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circos-remove-findbin.patch
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circos-remove-findbin.patch
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diff -crB circos-0.69-6/bin/circos circos-0.69-6-new/bin/circos
*** circos-0.69-6/bin/circos 2016-02-19 01:42:59.000000000 +0100
--- circos-0.69-6-new/bin/circos 2018-01-12 09:59:25.662731269 +0100
***************
*** 474,486 ****
use strict;
use warnings;
- use FindBin;
use Getopt::Long qw(:config pass_through posix_default auto_abbrev);
use Pod::Usage;
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
use Circos;
use Cwd;
--- 474,482 ----
diff -crB circos-0.69-6/lib/Circos/Colors.pm circos-0.69-6-new/lib/Circos/Colors.pm
*** circos-0.69-6/lib/Circos/Colors.pm 2015-03-17 01:25:43.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Colors.pm 2018-01-12 10:10:39.174797379 +0100
***************
*** 49,55 ****
use Carp qw( carp confess croak );
use Digest::MD5 qw(md5_hex);
- use FindBin;
use File::Basename;
use File::Spec::Functions;
use File::Temp qw(tempdir);
--- 49,54 ----
***************
*** 65,74 ****
#use Time::HiRes qw(gettimeofday tv_interval);
#use List::Util qw( max min );
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use POSIX qw(pow);
use Circos::Configuration;
--- 64,69 ----
diff -crB circos-0.69-6/lib/Circos/Configuration.pm circos-0.69-6-new/lib/Circos/Configuration.pm
*** circos-0.69-6/lib/Circos/Configuration.pm 2015-03-17 22:11:01.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Configuration.pm 2018-01-12 10:11:41.064008273 +0100
***************
*** 59,68 ****
use Params::Validate qw(:all);
use List::MoreUtils qw(uniq);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Constants;
use Circos::Debug;
use Circos::Utils;
--- 59,64 ----
diff -crB circos-0.69-6/lib/Circos/DataPoint.pm circos-0.69-6-new/lib/Circos/DataPoint.pm
*** circos-0.69-6/lib/Circos/DataPoint.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/DataPoint.pm 2018-01-12 10:11:54.888270731 +0100
***************
*** 38,51 ****
use Carp qw( carp confess croak );
use Data::Dumper;
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
use Circos::Debug;
--- 38,46 ----
diff -crB circos-0.69-6/lib/Circos/Debug.pm circos-0.69-6-new/lib/Circos/Debug.pm
*** circos-0.69-6/lib/Circos/Debug.pm 2015-03-24 01:26:13.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Debug.pm 2018-01-12 10:12:07.192502006 +0100
***************
*** 63,75 ****
use Carp qw( carp confess croak );
use Data::Dumper;
- use FindBin;
use Memoize;
use List::MoreUtils qw(uniq);
use Time::HiRes qw(gettimeofday tv_interval);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
use Circos::Constants;
--- 63,71 ----
diff -crB circos-0.69-6/lib/Circos/Division.pm circos-0.69-6-new/lib/Circos/Division.pm
*** circos-0.69-6/lib/Circos/Division.pm 2015-11-17 00:55:58.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Division.pm 2018-01-12 10:12:21.544769084 +0100
***************
*** 37,52 ****
our @EXPORT = qw();
use Carp qw( carp confess croak );
- use FindBin;
use GD;
use Math::Round;
use List::MoreUtils qw(uniq);
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Constants;
use Circos::Debug;
--- 37,47 ----
diff -crB circos-0.69-6/lib/Circos/Error.pm circos-0.69-6-new/lib/Circos/Error.pm
*** circos-0.69-6/lib/Circos/Error.pm 2015-03-17 22:46:36.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Error.pm 2018-01-12 10:12:32.472970548 +0100
***************
*** 44,53 ****
use Params::Validate;
use Text::Format;
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Constants;
use Circos::Debug;
use Circos::Utils;
--- 44,49 ----
diff -crB circos-0.69-6/lib/Circos/Expression.pm circos-0.69-6-new/lib/Circos/Expression.pm
*** circos-0.69-6/lib/Circos/Expression.pm 2015-11-30 23:49:36.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Expression.pm 2018-01-12 10:12:41.953144015 +0100
***************
*** 39,55 ****
use Carp qw( carp confess croak );
use Data::Dumper;
- use FindBin;
use Params::Validate qw(:all);
use Math::Round;
use Math::VecStat qw(average);
use List::Util qw(min max);
use Text::Balanced qw(extract_bracketed);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Constants;
use Circos::Debug;
--- 39,50 ----
diff -crB circos-0.69-6/lib/Circos/Font.pm circos-0.69-6-new/lib/Circos/Font.pm
*** circos-0.69-6/lib/Circos/Font.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Font.pm 2018-01-12 10:12:51.657320357 +0100
***************
*** 45,59 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Font::TTF::Font;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
use Circos::Constants;
use Circos::Colors;
--- 45,54 ----
diff -crB circos-0.69-6/lib/Circos/Geometry.pm circos-0.69-6-new/lib/Circos/Geometry.pm
*** circos-0.69-6/lib/Circos/Geometry.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Geometry.pm 2018-01-12 10:12:58.961452282 +0100
***************
*** 41,54 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
use Circos::Constants;
use Circos::Debug;
--- 41,49 ----
diff -crB circos-0.69-6/lib/Circos/Heatmap.pm circos-0.69-6-new/lib/Circos/Heatmap.pm
*** circos-0.69-6/lib/Circos/Heatmap.pm 2016-03-30 22:08:12.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Heatmap.pm 2018-01-12 10:13:09.953649538 +0100
***************
*** 24,40 ****
use Carp qw( carp confess croak );
use Clone;
use Data::Dumper;
- use FindBin;
use GD::Image;
use Math::VecStat qw(min max);
use Params::Validate qw(:all);
use List::MoreUtils qw(uniq);
use Regexp::Common qw(number);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Constants;
use Circos::Colors;
--- 24,35 ----
diff -crB circos-0.69-6/lib/Circos/Ideogram.pm circos-0.69-6-new/lib/Circos/Ideogram.pm
*** circos-0.69-6/lib/Circos/Ideogram.pm 2015-11-17 01:18:53.000000000 +0100
--- circos-0.69-6-new/lib/Circos/Ideogram.pm 2018-01-12 10:13:22.045864798 +0100
***************
*** 40,46 ****
use Carp qw( carp confess croak );
use Cwd;
- use FindBin;
use File::Spec::Functions;
use Math::Round;
use Math::VecStat qw(max);
--- 40,45 ----
***************
*** 50,59 ****
use POSIX qw(floor ceil);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Constants;
use Circos::Debug;
--- 49,54 ----
diff -crB circos-0.69-6/lib/Circos/Image.pm circos-0.69-6-new/lib/Circos/Image.pm
*** circos-0.69-6/lib/Circos/Image.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Image.pm 2018-01-12 10:13:31.094024696 +0100
***************
*** 45,58 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Colors;
use Circos::Constants;
--- 45,53 ----
diff -crB circos-0.69-6/lib/Circos/IO.pm circos-0.69-6-new/lib/Circos/IO.pm
*** circos-0.69-6/lib/Circos/IO.pm 2015-12-03 05:51:11.000000000 +0100
--- circos-0.69-6-new/lib/Circos/IO.pm 2018-01-12 10:13:41.686210640 +0100
***************
*** 39,45 ****
use Carp qw( carp confess croak );
use Storable qw(dclone);
use Cwd;
- use FindBin;
use Data::Dumper;
use File::Spec::Functions;
use Math::Round;
--- 39,44 ----
***************
*** 49,58 ****
use POSIX qw(floor ceil);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Constants;
use Circos::Colors;
use Circos::Configuration;
--- 48,53 ----
diff -crB circos-0.69-6/lib/Circos/Karyotype.pm circos-0.69-6-new/lib/Circos/Karyotype.pm
*** circos-0.69-6/lib/Circos/Karyotype.pm 2014-09-09 00:15:58.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Karyotype.pm 2018-01-12 10:13:53.318413330 +0100
***************
*** 38,44 ****
use Carp qw( carp confess croak );
use Cwd;
- use FindBin;
use Math::Round;
use Math::VecStat qw(max);
use Params::Validate qw(:all);
--- 38,43 ----
***************
*** 48,57 ****
#use Regexp::Common qw(number);
#use POSIX qw(floor ceil);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Constants;
use Circos::Debug;
--- 47,52 ----
diff -crB circos-0.69-6/lib/Circos/PNG.pm circos-0.69-6-new/lib/Circos/PNG.pm
*** circos-0.69-6/lib/Circos/PNG.pm 2014-09-17 05:33:06.000000000 +0200
--- circos-0.69-6-new/lib/Circos/PNG.pm 2018-01-12 10:14:31.011059637 +0100
***************
*** 37,51 ****
our @EXPORT = qw();
use Carp qw( carp confess croak );
- use FindBin;
use GD;
use Math::VecStat qw(min max);
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Colors;
use Circos::Constants;
--- 37,46 ----
diff -crB circos-0.69-6/lib/Circos/Rule.pm circos-0.69-6-new/lib/Circos/Rule.pm
*** circos-0.69-6/lib/Circos/Rule.pm 2014-10-02 01:14:25.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Rule.pm 2018-01-12 10:14:38.195181067 +0100
***************
*** 38,51 ****
use Carp qw( carp confess croak );
use Data::Dumper;
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
use Circos::DataPoint;
--- 38,46 ----
diff -crB circos-0.69-6/lib/Circos/SVG.pm circos-0.69-6-new/lib/Circos/SVG.pm
*** circos-0.69-6/lib/Circos/SVG.pm 2015-11-30 23:23:52.000000000 +0100
--- circos-0.69-6-new/lib/Circos/SVG.pm 2018-01-12 10:14:47.803342631 +0100
***************
*** 26,39 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
use Circos::Colors;
use Circos::Constants;
--- 26,34 ----
diff -crB circos-0.69-6/lib/Circos/Text.pm circos-0.69-6-new/lib/Circos/Text.pm
*** circos-0.69-6/lib/Circos/Text.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Text.pm 2018-01-12 10:14:57.083497772 +0100
***************
*** 42,55 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
use Circos::Colors;
--- 42,50 ----
diff -crB circos-0.69-6/lib/Circos/Track/Highlight.pm circos-0.69-6-new/lib/Circos/Track/Highlight.pm
*** circos-0.69-6/lib/Circos/Track/Highlight.pm 2014-10-01 00:43:27.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Track/Highlight.pm 2018-01-12 10:15:06.795659206 +0100
***************
*** 37,50 ****
our @EXPORT = qw();
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
#use Circos::Colors;
--- 37,45 ----
diff -crB circos-0.69-6/lib/Circos/Track/Link.pm circos-0.69-6-new/lib/Circos/Track/Link.pm
*** circos-0.69-6/lib/Circos/Track/Link.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Track/Link.pm 2018-01-12 10:15:17.387834198 +0100
***************
*** 37,50 ****
our @EXPORT = qw();
use Carp qw( carp confess croak );
- use FindBin;
use GD::Image;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
#use Circos::Colors;
--- 37,45 ----
diff -crB circos-0.69-6/lib/Circos/Track.pm circos-0.69-6-new/lib/Circos/Track.pm
*** circos-0.69-6/lib/Circos/Track.pm 2014-09-16 05:31:46.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Track.pm 2018-01-12 10:15:29.628035063 +0100
***************
*** 41,56 ****
use Carp qw( carp confess croak );
use Data::Dumper;
- use FindBin;
use GD::Image;
use List::MoreUtils qw(uniq);
use Math::VecStat qw(min max);
use Params::Validate qw(:all);
use Regexp::Common;
use Statistics::Basic qw(average stddev);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
--- 41,52 ----
diff -crB circos-0.69-6/lib/Circos/Unit.pm circos-0.69-6-new/lib/Circos/Unit.pm
*** circos-0.69-6/lib/Circos/Unit.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Unit.pm 2018-01-12 10:15:37.892169871 +0100
***************
*** 46,60 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use Data::Dumper;
use Params::Validate qw(:all);
use Regexp::Common qw(number);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration qw(%CONF $DIMS);
use Circos::Constants;
use Circos::Debug;
--- 46,55 ----
diff -crB circos-0.69-6/lib/Circos/URL.pm circos-0.69-6-new/lib/Circos/URL.pm
*** circos-0.69-6/lib/Circos/URL.pm 2014-05-12 18:20:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/URL.pm 2018-01-12 10:15:46.092303006 +0100
***************
*** 39,52 ****
);
use Carp qw( carp confess croak );
- use FindBin;
use GD;
use Params::Validate qw(:all);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Configuration;
#use Circos::Colors;
use Circos::Constants;
--- 39,47 ----
diff -crB circos-0.69-6/lib/Circos/Utils.pm circos-0.69-6-new/lib/Circos/Utils.pm
*** circos-0.69-6/lib/Circos/Utils.pm 2014-10-01 21:36:19.000000000 +0200
--- circos-0.69-6-new/lib/Circos/Utils.pm 2018-01-12 10:16:11.576712858 +0100
***************
*** 105,114 ****
use POSIX qw(floor ceil);
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
-
use Circos::Constants;
use Circos::Debug;
use Circos::Error;
--- 105,110 ----
diff -crB circos-0.69-6/lib/Circos.pm circos-0.69-6-new/lib/Circos.pm
*** circos-0.69-6/lib/Circos.pm 2016-06-25 00:19:27.000000000 +0200
--- circos-0.69-6-new/lib/Circos.pm 2018-01-12 10:16:35.801097176 +0100
***************
*** 49,57 ****
use strict;
use warnings;
- use lib "$FindBin::RealBin";
- use lib "$FindBin::RealBin/../lib";
- use lib "$FindBin::RealBin/lib";
BEGIN {
require Circos::Modules;
--- 49,54 ----