$2,$3 || 0)/e; + $v =~ s/(\.\d\d\d)000$/$1/; + $v =~ s/_.+$//; + if ( ref($v) ) { + # Numify + $v = $v + 0; + } + return $v; +} + +sub add_metadata { + my $self = shift; + my %hash = @_; + for my $key (keys %hash) { + warn "add_metadata: $key is not prefixed with 'x_'.\n" . + "Use appopriate function to add non-private metadata.\n" unless $key =~ /^x_/; + $self->{values}->{$key} = $hash{$key}; + } +} + + +###################################################################### +# MYMETA Support + +sub WriteMyMeta { + die "WriteMyMeta has been deprecated"; +} + +sub write_mymeta_yaml { + my $self = shift; + + # We need YAML::Tiny to write the MYMETA.yml file + unless ( eval { require YAML::Tiny; 1; } ) { + return 1; + } + + # Generate the data + my $meta = $self->_write_mymeta_data or return 1; + + # Save as the MYMETA.yml file + print "Writing MYMETA.yml\n"; + YAML::Tiny::DumpFile('MYMETA.yml', $meta); +} + +sub write_mymeta_json { + my $self = shift; + + # We need JSON to write the MYMETA.json file + unless ( eval { require JSON; 1; } ) { + return 1; + } + + # Generate the data + my $meta = $self->_write_mymeta_data or return 1; + + # Save as the MYMETA.yml file + print "Writing MYMETA.json\n"; + Module::Install::_write( + 'MYMETA.json', + JSON->new->pretty(1)->canonical->encode($meta), + ); +} + +sub _write_mymeta_data { + my $self = shift; + + # If there's no existing META.yml there is nothing we can do + return undef unless -f 'META.yml'; + + # We need Parse::CPAN::Meta to load the file + unless ( eval { require Parse::CPAN::Meta; 1; } ) { + return undef; + } + + # Merge the perl version into the dependencies + my $val = $self->Meta->{values}; + my $perl = delete $val->{perl_version}; + if ( $perl ) { + $val->{requires} ||= []; + my $requires = $val->{requires}; + + # Canonize to three-dot version after Perl 5.6 + if ( $perl >= 5.006 ) { + $perl =~ s{^(\d+)\.(\d\d\d)(\d*)}{join('.', $1, int($2||0), int($3||0))}e + } + unshift @$requires, [ perl => $perl ]; + } + + # Load the advisory META.yml file + my @yaml = Parse::CPAN::Meta::LoadFile('META.yml'); + my $meta = $yaml[0]; + + # Overwrite the non-configure dependency hashs + delete $meta->{requires}; + delete $meta->{build_requires}; + delete $meta->{recommends}; + if ( exists $val->{requires} ) { + $meta->{requires} = { map { @$_ } @{ $val->{requires} } }; + } + if ( exists $val->{build_requires} ) { + $meta->{build_requires} = { map { @$_ } @{ $val->{build_requires} } }; + } + + return $meta; +} + +1; diff --git a/inc/Module/Install/Win32.pm b/inc/Module/Install/Win32.pm new file mode 100644 index 0000000..99d9631 --- /dev/null +++ b/inc/Module/Install/Win32.pm @@ -0,0 +1,64 @@ +#line 1 +package Module::Install::Win32; + +use strict; +use Module::Install::Base (); + +use vars qw{$VERSION @ISA $ISCORE}; +BEGIN { + $VERSION = '1.04'; + @ISA = 'Module::Install::Base'; + $ISCORE = 1; +} + +# determine if the user needs nmake, and download it if needed +sub check_nmake { + my $self = shift; + $self->load('can_run'); + $self->load('get_file'); + + require Config; + return unless ( + $^O eq 'MSWin32' and + $Config::Config{make} and + $Config::Config{make} =~ /^nmake\b/i and + ! $self->can_run('nmake') + ); + + print "The required 'nmake' executable not found, fetching it...\n"; + + require File::Basename; + my $rv = $self->get_file( + url => 'http://download.microsoft.com/download/vc15/Patch/1.52/W95/EN-US/Nmake15.exe', + ftp_url => 'ftp://ftp.microsoft.com/Softlib/MSLFILES/Nmake15.exe', + local_dir => File::Basename::dirname($^X), + size => 51928, + run => 'Nmake15.exe /o > nul', + check_for => 'Nmake.exe', + remove => 1, + ); + + die <<'END_MESSAGE' unless $rv; + +------------------------------------------------------------------------------- + +Since you are using Microsoft Windows, you will need the 'nmake' utility +before installation. It's available at: + + http://download.microsoft.com/download/vc15/Patch/1.52/W95/EN-US/Nmake15.exe + or + ftp://ftp.microsoft.com/Softlib/MSLFILES/Nmake15.exe + +Please download the file manually, save it to a directory in %PATH% (e.g. +C:\WINDOWS\COMMAND\), then launch the MS-DOS command line shell, "cd" to +that directory, and run "Nmake15.exe" from there; that will create the +'nmake.exe' file needed by this module. + +You may then resume the installation process described in README. + +------------------------------------------------------------------------------- +END_MESSAGE + +} + +1; diff --git a/inc/Module/Install/WriteAll.pm b/inc/Module/Install/WriteAll.pm new file mode 100644 index 0000000..86bb25e --- /dev/null +++ b/inc/Module/Install/WriteAll.pm @@ -0,0 +1,63 @@ +#line 1 +package Module::Install::WriteAll; + +use strict; +use Module::Install::Base (); + +use vars qw{$VERSION @ISA $ISCORE}; +BEGIN { + $VERSION = '1.04'; + @ISA = qw{Module::Install::Base}; + $ISCORE = 1; +} + +sub WriteAll { + my $self = shift; + my %args = ( + meta => 1, + sign => 0, + inline => 0, + check_nmake => 1, + @_, + ); + + $self->sign(1) if $args{sign}; + $self->admin->WriteAll(%args) if $self->is_admin; + + $self->check_nmake if $args{check_nmake}; + unless ( $self->makemaker_args->{PL_FILES} ) { + # XXX: This still may be a bit over-defensive... + unless ($self->makemaker(6.25)) { + $self->makemaker_args( PL_FILES => {} ) if -f 'Build.PL'; + } + } + + # Until ExtUtils::MakeMaker support MYMETA.yml, make sure + # we clean it up properly ourself. + $self->realclean_files('MYMETA.yml'); + + if ( $args{inline} ) { + $self->Inline->write; + } else { + $self->Makefile->write; + } + + # The Makefile write process adds a couple of dependencies, + # so write the META.yml files after the Makefile. + if ( $args{meta} ) { + $self->Meta->write; + } + + # Experimental support for MYMETA + if ( $ENV{X_MYMETA} ) { + if ( $ENV{X_MYMETA} eq 'JSON' ) { + $self->Meta->write_mymeta_json; + } else { + $self->Meta->write_mymeta_yaml; + } + } + + return 1; +} + +1; diff --git a/lib/Statistics/R.pm b/lib/Statistics/R.pm new file mode 100644 index 0000000..8b3371d --- /dev/null +++ b/lib/Statistics/R.pm @@ -0,0 +1,617 @@ +package Statistics::R; + + +use 5.006; +use strict; +use warnings; +use Regexp::Common; +use File::Spec::Functions; +use Statistics::R::Legacy; +use IPC::Run qw( harness start pump finish ); +use Text::Balanced qw ( extract_delimited extract_multiple ); + +if ( $^O =~ m/^(?:.*?win32|dos)$/i ) { + require Statistics::R::Win32; +} + +our $VERSION = '0.24'; + +our ($SHARED_BRIDGE, $SHARED_STDIN, $SHARED_STDOUT, $SHARED_STDERR); + +my $prog = 'R'; # executable we are after... R +my $eos = 'Statistics::R::EOS'; # string to signal the R output stream end +my $eos_re = qr/$eos\n$/; # regexp to match end of R stream + +=head1 NAME + +Statistics::R - Perl interface with the R statistical program + +=head1 DESCRIPTION + +I is a module to controls the R interpreter (R project for statistical +computing: L). It lets you start R, pass commands to +it and retrieve the output. A shared mode allow to have several instances of +I talk to the same R process. + +The current I implementation uses pipes (for stdin, stdout and +and stderr) to communicate with R. This implementation should be more efficient +and reliable than that in previous version, which relied on reading and writing +files. As before, this module works on GNU/Linux, MS Windows and probably many +more systems. + +=head1 SYNOPSIS + + use Statistics::R; + + # Create a communication bridge with R and start R + my $R = Statistics::R->new(); + + # Run simple R commands + my $output_file = "file.ps"; + $R->run(qq`postscript("$output_file" , horizontal=FALSE , width=500 , height=500 , pointsize=1)`); + $R->run(q`plot(c(1, 5, 10), type = "l")`); + $R->run(q`dev.off()`); + + # Pass and retrieve data (scalars or arrays) + my $input_value = 1; + $R->set('x', $input_value); + $R->run(q`y <- x^2`); + my $output_value = $R->get('y'); + print "y = $output_value\n"; + + $R->stop(); + +=head1 METHODS + +=over 4 + +=item new() + +Build a I bridge object between Perl and R. Available options are: + + +=over 4 + +=item r_bin + +Specify the full path to R if it is not automatically found. See L. + +=item shared + +Start a shared bridge. When using a shared bridge, several instances of +Statistics::R can communicate with the same unique R instance. Example: + + use Statistics::R; + + my $R1 = Statistics::R->new( shared => 1); + my $R2 = Statistics::R->new( shared => 1); + + $R1->set( 'x', 'pear' ); + my $x = $R2->get( 'x' ); + print "x = $x\n"; + +Do not call the I method is you still have processes that need to interact +with R. + +=back + + +=item run() + +First, start() R if it is not yet running. Then, execute R commands passed as a +string and return the output as a string. If your command fails to run in R, an +error message will be displayed. + +Example: + + my $out = $R->run( q`print( 1 + 2 )` ); + +If you intend on runnning many R commands, it may be convenient to pass an array +of commands or put multiple commands in an here-doc: + + # Array of R commands: + my $out1 = $R->run( + q`a <- 2`, + q`b <- 5`, + q`c <- a * b`, + q`print("ok")` + ); + + # Here-doc with multiple R commands: + my $cmds = <run($cmds); + +To run commands from a file, see the run_from_file() method. + +The output you get from run() is the combination of what R would display on the +standard output and the standard error, but the order may differ. When loading +modules, some may write numerous messages on standard error. You can disable +this behavior using the following R command: + + suppressPackageStartupMessages(library(library_to_load)) + + +=item run_from_file() + +Similar to run() but reads the R commands from the specified file. Internally, +this method uses the R source() command to read the file. + +=item set() + +Set the value of an R variable (scalar or arrayref). Example: + + $R->set( 'x', 'pear' ); + +or + + $R->set( 'y', [1, 2, 3] ); + + +=item get() + +Get the value of an R variable (scalar or arrayref). Example: + + my $x = $R->get( 'x' ); # $y is an scalar + +or + + my $y = $R->get( 'y' ); # $x is an arrayref + +=item start() + +Explicitly start R. Most times, you do not need to do that because the first +execution of run() or set() will automatically call start(). + +=item stop() + +Stop a running instance of R. + +=item restart() + +stop() and start() R. + +=item bin() + +Get or set the path to the R executable. + +=item is_shared() + +Was R started in shared mode? + +=item is_started() + +Is R running? + +=item pid() + +Return the pid of the running R process + +=back + +=head1 INSTALLATION + +Since I relies on R to work, you need to install R first. See this +page for downloads, L. If R is in your PATH environment +variable, then it should be available from a terminal and be detected +automatically by I. This means that you don't have to do anything +on Linux systems to get I working. On Windows systems, in addition +to the folders described in PATH, the usual suspects will be checked for the +presence of the R binary, e.g. C:\Program Files\R. If I does not +find R installation, your last recourse is to specify its full path when calling +new(): + + my $R = Statistics::R->new( r_bin => $fullpath ); + +You also need to have the following CPAN Perl modules installed: + +=over 4 + +=item Text::Balanced (>= 1.97) + +=item Regexp::Common + +=item IPC::Run + +=back + +=head1 SEE ALSO + +=over 4 + +=item * L + +=item * L + +=item * The R-project web site: L + +=item * Statistics:: modules for Perl: L + +=back + +=head1 AUTHORS + +Florent Angly Eflorent.angly@gmail.comE (2011 rewrite) + +Graciliano M. P. Egm@virtuasites.com.brE (original code) + +=head1 MAINTAINER + +Brian Cassidy Ebricas@cpan.orgE + +=head1 COPYRIGHT & LICENSE + +This program is free software; you can redistribute it and/or +modify it under the same terms as Perl itself. + +=head1 BUGS + +All complex software has bugs lurking in it, and this program is no exception. +If you find a bug, please report it on the CPAN Tracker of Statistics::R: +L + +Bug reports, suggestions and patches are welcome. The Statistics::R code is +developed on Github (L) and is under Git +revision control. To get the latest revision, run: + + git clone git@github.com:bricas/statistics-r.git + +=cut + + +sub new { + # Create a new R communication object + my ($class, %args) = @_; + my $self = {}; + bless $self, ref($class) || $class; + $self->initialize( %args ); + return $self; +} + + +sub is_shared { + # Get (/ set) the whether or not Statistics::R is setup to run in shared mode + my ($self, $val) = @_; + if (defined $val) { + $self->{is_shared} = $val; + } + return $self->{is_shared}; +} + + +{ +no warnings 'redefine'; +sub start { + my ($self, %args) = @_; + my $status = 1; + if (not $self->is_started) { + + # If shared mode option of start() requested, rebuild the bridge in shared + # mode. Don't use this option though. It is only here to cater for the legacy + # method start_shared() + if ( exists($args{shared}) && ($args{shared} == 1) ) { + $self->is_shared( 1 ); + $self->bridge( 1 ); + } + + # Now, start R + my $bridge = $self->bridge; + $status = $bridge->start or die "Error starting $prog: $?\n"; + $self->bin( $bridge->{KIDS}->[0]->{PATH} ); + } + + return $status; +} +} + + +sub stop { + my ($self) = @_; + my $status = 1; + if ($self->is_started) { + $status = $self->bridge->finish or die "Error stopping $prog: $?\n"; + } + return $status; +} + + +sub restart { + my ($self) = @_; + return $self->stop && $self->start; +} + + +sub is_started { + # Query whether or not R is currently running + return shift->bridge->{STATE} eq IPC::Run::_started ? 1 : 0; +} + + +sub pid { + # Get (/ set) the PID of the running R process. It is accessible only after + # the bridge has start()ed + return shift->bridge->{KIDS}->[0]->{PID}; +} + + +sub bin { + # Get / set the full path to the R binary program to use. Unless you have set + # the path yourself, it is accessible only after the bridge has start()ed + my ($self, $val) = @_; + if (defined $val) { + $self->{bin} = $val; + } + return $self->{bin}; +} + + +sub run { + # Pass the input and get the output + my ($self, @cmds) = @_; + + # Need to start R now if it is not already running + $self->start if not $self->is_started; + + + # Process each command + my $results = ''; + for my $cmd (@cmds) { + + # Wrap command for execution in R + $self->stdin( $self->wrap_cmd($cmd) ); + + # Pass input to R and get its output + my $bridge = $self->bridge; + while ( $self->stdout !~ m/$eos_re/gc && $bridge->pumpable ) { + $bridge->pump; + } + + # Parse outputs, detect errors + my $out = $self->stdout; + $out =~ s/$eos_re//g; + chomp $out; + my $err = $self->stderr; + chomp $err; + if ($out =~ m//sg) { + # Parse (multi-line) error message + my $err_msg = $1."\n".$err; + die "Problem running the R command:\n$cmd\n\nGot the error:\n$err_msg\n"; + } + + # Save results and reinitialize + $results .= "\n" if $results; + $results .= $err.$out; + $self->stdout(''); + $self->stderr(''); + + } + + $self->result($results); + + return $results; +} + + +sub run_from_file { + my ($self, $file) = @_; + my $results = $self->run( qq`source('$file')` ); + return $results; +} + + +sub set { + # Assign a variable or array of variables in R. Use undef if you want to + # assign NULL to an R variable + my ($self, $varname, $arr) = @_; + + # Check variable type, convert everything into an arrayref + my $ref = ref $arr; + if ($ref eq '') { + # This is a scalar + $arr = [ $arr ]; + } elsif ($ref eq 'ARRAY') { + # This is an array reference, nothing to do + } else { + die "Error: Import variable of type $ref is not supported\n"; + } + + # Quote strings and nullify undef variables + for (my $i = 0; $i < scalar @$arr; $i++) { + if (defined $$arr[$i]) { + if ( $$arr[$i] !~ /^$RE{num}{real}$/ ) { + $$arr[$i] = '"'.$$arr[$i].'"'; + } + } else { + $$arr[$i] = 'NULL'; + } + } + + # Build a string and run it to import data + my $cmd = $varname.' <- c('.join(', ',@$arr).')'; + $self->run($cmd); + return 1; +} + + +sub get { + # Get the value of an R variable + my ($self, $varname) = @_; + my $string = $self->run(qq`print($varname)`); + + # Parse R output + my $value; + if ($string eq 'NULL') { + $value = undef; + } elsif ($string =~ m/^\s*\[\d+\]/) { + # Vector: its string look like: + # ' [1] 6.4 13.3 4.1 1.3 14.1 10.6 9.9 9.6 15.3 + # [16] 5.2 10.9 14.4' + my @lines = split /\n/, $string; + for (my $i = 0; $i < scalar @lines; $i++) { + $lines[$i] =~ s/^\s*\[\d+\] //; + } + $value = join ' ', @lines; + } else { + my @lines = split /\n/, $string; + if (scalar @lines == 2) { + # String looks like: ' mean + # 10.41111 ' + # Extract value from second line + $value = $lines[1]; + $value =~ s/^\s*(\S+)\s*$/$1/; + } else { + #die "Error: Don't know how to handle this R output\n$string\n"; + $value = $string; + } + } + + # Clean + my @arr; + if (not defined $value) { + @arr = ( undef ); + } else { + # Split string into an array, paying attention to strings containing spaces + @arr = extract_multiple( $value, [sub { extract_delimited($_[0],q{ '"}) },] ); + for (my $i = 0; $i < scalar @arr; $i++) { + my $elem = $arr[$i]; + if ($elem =~ m/^\s*$/) { + # Remove elements that are simply whitespaces + splice @arr, $i, 1; + $i--; + } else { + # Trim whitespaces + $arr[$i] =~ s/^\s*(.*?)\s*$/$1/; + # Remove double-quotes + $arr[$i] =~ s/^"(.*)"$/$1/; + } + } + } + + # Return either a scalar of an arrayref + my $ret_val; + if (scalar @arr == 1) { + $ret_val = $arr[0]; + } else { + $ret_val = \@arr; + } + + return $ret_val; +} + + +#---------- INTERNAL METHODS --------------------------------------------------# + + +sub initialize { + my ($self, %args) = @_; + + # Path of R binary + my $bin; + if ( $args{ r_bin } || $args{ R_bin } ) { + $bin = $args{ r_bin } || $args{ R_bin }; + } else { + $bin = $prog; # IPC::Run will find the full path for the program later + } + $self->bin( $bin ); + + # Using shared mode? + if ( exists($args{shared}) && ($args{shared} == 1) ) { + $self->is_shared( 1 ); + } else { + $self->is_shared( 0 ); + } + + # Build the bridge + $self->bridge( 1 ); + + return 1; +} + + +sub bridge { + # Get or build the communication bridge and IOs with R + my ($self, $build) = @_; + if ($build) { + my $cmd = [ $self->bin, '--vanilla', '--slave' ]; + if (not $self->is_shared) { + my ($stdin, $stdout, $stderr); + $self->{stdin} = \$stdin; + $self->{stdout} = \$stdout; + $self->{stderr} = \$stderr; + $self->{bridge} = harness $cmd, $self->{stdin}, $self->{stdout}, $self->{stderr}; + } else { + $self->{stdin} = \$SHARED_STDIN ; + $self->{stdout} = \$SHARED_STDOUT; + $self->{stderr} = \$SHARED_STDERR; + if (not defined $SHARED_BRIDGE) { + # The first Statics::R instance builds the bridge + $SHARED_BRIDGE = harness $cmd, $self->{stdin}, $self->{stdout}, $self->{stderr}; + } + $self->{bridge} = $SHARED_BRIDGE; + } + } + return $self->{bridge}; +} + + +sub stdin { + # Get / set standard input string for R + my ($self, $val) = @_; + if (defined $val) { + ${$self->{stdin}} = $val; + } + return ${$self->{stdin}}; +} + + +sub stdout { + # Get / set standard output string for R + my ($self, $val) = @_; + if (defined $val) { + ${$self->{stdout}} = $val; + } + return ${$self->{stdout}}; +} + + +sub stderr { + # Get / set standard error string for R + my ($self, $val) = @_; + if (defined $val) { + ${$self->{stderr}} = $val; + } + return ${$self->{stderr}}; +} + + +sub result { + # Get / set result of last R command + my ($self, $val) = @_; + if (defined $val) { + $self->{result} = $val; + } + return $self->{result}; +} + + +sub wrap_cmd { + # Wrap a command to pass to R. Whether the command is successful or not, the + # end of stream string will appear on stdout and indicate that R has finished + # processing the data. Note that $cmd can be multiple R commands. + my ($self, $cmd) = @_; + + # Escape double-quotes + $cmd =~ s/"/\\"/g; + + # Evaluate command (and catch syntax and runtime errors) + $cmd = qq`tryCatch( eval(parse(text="$cmd")) , error = function(e){print(e)} ); write("$eos",stdout())\n`; + + return $cmd; +} + + +1; diff --git a/lib/Statistics/R/Legacy.pm b/lib/Statistics/R/Legacy.pm new file mode 100644 index 0000000..8acd396 --- /dev/null +++ b/lib/Statistics/R/Legacy.pm @@ -0,0 +1,188 @@ +package Statistics::R::Legacy; + + +use strict; +use warnings; + +use base qw( Statistics::R ); + +use vars qw{@ISA @EXPORT}; + +BEGIN { + @ISA = 'Exporter'; + @EXPORT = qw{ + startR + stopR + restartR + Rbin + start_sharedR + start_shared + read + receive + is_blocked + is_locked + receive + lock + unlock + send + error + clean_up + }; +} + +=head1 NAME + +Statistics::R::Legacy - Legacy methods for Statistics::R + +=head1 DESCRIPTION + +This module contains legacy methods for I. They are provided +solely so that code that uses older versions of I does not crash +with recent version. Do not use these methods in new code! + +Some of these legacy methods simply had their name changed, but some others were +changed to do nothing and return only single value because it did not make sense +to keep these methods as originally intended anymore. + +=head1 METHODS + +=over 4 + +=item startR() + +This is the same thing as start(). + +=item stopR() + +This is the same thing as stop(). + +=item restartR() + +This is the same thing as restart(). + +=item Rbin() + +This is the same thing as bin(). + +=item start_sharedR() / start_shared() + +Use the shared option of new() instead. + +=item send / read() / receive() + +Use run() instead. + +=item lock() + +Does nothing anymore. + +=item unlock() + +Does nothing anymore. + +=item is_blocked() / is_locked() + +Return 0. + +=item + +Return the empty string. + +=item clean_up() + +Does nothing anymore. + +=back + +=head1 SEE ALSO + +=over 4 + +=item * L + +=back + +=head1 AUTHORS + +Florent Angly Eflorent.angly@gmail.comE (2011 rewrite) + +Graciliano M. P. Egm@virtuasites.com.brE (original code) + +=head1 MAINTAINER + +Brian Cassidy Ebricas@cpan.orgE + +=head1 COPYRIGHT & LICENSE + +This program is free software; you can redistribute it and/or +modify it under the same terms as Perl itself. + +=head1 BUGS + +All complex software has bugs lurking in it, and this program is no exception. +If you find a bug, please report it on the CPAN Tracker of Statistics::R: +L + +Bug reports, suggestions and patches are welcome. The Statistics::R code is +developed on Github (L) and is under Git +revision control. To get the latest revision, run: + + git clone git@github.com:bricas/statistics-r.git + +=cut + + +{ + # Prevent "Name XXX used only once" warnings in this block + no warnings 'once'; + *startR = \&Statistics::R::start; + *stopR = \&Statistics::R::stop; + *restartR = \&Statistics::R::restart; + *Rbin = \&Statistics::R::bin; + *receive = \&Statistics::R::result; + *start_sharedR = \&start_shared; + *read = \&receive; + *is_blocked = \&is_locked; +} + + +sub start_shared { + my $self = shift; + $self->start( shared => 1 ); +} + + +sub lock { + return 1; +} + + +sub unlock { + return 1; +} + + +sub is_locked { + return 0; +} + + +sub send { + # Send a command to R. Do not return the output. + my ($self, $cmd) = @_; + $self->run($cmd); + return 1; +} + + +sub error { + return ''; +} + + +sub clean_up { + return 1; +} + + +1; diff --git a/lib/Statistics/R/Win32.pm b/lib/Statistics/R/Win32.pm new file mode 100644 index 0000000..8ad6467 --- /dev/null +++ b/lib/Statistics/R/Win32.pm @@ -0,0 +1,191 @@ +package Statistics::R::Win32; + + +use strict; +use warnings; +use File::Spec::Functions; +use File::DosGlob qw( glob ); +use Env qw( @PATH $PROGRAMFILES ); + +use vars qw{@ISA @EXPORT}; + +BEGIN { + @ISA = 'Exporter'; + @EXPORT = qw{ + win32_path_adjust + win32_space_quote + win32_space_escape + win32_double_bs + }; +} + +our $PROG = 'R'; + + +=head1 NAME + +Statistics::R::Win32 - Helper functions for Statistics::R on MS Windows platforms + +=head1 DESCRIPTION + +Helper functions to deal with environment variables and escape file paths on +MS Windows platforms. + +=head1 SYNOPSIS + + if ( $^O =~ m/^(?:.*?win32|dos)$/i ) { + require Statistics::R::Win32; + } + +=head1 METHODS + +=over 4 + +=item win32_path_adjust( ) + +Looks for paths where R could be installed, e.g. C:\Program Files (x86)\R-2.1\bin +and add it to the PATH environment variable. + +=item win32_space_quote( ) + +Takes a path and return a path that is surrounded by double-quotes if the path +contains whitespaces. Example: + + C:\Program Files\R\bin\x64 + +becomes + + "C:\Program Files\R\bin\x64" + +=item win32_space_escape( ) + +Takes a path and return a path where spaces have been escaped by a backslash. +contains whitespaces. Example: + + C:\Program Files\R\bin\x64 + +becomes + + C:\Program\ Files\R\bin\x64 + +=item win32_double_bs + +Takes a path and return a path where each backslash was replaced by two backslashes. + Example: + + C:\Program Files\R\bin\x64 + +becomes + + C:\\Program Files\\R\\bin\\x64 + +=back + +=head1 SEE ALSO + +=over 4 + +=item * L + +=back + +=head1 AUTHORS + +Florent Angly Eflorent.angly@gmail.comE (2011 rewrite) + +Graciliano M. P. Egm@virtuasites.com.brE (original code) + +=head1 MAINTAINER + +Brian Cassidy Ebricas@cpan.orgE + +=head1 COPYRIGHT & LICENSE + +This program is free software; you can redistribute it and/or +modify it under the same terms as Perl itself. + +=head1 BUGS + +All complex software has bugs lurking in it, and this program is no exception. +If you find a bug, please report it on the CPAN Tracker of Statistics::R: +L + +Bug reports, suggestions and patches are welcome. The Statistics::R code is +developed on Github (L) and is under Git +revision control. To get the latest revision, run: + + git clone git@github.com:bricas/statistics-r.git + +=cut + + +# Adjust PATH environment variable when this module is loaded. +win32_path_adjust(); + + +sub win32_path_adjust { + # Find potential R directories in the Windows Program Files folder and add + # them to the PATH environment variable + + # Find potential R directories, e.g. C:\Program Files (x86)\R-2.1\bin + # or C:\Program Files\R\bin\x64 + my @r_dirs; + my @prog_file_dirs; + if (defined $PROGRAMFILES) { + push @prog_file_dirs, $PROGRAMFILES; # e.g. C:\Program Files (x86) + my ($programfiles_2) = ($PROGRAMFILES =~ m/^(.*) \(/); # e.g. C:\Program Files + push @prog_file_dirs, $programfiles_2 if not $programfiles_2 eq $PROGRAMFILES; + } + for my $prog_file_dir ( @prog_file_dirs ) { + next if not -d $prog_file_dir; + my @subdirs; + my @globs = ( catfile($prog_file_dir, $PROG), catfile($prog_file_dir, $PROG.'-*') ); + for my $glob ( @globs ) { + $glob = win32_space_escape( win32_double_bs( $glob ) ); + push @subdirs, glob $glob; # DosGlob + } + for my $subdir (@subdirs) { + my $subdir2 = catfile($subdir, 'bin'); + if ( -d $subdir2 ) { + my $subdir3 = catfile($subdir2, 'x64'); + if ( -d $subdir3 ) { + push @r_dirs, $subdir3; + } + push @r_dirs, $subdir2; + } + push @r_dirs, $subdir; + } + } + + # Append R directories to PATH (order is important) + push @PATH, @r_dirs; + + return 1; +} + + +sub win32_space_quote { + # Quote a path if it contains whitespaces + my $path = shift; + $path = '"'.$path.'"' if $path =~ /\s/; + return $path; +} + + +sub win32_space_escape { + # Escape spaces with a single backslash + my $path = shift; + $path =~ s/ /\\ /g; + return $path; +} + + +sub win32_double_bs { + # Double the backslashes + my $path = shift; + $path =~ s/\\/\\\\/g; + return $path; +} + + +1; diff --git a/t/00-load.t b/t/00-load.t new file mode 100644 index 0000000..e43ba72 --- /dev/null +++ b/t/00-load.t @@ -0,0 +1,12 @@ +#! perl + +use strict; +use warnings; +use Test::More tests => 1; + + +BEGIN { + use_ok( 'Statistics::R' ); +} + +diag( "Testing Statistics::R $Statistics::R::VERSION, Perl $], $^X" ); diff --git a/t/01-pod.t b/t/01-pod.t new file mode 100644 index 0000000..d0907bc --- /dev/null +++ b/t/01-pod.t @@ -0,0 +1,9 @@ +#! perl + +use strict; +use warnings; +use Test::More; + +eval 'use Test::Pod 1.00'; +plan skip_all => 'Test::Pod 1.00 required for testing POD' if $@; +all_pod_files_ok(); diff --git a/t/02-legacy.t b/t/02-legacy.t new file mode 100644 index 0000000..2c9ef95 --- /dev/null +++ b/t/02-legacy.t @@ -0,0 +1,57 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; + +plan tests => 20; + + +my $R; + +my $file = "file.ps"; + +ok $R = Statistics::R->new(); + +ok $R->startR(); + +ok $R->restartR(); + +ok $R->send(qq`postscript("$file" , horizontal=FALSE , width=500 , height=500 , pointsize=1)`); + +ok $R->send( q`plot(c(1, 5, 10), type = "l")` ); + +ok $R->send( qq`x = 123 \n print(x)` ); + +my $ret = $R->read(); +ok $ret =~ /^\[\d+\]\s+123\s*$/; + +ok $R->send( qq`x = 456 \n print(x)` ); + +$ret = $R->read(); +ok $ret =~ /^\[\d+\]\s+456\s*$/; + +ok $R->lock; + +ok $R->unlock; + +is $R->is_blocked, 0; + +is $R->is_locked, 0; + +ok $R->clean_up(); + +ok $R->Rbin() =~ /\S+/; + +ok $R->stopR(); + +is $R->error(), ''; + +ok $R->start_shared(); + +ok $R->start_sharedR(); + +ok $R->stop(); + +unlink $file; diff --git a/t/03-run.t b/t/03-run.t new file mode 100644 index 0000000..cf3ea5a --- /dev/null +++ b/t/03-run.t @@ -0,0 +1,80 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; + +plan tests => 15; + + +my ($R, $expected); + +my $file = 'file.ps'; + +ok $R = Statistics::R->new(); + +ok $R->bin() =~ /\S+/, 'Binary'; + +$expected = ''; +is $R->run( ), $expected; + +$expected = ''; +is $R->run( qq`postscript("$file" , horizontal=FALSE , width=500 , height=500 , pointsize=1)`), $expected, 'Basic'; + +$expected = ''; +is $R->run( q`plot(c(1, 5, 10), type = "l")` ), $expected; + +$expected = +'null device + 1 '; +is $R->run( q`dev.off()` ), $expected; # RT bug #66190 + +ok -e $file; # RT bug #70307 +unlink $file; + +$expected = +'loop iteration 1 +loop iteration 2 +loop iteration 3'; +is $R->run( q`for (j in 1:3) { cat("loop iteration "); cat(j); cat("\n") }` ), $expected; + +$expected = 'Some innocuous message on stderr'; +is $R->run( q`write("Some innocuous message on stderr", stderr())` ), $expected, 'IO'; + +$expected = 'Some innocuous message on stdout'; +is $R->run( q`write("Some innocuous message on stdout", stdout())` ), $expected; + +$expected = '[1] 123'; +is $R->run( qq`x <- 123 \n print(x)` ), $expected, 'Multi-line commands'; + +$expected = '456'; +my $cmd1 = 'x <- 456 ; write.table(x, file="", row.names=FALSE, col.names=FALSE)'; +is $R->run( $cmd1 ), $expected; # RT bug #70314 + +my $cmd2 = <run( $cmd2 ), $expected, 'Heredoc commands'; + +$expected = +'456 +[1] "ok"'; +is $R->run( $cmd1, $cmd2 ), $expected, 'Multiple commands'; + +$expected = +'Some innocuous message on stderr +loop iteration: [1] 1 +loop iteration: [1] 2 +loop iteration: [1] 3 +Some innocuous message on stdout + +[1] 123 +456 +[1] "ok"'; +is $R->run_from_file( './t/data/script.R' ), $expected, 'Commands from file'; + diff --git a/t/04-start-stop.t b/t/04-start-stop.t new file mode 100644 index 0000000..ed30915 --- /dev/null +++ b/t/04-start-stop.t @@ -0,0 +1,46 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; +use Cwd; + +plan tests => 16; + + +my $R; + +my $initial_dir = cwd; + +ok $R = Statistics::R->new(); + +is $R->is_started, 0; + +is $R->is_shared, 0; + +ok $R->stop(); + +ok $R->stop(); + +ok $R->start(); + +is $R->is_started, 1; + +is $R->is_shared, 0; + +ok $R->start(); + +is cwd, $initial_dir; # Bug RT #6724 and #70307 + +ok $R->restart(); + +ok $R->stop(); + +ok $R->start( shared => 1); + +is $R->is_shared, 1; + +ok $R->stop(); + +is cwd, $initial_dir; # Bug RT #6724 and #70307 diff --git a/t/05-shared.t b/t/05-shared.t new file mode 100644 index 0000000..904bc26 --- /dev/null +++ b/t/05-shared.t @@ -0,0 +1,53 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; + +plan tests => 29; + + +my ($R1, $R2, $R3, $R4); + +ok $R1 = Statistics::R->new( shared => 1 ), 'Starting in shared mode'; +ok $R2 = Statistics::R->new( shared => 1 ); +ok $R3 = Statistics::R->new( shared => 1 ); +ok $R4 = Statistics::R->new( shared => 1 ); + +is $R1->is_shared, 1; +is $R2->is_shared, 1; +is $R3->is_shared, 1; +is $R4->is_shared, 1; + +ok $R2->start; +ok $R4->start; + +is $R1->is_started, 1; +is $R2->is_started, 1; +is $R3->is_started, 1; +is $R4->is_started, 1; + +ok $R1 =~ m/\d+/, 'PIDs'; +is $R1->pid, $R2->pid; +is $R1->pid, $R3->pid; +is $R1->pid, $R4->pid; + +ok $R1->set( 'x', "string" ), 'Sharing data'; + +ok $R2->set( 'y', 3 ); + +is $R2->get( 'x' ), "string"; + +ok $R3->set( 'z', 10 ); + +is $R4->run( q`a <- y / z` ), ''; + +is $R4->get( 'a' ), 0.3; + +ok $R3->stop(); + +is $R1->is_started, 0; +is $R2->is_started, 0; +is $R3->is_started, 0; +is $R4->is_started, 0; diff --git a/t/06-get-set.t b/t/06-get-set.t new file mode 100644 index 0000000..202bee1 --- /dev/null +++ b/t/06-get-set.t @@ -0,0 +1,99 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; + +plan tests => 86; + + +my ($R, $input, $output); + + +ok $R = Statistics::R->new(); + + +$input = undef; +ok $R->set('x', $input), 'undef'; +is $R->get('x'), undef; + + +$input = 123; +ok $R->set('x', $input); +ok $output = $R->get('x'), 'integer'; +is ref($output), ''; +is $output, 123; + + +# R default number of digits is 7 +$input = 0.93945768644; +ok $R->set('x', $input), 'real number'; +ok $output = $R->get('x'); +is ref($output), ''; +is $output, sprintf("%.7f", $input); + + +$input = "apocalypse"; +ok $R->set('x', $input), 'string'; +ok $output = $R->get('x'); +is ref($output), ''; +is $output, "apocalypse"; + + +$input = "a string"; +ok $R->set('x', $input), 'string with witespace'; +ok $output = $R->get('x'); +is ref($output), ''; +is $output, "a string"; + + +$input = 'gi|57116681|ref|NC_000962.2|'; +ok $R->set('x', $input), 'number-containing string'; +ok $output = $R->get('x'); +is ref($output), ''; +is $output, 'gi|57116681|ref|NC_000962.2|'; + + +# Mixed arrays are considered as string arrays by R, thus there is no digit limit +$input = [123, "a string", 'two strings', 0.93945768644]; +ok $R->set('x', $input), 'mixed array'; +ok $output = $R->get('x'); +is ref($output), 'ARRAY'; +is $$output[0], 123; +is $$output[1], "a string"; +is $$output[2], "two strings"; +is $$output[3], 0.93945768644; + + +# RT bug #71988 +$input = [ q{statistics-r-0.22}, "abc 123 xyz", 'gi|57116681|ref|NC_000962.2|']; +ok $R->set('x', $input), 'array of number-containing strings'; +ok $output = $R->get('x'); +is ref($output), 'ARRAY'; +is $$output[0], q{statistics-r-0.22}; +is $$output[1], "abc 123 xyz"; +is $$output[2], 'gi|57116681|ref|NC_000962.2|'; + + +$input = [123,142,147,153,145,151,165,129,133,150,142,154,131,146,151,136,147,156,141,155,147,165,168,146,148,146,142,145,161,157,154,137,130,161,130,156,140,145,154]; +ok $R->set('x', $input), 'large array of integers'; +ok $output = $R->get('x'); +is ref($output), 'ARRAY'; +for (my $i = 0; $i < scalar @$input; $i++) { + is $$output[$i], $$input[$i]; +} + + +$input = [1, 2, 3]; +ok $R->set('x', $input), 'data frame'; +is $R->run(q`a <- data.frame(first=x)`), ''; +ok $output = $R->get('a$first'); +is ref($output), 'ARRAY'; +is $$output[0], 1; +is $$output[1], 2; +is $$output[2], 3; + + +ok $R->stop(); + diff --git a/t/07-robust.t b/t/07-robust.t new file mode 100644 index 0000000..51b6f85 --- /dev/null +++ b/t/07-robust.t @@ -0,0 +1,25 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; + +plan tests => 10003; + + +# Test that the IOs are well-oiled. In Statistics::R version 0.20, a slight +# imprecision in the regular expression to parse the output stream caused a +# problem was apparent only once every few thousands times + +my ($R, $input); + +ok $R = Statistics::R->new(); + +ok $R->set('x', $input); + +for my $i (1 .. 10000) { + is($R->get('x'), undef); +} + +ok $R->stop(); diff --git a/t/08-errors.t b/t/08-errors.t new file mode 100644 index 0000000..04b4a0c --- /dev/null +++ b/t/08-errors.t @@ -0,0 +1,26 @@ +#! perl + +use strict; +use warnings; +use Test::More; +use Statistics::R; + +plan tests => 3; + +my $R; + +ok $R = Statistics::R->new(); + + +eval { + $R->run( q`print "ASDF"` ); +}; +ok $@, 'Syntax error'; +# Actual error message vary depending on locale + + +eval { + $R->run( q`print(ASDF)` ); +}; +ok $@, 'Runtime error'; + diff --git a/t/data/script.R b/t/data/script.R new file mode 100644 index 0000000..deb371d --- /dev/null +++ b/t/data/script.R @@ -0,0 +1,24 @@ +postscript("file2.ps" , horizontal=FALSE , width=500 , height=500 , pointsize=1) + +plot(c(1, 5, 10), type = "l") + +dev.off() + +unlink("file2.ps") + +for (j in 1:3) { cat("loop iteration: "); print(j); } + +write("Some innocuous message on stdout\n", stdout()) + +write("Some innocuous message on stderr\n", stderr()) + +x <- 123 +print(x) + +x <- 456 ; write.table(x, file="", row.names=FALSE, col.names=FALSE) + +a <- 2 +b <- 5 +c <- a * b +print('ok') + -- 2.39.2