lib/SGN/Build.pm

   1 package SGN::Build;
   2 use strict;
   3 use warnings;
   4
   5 use version;
   6
   7 my $HAVE_PARSE_DEB_CONTROL;
   8
   9 BEGIN {
  10     eval { require Parse::Deb::Control };
  11     if( $@ ) {
  12         warn "WARNING: Failed to load Parse::Deb::Control, and it is needed to check R dependencies:\n$@\n"
  13     }
  14     $HAVE_PARSE_DEB_CONTROL = !$@;
  15 }
  16
  17 use Module::Build;
  18 use base 'Module::Build';
  19
  20 my $HAVE_CAPTURE;
  21 BEGIN {
  22     eval { require Capture::Tiny };
  23     $HAVE_CAPTURE = !$@;
  24 }
  25
  26 # we should probably convert this to autodie at some point
  27
  28 # build action just runs make on programs
  29 sub ACTION_build {
  30    my $self = shift;
  31    $self->SUPER::ACTION_build(@_);
  32    system "make -C programs";
  33    if($?) {
  34         _handle_errors($?);
  35         die "make -C programs failed\!n";
  36    }
  37
  38    unless( $ENV{SGN_SHIPWRIGHT_BUILDING} ) {
  39        $self->check_R
  40            or die "R dependency check failed, aborting.\n";
  41    }
  42
  43 }
  44
  45 # override install to just copy the whole dir into the install_base
  46 sub ACTION_install {
  47    my $self = shift;
  48
  49    # installation is just copying the entire dist into
  50    # install_base/sgn
  51    require File::Spec;
  52    my $tgt_dir = File::Spec->catdir($self->install_base,'sgn');
  53    system 'cp', '-rl', '.', $tgt_dir;
  54    if($?) {
  55       _handle_errors($?);
  56       die "SGN site copy ( cp -rl . $tgt_dir ) failed!\n";
  57    }
  58 }
  59
  60 sub ACTION_clean {
  61    shift->SUPER::ACTION_clean(@_);
  62    system "make -C programs clean";
  63    if($?) {
  64       _handle_errors($?);
  65       die "make -C programs clean failed!\n";
  66    }
  67 }
  68
  69 sub ACTION_installdeps {
  70     my $self = shift;
  71
  72     $self->_R_installdeps;
  73
  74     $self->SUPER::ACTION_installdeps( @_ );
  75 }
  76
  77 sub create_build_script {
  78     my $self = shift;
  79
  80     $self->check_R
  81         or warn $self->{R}{check_output};
  82
  83     return $self->SUPER::create_build_script(@_);
  84 }
  85
  86 sub check_R {
  87     my ( $self, @args ) = @_;
  88
  89     if( $HAVE_CAPTURE ) {
  90         my $ret;
  91         my $out = Capture::Tiny::capture_merged {
  92             $ret = $self->_check_R_version;
  93         };
  94
  95          $self->{R}{check_output} = $out;
  96
  97         return $ret;
  98     } else {
  99         return $self->_check_R_version
 100     }
 101 }
 102
 103 sub _R_installdeps {
 104     my ( $self ) = @_;
 105
 106     print "\n\nInstalling R dependencies in ~/cxgn/R_libs. \nDepending on the number of deps to install, this may take long time.\n\nAfter the installation completes, set the env variable R_LIBS_USER in your system (/etc/R/Renviron) to \"~/cxgn/R_libs\". This will ensure deps you manually install in R will be in the same place as sgn R libraries and avoid installation of the same R packages in multiple places. It will also add packages in the \"~/cxgn/R_libs\" to the search path\n\n";
 107
 108     my $rout = qx /Rscript R\/sgnPackages.r 2>&1 /;
 109
 110     print "\nR dependencies installation output:\n $rout\n";
 111
 112     if( $? ) {
 113         _handle_errors($?);
 114         warn "Failed to automatically install R dependencies\n\n";
 115     } else  {
 116         print "Successfully installed R dependencies.\n\n";
 117     }
 118
 119 }
 120
 121 sub _handle_errors {
 122     my ($exit_code) = @_;
 123     if ($exit_code == -1) {
 124         print "Error: failed to execute: $!\n";
 125     } elsif ($exit_code & 127) {
 126         warn sprintf("Error: child died with signal %d, %s coredump\n",
 127             ($exit_code & 127),  ($exit_code & 128) ? 'with' : 'without');
 128     } else {
 129         warn sprintf("Error: child exited with value %d\n",$exit_code >> 8);
 130     }
 131 }
 132
 133 sub _run_R_check {
 134     my $self = shift;
 135
 136     # check the R version ourself, since R CMD check apparently does
 137     # not do it.
 138     $self->_check_R_version
 139         or return 0;
 140
 141     if ( $? ) {
 142         _handle_errors($?);
 143         warn "\nR version PREREQUISITE CHECK FAILED.\n\n";
 144         return 0;
 145     } else {
 146         print "\nR version prerequisite OK.\n\n";
 147         return 1;
 148     }
 149 }
 150
 151 sub _check_R_version {
 152     my $self = shift;
 153
 154     unless ($HAVE_PARSE_DEB_CONTROL) {
 155         warn "Parse::Deb::Control not present, skipping R configuration";
 156         return 0;
 157     }
 158     my ( $cmp, $v ) = $self->_R_version_required;
 159
 160     if( eval '$self->_R_version_current'." $cmp version->parse('$v')" ) {
 161         return 1;
 162     } else {
 163         warn "R VERSION CHECK FAILED, we have ".$self->_R_version_current.", but we require $cmp $v.\n";
 164         warn "To install R : sudo apt-get update; sudo apt-get install r-base r-base-dev\n\n";
 165         return 0;
 166     }
 167 }
 168
 169 # parse and return the R cran deps file
 170 sub _R_desc {
 171     return Parse::Deb::Control->new([qw[ R_files cran ]]);
 172 }
 173
 174 # parse and return the version of R we require as string list like
 175 # ('>=','2.10.0')
 176 sub _R_version_required {
 177     my $self = shift;
 178
 179     my @k = $self->_R_desc->get_keys('Depends')
 180         or return ( '>=', 0 );
 181     my ($version) = ${$k[0]->{value}} =~ / \b R \s* \( ([^\)]+) /x
 182         or return ( '>=', 0 );
 183
 184     my @v = split /\s+/, $version;
 185     unshift @v, '==' unless @v > 1;
 186
 187     return @v;
 188 }
 189
 190 # parse and return the current R version as a version object
 191 sub _R_version_current {
 192     my $r = `R --version`;
 193     return 0 unless $r;
 194
 195     $r =~ /R version ([\d\.]+)/;
 196
 197     return version->new($1);
 198 }
 199
 200
 201 1;
 202