[Bioperl-guts-l] bioperl-live/Bio/Tools/Run StandAloneBlast.pm, 1.66, 1.67 WrapperBase.pm, 1.23, 1.24

Torsten Seemann tseemann at dev.open-bio.org
Wed Oct 4 01:52:08 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Run
In directory dev.open-bio.org:/tmp/cvs-serv7557/Bio/Tools/Run

Modified Files:
	StandAloneBlast.pm WrapperBase.pm 
Log Message:
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and
File::Path native Perl 5.6.1 equivalents.


Index: WrapperBase.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Run/WrapperBase.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** WrapperBase.pm	26 Sep 2006 22:03:19 -0000	1.23
--- WrapperBase.pm	4 Oct 2006 05:52:06 -0000	1.24
***************
*** 74,81 ****
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::IO;
- 
  use base qw(Bio::Root::RootI);
  
  =head2 run
  
--- 74,82 ----
  # Object preamble - inherits from Bio::Root::Root
  
  use base qw(Bio::Root::RootI);
  
+ use File::Spec;
+ use File::Path qw(); # don't import anything
+ 
  =head2 run
  
***************
*** 235,241 ****
     my ($self) = @_;
     $self->io->_io_cleanup();
!    if( defined $self->{'_tmpdir'} &&
!        -d $self->{'_tmpdir'} ) {
!        $self->io->rmtree($self->{'_tmpdir'});
     }
  }
--- 236,242 ----
     my ($self) = @_;
     $self->io->_io_cleanup();
!    if( defined $self->{'_tmpdir'} && -d $self->{'_tmpdir'} ) {
!        # $self->io->rmtree($self->{'_tmpdir'});
!        File::Path->rmtree( $self->{'_tmpdir'} );
     }
  }
***************
*** 327,331 ****
      push @path, $self->program_name.($^O =~ /mswin/i ?'.exe':'');
  
!     return Bio::Root::IO->catfile(@path);
  }
  
--- 328,332 ----
      push @path, $self->program_name.($^O =~ /mswin/i ?'.exe':'');
  
!     return File::Spec->catfile(@path);
  }
  

Index: StandAloneBlast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Run/StandAloneBlast.pm,v
retrieving revision 1.66
retrieving revision 1.67
diff -C2 -d -r1.66 -r1.67
*** StandAloneBlast.pm	27 Sep 2006 02:02:32 -0000	1.66
--- StandAloneBlast.pm	4 Oct 2006 05:52:06 -0000	1.67
***************
*** 507,511 ****
      push @path, $program_name .($^O =~ /mswin/i ?'.exe':'');
  
!     return Bio::Root::IO->catfile(@path);
  }
  
--- 507,511 ----
      push @path, $program_name .($^O =~ /mswin/i ?'.exe':'');
  
!     return File::Spec->catfile(@path);
  }
  



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