[Bioperl-guts-l] bioperl-live INSTALL, 1.47, 1.47.4.1 Makefile.PL, 1.94, 1.94.4.1

Sat Sep 2 09:26:03 EDT 2006

Update of /home/repository/bioperl/bioperl-live
In directory dev.open-bio.org:/tmp/cvs-serv14753

Modified Files:
      Tag: branch-1-5-2
	INSTALL Makefile.PL 
Log Message:
merge from HEAD, server problems should skip and pass in test suite

Index: Makefile.PL
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Makefile.PL,v
retrieving revision 1.94
retrieving revision 1.94.4.1
diff -C2 -d -r1.94 -r1.94.4.1
*** Makefile.PL	15 Jun 2006 13:57:04 -0000	1.94
--- Makefile.PL	2 Sep 2006 13:26:01 -0000	1.94.4.1
***************
*** 13,56 ****
  # All Bioperl dependencies on external modules are defined here
  %packages = (
! 	     'Set::Scalar'              => '0.0/Bio::Tree::Compatible/proper operation/Bio::Tree::Compatible',
! 	     'HTTP::Request::Common'    => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
! 	     'LWP::UserAgent'           => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
! 	     'HTML::Entities'           => '0.0/To parse POST request URL formas/Remote Analysis POST submissions/Bio::Tools::Run::Analysis::*',
! 	     'HTML::Parser'             => '3.0/Parse HTML documents/screen scraping www.gdb.org/Bio::DB::GDB',
! 	     'Ace'                      => '0.0/Aceperl/access of ACeDB database/Bio::DB::Ace',
! #	     'IO::Scalar'               => '0.0/IO handle to read or write to a scalar/remote http Blast jobs/Bio::Tools::Blast::Run::Webblast',
! 	     'IO::String'               => '0.0/IO handle to read or write to a string/GenBank+GenPept sequence retrieval, Variation code/Bio::DB::*,Bio::Variation::*,Bio::Tools::Blast::Run::Webblast, Bio::Index::Blast',
! 	     'XML::Parser'              => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
! 	     'XML::Writer'              => '0.0/Parsing + writing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
! 	     'XML::Parser::PerlSAX'     => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
! 	     'XML::Twig'         	     => '0.0/Available on CPAN/parsing of XML documents/Module Bio::Variation::IO::xml.pm',
! 	     'File::Temp'               => '0.0/Temporary File creation/Bio::Root::IO uses if present/Bio::DB::WebDBSeqI, Bio::Seq::LargePrimarySeq',
! 	     'SOAP::Lite'               => '0.0/SOAP protocol/XEMBL Services (also Bibliographic queries in Biblio::) /Bio::DB::XEMBLService',
! 	     'HTML::Parser'             => '0.0/HTML parsing/HTML parsing of GDB page/Bio::DB::GDB',
! 	     'DBD::mysql'               => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF',
! 	     'GD'                       => '1.3/Graphical Drawing Toolkit/rendering Sequences and Features/Bio::Graphics',
! 	     'Text::Shellwords'         => '0.0/Execute shell commands/test scripts/Bio::Graphics',
! 	     'SVG'                      => '2.26/Generate optional SVG output/Bio::Graphics/Bio::Graphics::Pictogram',
! 	     'SVG::Graph'               => '0.01/Generate optional SVG output/creating SVG images/Bio::TreeIO::svggraph',
! 	     'GD::SVG'                  => '0.0/Generate optional SVG output/creating SVG images/Bio::Graphics::Panel',
! 	     'Storable'                 => '0.0/Persistent object storage and retrieval/storing sequence objects in local file cache/Bio::DB::FileCache',
! 	     'DB_File'                  => '0.0/Persistent object storage and retrieval/Bio::DB::GFF::Adaptor::berkeleydb',
! 	     'Graph::Directed'          => '0.0/Generic Graph data structure and algorithms/ontology engine implementation for the GO parser/Bio::Ontology::OBOEngine',
! 	     'Class::AutoClass'         => '0.0/Protocol for object creation/creating objects/Bio::Graph::SimpleGraph',
! 	     'Clone'                    => '0.0/Recursively copy Perl datatypes/cloning ProteinGraph objects/Bio::Graph::ProteinGraph',
! 	     'XML::SAX'                 => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
! 	     'XML::SAX::Base'           => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
! 	     'XML::SAX::Writer'         => '0.0/New style SAX parser/Writers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
! 	     'XML::DOM::XPath'          => '0.0/XML parser/Bio::SeqIO::interpro',
! 
!  	     'Bio::ASN1::EntrezGene'    => '0.0/Entrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene',
!  	     'Convert::Binary::C'       => '0.0/Binary Data Conversion using C Types/Parsers/Bio::SeqIO::strider',
!  	     'Spreadsheet::ParseExcel'  => '0.0/Excel parser/Test suite',
!              'Data::Stag::Writer'       => '0.0/XML writer/Bio::SeqIO::chaosxml',
  # Bio::Microarray is not in core bioperl yet
! #	     'enum'                     => '0.0/C style enumerated types and bitmask flags 
  # in Perl/Bio::Microarray::Affymetrix::*',
! 
! 	    );
  
  sub check_package {
--- 13,54 ----
  # All Bioperl dependencies on external modules are defined here
  %packages = (
!     'Ace'                       => '0.0/Aceperl/access of ACeDB database/Bio::DB::Ace',
!     'Bio::ASN1::EntrezGene'     => '0.0/Entrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene',
!     'Class::AutoClass'          => '0.0/Protocol for object creation/creating objects/Bio::Graph::SimpleGraph',
!     'Clone'                     => '0.0/Recursively copy Perl datatypes/cloning ProteinGraph objects/Bio::Graph::ProteinGraph',
!     'Convert::Binary::C'        => '0.0/Binary Data Conversion using C Types/Parsers/Bio::SeqIO::strider',
!     'Data::Stag::Writer'        => '0.0/XML writer/Bio::SeqIO::chaosxml',
!     'DB_File'                   => '0.0/Persistent object storage and retrieval/Bio::DB::GFF::Adaptor::berkeleydb',
!     'DBD::mysql'                => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF',
  # Bio::Microarray is not in core bioperl yet
! #    'enum'                      => '0.0/C style enumerated types and bitmask flags
  # in Perl/Bio::Microarray::Affymetrix::*',
!     'File::Temp'                => '0.0/Temporary File creation/Bio::Root::IO uses if present/Bio::DB::WebDBSeqI, Bio::Seq::LargePrimarySeq',
!     'GD'                        => '1.3/Graphical Drawing Toolkit/rendering Sequences and Features/Bio::Graphics',
!     'GD::SVG'                   => '0.0/Generate optional SVG output/creating SVG images/Bio::Graphics::Panel',
!     'Graph::Directed'           => '0.0/Generic Graph data structure and algorithms/ontology engine implementation for the GO parser/Bio::Ontology::OBOEngine',
!     'HTML::Entities'            => '0.0/To parse POST request URL formas/Remote Analysis POST submissions/Bio::Tools::Run::Analysis::*',
!     'HTML::Parser'              => '3.0/Parse HTML documents/screen scraping www.gdb.org/Bio::DB::GDB',
!     'HTTP::Request::Common'     => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
! #    'IO::Scalar'                => '0.0/IO handle to read or write to a scalar/remote http Blast jobs/Bio::Tools::Blast::Run::Webblast',
!     'IO::String'                => '0.0/IO handle to read or write to a string/GenBank+GenPept sequence retrieval, Variation code/Bio::DB::*,Bio::Variation::*,Bio::Tools::Blast::Run::Webblast, Bio::Index::Blast',
!     'LWP::UserAgent'            => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
!     'Set::Scalar'               => '0.0/Bio::Tree::Compatible/proper operation/Bio::Tree::Compatible',
!     'SOAP::Lite'                => '0.0/SOAP protocol/XEMBL Services (also Bibliographic queries in Biblio::) /Bio::DB::XEMBLService',
!     'Spreadsheet::ParseExcel'   => '0.0/Excel parser/Test suite',
!     'Storable'                  => '0.0/Persistent object storage and retrieval/storing sequence objects in local file cache/Bio::DB::FileCache',
!     'SVG'                       => '2.26/Generate optional SVG output/Bio::Graphics/Bio::Graphics::Pictogram',
!     'SVG::Graph'                => '0.01/Generate optional SVG output/creating SVG images/Bio::TreeIO::svggraph',
!     'Text::Shellwords'          => '0.0/Execute shell commands/test scripts/Bio::Graphics',
!     'XML::DOM::XPath'           => '0.0/XML parser/Bio::SeqIO::interpro',
!     'XML::Parser'               => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
!     'XML::Parser::PerlSAX'      => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
!     'XML::SAX'                  => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
!     'XML::SAX::Base'            => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
!     'XML::SAX::Writer'          => '0.0/New style SAX parser/Writers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
!     'XML::Simple'               => '0.0/Simple XML parser/Parsers/Bio::DB::EUtilities',
!     'XML::Twig'                 => '0.0/Available on CPAN/parsing of XML documents/Module Bio::Variation::IO::xml.pm',
!     'XML::Writer'               => '0.0/Parsing + writing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
! );
  
  sub check_package {
***************
*** 58,63 ****
      my ($ver,$desc,$expl,$module) = split( /\// , $str);
      if( !eval "require($name)") {
! 	print "External Module $name, $desc,\n is not installed on this computer.\n  The $module in Bioperl needs it for $expl\n\n";
! 	return 1;
      }
  
--- 56,61 ----
      my ($ver,$desc,$expl,$module) = split( /\// , $str);
      if( !eval "require($name)") {
!     print "External Module $name, $desc,\n is not installed on this computer.\n  The $module in Bioperl needs it for $expl\n\n";
!     return 1;
      }
  
***************
*** 103,114 ****
        GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
        if (open T,">t/do_biodbgff.tests") {
! 	foreach (keys %$cfg) {
! 	  print T $_,"\t",$cfg->{$_},"\n";
! 	}
! 	close T;
        }
      } else {
        if( -e "t/do_biodbgff.tests" ) {
! 	unlink "t/do_biodbgff.tests";
        }
      }
--- 101,112 ----
        GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
        if (open T,">t/do_biodbgff.tests") {
!     foreach (keys %$cfg) {
!       print T $_,"\t",$cfg->{$_},"\n";
!     }
!     close T;
        }
      } else {
        if( -e "t/do_biodbgff.tests" ) {
!     unlink "t/do_biodbgff.tests";
        }
      }
***************
*** 116,119 ****
--- 114,140 ----
  }
  
+ sub setup_bioseqfeaturestore {
+   if ( eval "require DB_File; 1" ) {
+     warn "I see you have Berkeleydb installed. I will create the BDB tests for Bio::DB::SeqFeature::Store...\n";
+     open F,">t/BioDBSeqFeature_BDB.t";
+     print F <<END;
+ system "perl t/BioDBSeqFeature.t -adaptor berkeleydb -create 1 -temp 1";
+ END
+     close F;
+   }
+ 
+   if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
+     if (DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})) {
+       warn "I see you have mysql running and have a connectable 'test' database. I will create the mysql tests for Bio::DB::SeqFeature::Store...\n";
+       open F,">t/BioDBSeqFeature_mysql.t";
+       print F <<END;
+ system "perl t/BioDBSeqFeature.t -adaptor DBI::mysql -create 1 -temp 1 -dsn test";
+ END
+       close F;
+     }
+   }
+ 
+ }
+ 
  sub MY::install {
    package MY;
***************
*** 185,189 ****
        next if $doneit;
        if (s/^\#\!\S+/$bangline/) {
! 	$doneit++;
        }
      } continue {
--- 206,210 ----
        next if $doneit;
        if (s/^\#\!\S+/$bangline/) {
!     $doneit++;
        }
      } continue {
***************
*** 222,226 ****
  
    $driver  = prompt("Which database driver should I use for testing BioDBGFF (mysql,Pg,Oracle)?",
! 		    $driver) if $prompt;
  
    my $d = lc $driver;
--- 243,247 ----
  
    $driver  = prompt("Which database driver should I use for testing BioDBGFF (mysql,Pg,Oracle)?",
!             $driver) if $prompt;
  
    my $d = lc $driver;
***************
*** 263,267 ****
    }
    if ($d eq 'pg') {
!     $test_dsn = "dbi:$driver:dbname=$test_db"; 
    } else {
      $test_dsn = "dbi:$driver:database=$test_db";
--- 284,288 ----
    }
    if ($d eq 'pg') {
!     $test_dsn = "dbi:$driver:dbname=$test_db";
    } else {
      $test_dsn = "dbi:$driver:database=$test_db";
***************
*** 276,288 ****
      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");
    }
  }
  
! 				           
  #
  # Talk to Ewan (<birney at ebi.ac.uk>) or bioperl-l at bioperl.org for more info.
--- 297,309 ----
      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");
    }
  }
  
! 
  #
  # Talk to Ewan (<birney at ebi.ac.uk>) or bioperl-l at bioperl.org for more info.
***************
*** 300,303 ****
--- 321,325 ----
  my @scripts_to_install = eval {get_scripts_to_install()};
  prompt_for_biodbgff();
+ setup_bioseqfeaturestore();
  
  
***************
*** 329,333 ****
  foreach $name ( keys %packages ) {
      if( &check_package($name,$packages{$name}) == 1 ) {
! 	$error = 1;
      }
  }
--- 351,355 ----
  foreach $name ( keys %packages ) {
      if( &check_package($name,$packages{$name}) == 1 ) {
!     $error = 1;
      }
  }
***************
*** 354,379 ****
  
  WriteMakefile(
!     NAME	=> $NAME,
!     DISTNAME    => $DISTNAME,
      VERSION_FROM => "Bio/Root/Version.pm",
!     'dist'      => {  COMPRESS     => 'gzip -9f',
!                       SUFFIX       => '.gz', 
                        DIST_DEFAULT => 'all tardist',
!                    },
!     ($] ge '5.005')  ? (
!      'AUTHOR'   => 'Bioperl Team (bioperl-l at bioperl.org)',
!      'ABSTRACT' => 'Bioinformatics Toolkit',
      ) : (),
!     'realclean' => {  FILES        => join(' ', at BACKUP_FILES) },
      DIR         => [  ], # directories with other Makefile.PL's in them
      EXE_FILES   => \@scripts_to_install,
!     PL_FILES	=> {'maintenance/symlink_scripts.PLS' => 'maintenance/symlink_scripts.pl' },
      PREREQ_PM   => {
! 	'IO::String'       => 0,
!     	'File::Temp'       => 0,
! 	'File::Spec'       => 0,
! 	'HTML::Entities'   => 0,
! 	'DB_File'          => 0,
! 	'IO::Scalar'       => 0,
      },
  );
--- 376,401 ----
  
  WriteMakefile(
!     NAME         => $NAME,
!     DISTNAME     => $DISTNAME,
      VERSION_FROM => "Bio/Root/Version.pm",
!     'dist'       => { COMPRESS     => 'gzip -9f',
!                       SUFFIX       => '.gz',
                        DIST_DEFAULT => 'all tardist',
!                     },
!     ($] ge '5.005') ? (
!         'AUTHOR'   => 'Bioperl Team (bioperl-l at bioperl.org)',
!         'ABSTRACT' => 'Bioinformatics Toolkit',
      ) : (),
!     'realclean' => { FILES => join(' ', @BACKUP_FILES) },
      DIR         => [  ], # directories with other Makefile.PL's in them
      EXE_FILES   => \@scripts_to_install,
!     PL_FILES    => {'maintenance/symlink_scripts.PLS' => 'maintenance/symlink_scripts.pl' },
      PREREQ_PM   => {
!         'IO::String'     => 0,
!         'File::Temp'     => 0,
!         'File::Spec'     => 0,
!         'HTML::Entities' => 0,
!         'DB_File'        => 0,
!         'IO::Scalar'     => 0,
      },
  );
***************
*** 394,398 ****
    package MY;
    return shift->SUPER::clean(@_) . <<END;
! 	-rm -rf scripts_temp
  END
  }
--- 416,420 ----
    package MY;
    return shift->SUPER::clean(@_) . <<END;
! \t-rm -rf scripts_temp
  END
  }

Index: INSTALL
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v
retrieving revision 1.47
retrieving revision 1.47.4.1
diff -C2 -d -r1.47 -r1.47.4.1
*** INSTALL	5 Jul 2006 03:28:12 -0000	1.47
--- INSTALL	2 Sep 2006 13:26:01 -0000	1.47.4.1
***************
*** 533,536 ****
--- 533,538 ----
                                           Bio::Graph::SimpleGraph*
  
+  Requires Class::AutoClass v 1.01
+ 
   Clone                    Used to clone objects
                                           Bio::Graph::ProteinGraph