New Bioperl version 1.2.2 -

3 files changed, 118 insertions, 0 deletions

diff --git a/app-sci/bioperl/files/biodbgff-enable-1.2.2.patch b/app-sci/bioperl/files/biodbgff-enable-1.2.2.patch
new file mode 100644
index 000000000000..7bd66206a0b4
--- /dev/null
+++ b/app-sci/bioperl/files/biodbgff-enable-1.2.2.patch
@@ -0,0 +1,98 @@
+--- Makefile.PL.orig	2003-07-14 16:09:49.000000000 +0100
++++ Makefile.PL	2003-07-14 16:15:56.000000000 +0100
+@@ -83,9 +83,6 @@
+ # Prompt user for BioDBGFF stuff
+ #
+ 
+-if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
+-  my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql database) y/n",'n');
+-  if( $proceed =~ /^[yY]/) {
+     my $cfg = {dbd_driver => 'mysql'};
+     GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
+     if (open T,">t/do_biodbgff.tests") {
+@@ -94,13 +91,6 @@
+       }
+       close T;
+     }
+-  } else {
+-    if( -e "t/do_biodbgff.tests" ) {
+-      unlink "t/do_biodbgff.tests";
+-    }
+-  }
+-}
+-
+ 
+ ############################################################################
+ #
+@@ -124,55 +114,27 @@
+   my $d = lc $driver;
+   my $prompt = $options->{'prompt'};
+ 
+-  my $test_db =  exists($options->{"$d-test-db"}) ?
+-    $options->{"$d-test-db"} : ($cfg->{'test_db'} || 'test');
+-  $test_db = prompt
+-    ("Which database should I use for testing the $db drivers?",
+-     $test_db) if $prompt;
+-
+-  my $test_host = exists($options->{"$d-test-host"}) ?
+-    $options->{"$d-test-host"} : ($cfg->{'test_host'} || 'localhost');
+-  $test_host = prompt
+-    ("On which host is database $test_db running (hostname, ip address or host:port)", $test_host) if $prompt;
+-
+-  my($test_user, $test_pass);
+-
+-  $test_user = exists($options->{"$d-test-user"}) ?
+-    $options->{"$d-test-user"} : ($cfg->{'test_user'} || "undef");
+-  $test_user = prompt
+-    ("User name for connecting to database $test_db?", $test_user)
+-      if $prompt;
+-  $test_user = undef if $test_user eq 'undef';
+-
+-  $test_pass = exists($options->{"$d-test-pass"}) ?
+-    $options->{"$d-test-pass"} : ($cfg->{'test_pass'} || "undef");
+-  $test_pass = prompt
+-    ("Password for connecting to database $test_db?", $test_pass)
+-      if $prompt;
+-  $test_pass = undef if $test_pass eq 'undef';
+-
+-  $cfg->{'test_db'}   = $test_db;
+-  $cfg->{'test_host'} = $test_host;
+-  $cfg->{'test_user'} = $test_user;
+-  $cfg->{'test_pass'} = $test_pass;
+-  if ($test_host eq 'undef'  ||  $test_host eq 'localhost') {
+-    $test_host = '';
+-  }
+-  my $test_dsn = "DBI:$driver:database=$test_db";
+-  $cfg->{test_dsn} = $test_dsn;
+-  if ($test_host) {
+-    $cfg->{'test_dsn'} .= ";host=$test_host";
+-  }
++  $options->{"$d-test-db"} = 'test';
++  $options->{"$d-test-host"} = 'localhost';
++  $options->{"$d-test-user"} = n0b0dy;
++  $options->{"$d-test-pass"} = undef;
++
++  $cfg->{'test_db'}   = $options->{"$d-test-db"};
++  $cfg->{'test_host'} = $options->{"$d-test-host"};
++  $cfg->{'test_user'} = $options->{"$d-test-user"};
++  $cfg->{'test_pass'} = $options->{"$d-test-pass"};
+ 
++  my $test_dsn = "DBI:$driver:database=" . $cfg->{test_db};
++  $cfg->{'test_dsn'} = $test_dsn;
+ 
+   if ($options->{'verbose'}) {
+     local $^W=0;  # some uninitialized variable warning coming through
+     print("Driver $driver is using the following settings for tests:\n",
+-	  "    Database $test_db\n",
+-	  "    Host     $test_host\n",
+-	  "    DSN      $test_dsn\n",
+-	  "    User     $test_user\n",
+-	  "    Password $test_pass\n");
++	  "    Database ".$cfg->{test_db}.  "\n",
++	  "    Host     ".$cfg->{test_host}."\n",
++	  "    DSN      ".$cfg->{test_dsn}. "\n",
++	  "    User     ".$cfg->{test_user}."\n",
++	  "    Password ".$cfg->{test_pass}."\n");
+   }
+ }
+ 
diff --git a/app-sci/bioperl/files/digest-bioperl-1.2.2 b/app-sci/bioperl/files/digest-bioperl-1.2.2
new file mode 100644
index 000000000000..f9d1b2b95180
--- /dev/null
+++ b/app-sci/bioperl/files/digest-bioperl-1.2.2
@@ -0,0 +1 @@
+MD5 c630a5f13a452a65cfa1cbbed1d10378 bioperl-1.2.2.tar.gz 3585206
diff --git a/app-sci/bioperl/files/domanpages-1.2.2.patch b/app-sci/bioperl/files/domanpages-1.2.2.patch
new file mode 100644
index 000000000000..14cbe35de59a
--- /dev/null
+++ b/app-sci/bioperl/files/domanpages-1.2.2.patch
@@ -0,0 +1,19 @@
+--- Makefile.PL.orig	2003-07-14 17:31:03.000000000 +0100
++++ Makefile.PL	2003-07-14 17:31:15.000000000 +0100
+@@ -270,16 +270,3 @@
+ 		   },
+ );
+ 
+-
+-sub MY::manifypods {
+-    my $self = shift;
+-    #print STDERR "In manifypods moment\n";
+-    if( 1 ) {
+-        return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
+-      }
+-      else {
+-        return $self->SUPER::manifypods(@_);
+-      }
+-    }
+-
+-