projects/guix·blob python-team · refs

544 lines · 15.9 KiB

1This patch was created by Roel Janssen <[email protected]>.
2
3Circos uses paths relative to the "circos" script to find its Perl modules.
4This patch removes that mechanism, and instead expects the 'Circos' modules
5to be available in the global Perl path.
6
7diff -crB circos-0.69-6/bin/circos circos-0.69-6-new/bin/circos
8*** circos-0.69-6/bin/circos 2016-02-19 01:42:59.000000000 +0100
9--- circos-0.69-6-new/bin/circos 2018-01-12 09:59:25.662731269 +0100
10***************
11*** 474,486 ****
12
13 use strict;
14 use warnings;
15- use FindBin;
16 use Getopt::Long qw(:config pass_through posix_default auto_abbrev);
17 use Pod::Usage;
18
19- use lib "$FindBin::RealBin";
20- use lib "$FindBin::RealBin/../lib";
21- use lib "$FindBin::RealBin/lib";
22 use Circos;
23
24 use Cwd;
25--- 474,482 ----
26diff -crB circos-0.69-6/lib/Circos/Colors.pm circos-0.69-6-new/lib/Circos/Colors.pm
27*** circos-0.69-6/lib/Circos/Colors.pm 2015-03-17 01:25:43.000000000 +0100
28--- circos-0.69-6-new/lib/Circos/Colors.pm 2018-01-12 10:10:39.174797379 +0100
29***************
30*** 49,55 ****
31
32 use Carp qw( carp confess croak );
33 use Digest::MD5 qw(md5_hex);
34- use FindBin;
35 use File::Basename;
36 use File::Spec::Functions;
37 use File::Temp qw(tempdir);
38--- 49,54 ----
39***************
40*** 65,74 ****
41 #use Time::HiRes qw(gettimeofday tv_interval);
42 #use List::Util qw( max min );
43
44- use lib "$FindBin::RealBin";
45- use lib "$FindBin::RealBin/../lib";
46- use lib "$FindBin::RealBin/lib";
47-
48 use POSIX qw(pow);
49
50 use Circos::Configuration;
51--- 64,69 ----
52diff -crB circos-0.69-6/lib/Circos/Configuration.pm circos-0.69-6-new/lib/Circos/Configuration.pm
53*** circos-0.69-6/lib/Circos/Configuration.pm 2015-03-17 22:11:01.000000000 +0100
54--- circos-0.69-6-new/lib/Circos/Configuration.pm 2018-01-12 10:11:41.064008273 +0100
55***************
56*** 59,68 ****
57 use Params::Validate qw(:all);
58 use List::MoreUtils qw(uniq);
59
60- use lib "$FindBin::RealBin";
61- use lib "$FindBin::RealBin/../lib";
62- use lib "$FindBin::RealBin/lib";
63-
64 use Circos::Constants;
65 use Circos::Debug;
66 use Circos::Utils;
67--- 59,64 ----
68diff -crB circos-0.69-6/lib/Circos/DataPoint.pm circos-0.69-6-new/lib/Circos/DataPoint.pm
69*** circos-0.69-6/lib/Circos/DataPoint.pm 2014-05-12 18:20:19.000000000 +0200
70--- circos-0.69-6-new/lib/Circos/DataPoint.pm 2018-01-12 10:11:54.888270731 +0100
71***************
72*** 38,51 ****
73
74 use Carp qw( carp confess croak );
75 use Data::Dumper;
76- use FindBin;
77 use GD::Image;
78 use Params::Validate qw(:all);
79
80- use lib "$FindBin::RealBin";
81- use lib "$FindBin::RealBin/../lib";
82- use lib "$FindBin::RealBin/lib";
83-
84 use Circos::Configuration; # qw(%CONF $DIMS);
85 use Circos::Constants;
86 use Circos::Debug;
87--- 38,46 ----
88diff -crB circos-0.69-6/lib/Circos/Debug.pm circos-0.69-6-new/lib/Circos/Debug.pm
89*** circos-0.69-6/lib/Circos/Debug.pm 2015-03-24 01:26:13.000000000 +0100
90--- circos-0.69-6-new/lib/Circos/Debug.pm 2018-01-12 10:12:07.192502006 +0100
91***************
92*** 63,75 ****
93
94 use Carp qw( carp confess croak );
95 use Data::Dumper;
96- use FindBin;
97 use Memoize;
98 use List::MoreUtils qw(uniq);
99 use Time::HiRes qw(gettimeofday tv_interval);
100- use lib "$FindBin::RealBin";
101- use lib "$FindBin::RealBin/../lib";
102- use lib "$FindBin::RealBin/lib";
103
104 use Circos::Constants;
105
106--- 63,71 ----
107diff -crB circos-0.69-6/lib/Circos/Division.pm circos-0.69-6-new/lib/Circos/Division.pm
108*** circos-0.69-6/lib/Circos/Division.pm 2015-11-17 00:55:58.000000000 +0100
109--- circos-0.69-6-new/lib/Circos/Division.pm 2018-01-12 10:12:21.544769084 +0100
110***************
111*** 37,52 ****
112 our @EXPORT = qw();
113
114 use Carp qw( carp confess croak );
115- use FindBin;
116 use GD;
117 use Math::Round;
118 use List::MoreUtils qw(uniq);
119 use Params::Validate qw(:all);
120
121- use lib "$FindBin::RealBin";
122- use lib "$FindBin::RealBin/../lib";
123- use lib "$FindBin::RealBin/lib";
124-
125 use Circos::Configuration;
126 use Circos::Constants;
127 use Circos::Debug;
128--- 37,47 ----
129diff -crB circos-0.69-6/lib/Circos/Error.pm circos-0.69-6-new/lib/Circos/Error.pm
130*** circos-0.69-6/lib/Circos/Error.pm 2015-03-17 22:46:36.000000000 +0100
131--- circos-0.69-6-new/lib/Circos/Error.pm 2018-01-12 10:12:32.472970548 +0100
132***************
133*** 44,53 ****
134 use Params::Validate;
135 use Text::Format;
136
137- use lib "$FindBin::RealBin";
138- use lib "$FindBin::RealBin/../lib";
139- use lib "$FindBin::RealBin/lib";
140-
141 use Circos::Constants;
142 use Circos::Debug;
143 use Circos::Utils;
144--- 44,49 ----
145diff -crB circos-0.69-6/lib/Circos/Expression.pm circos-0.69-6-new/lib/Circos/Expression.pm
146*** circos-0.69-6/lib/Circos/Expression.pm 2015-11-30 23:49:36.000000000 +0100
147--- circos-0.69-6-new/lib/Circos/Expression.pm 2018-01-12 10:12:41.953144015 +0100
148***************
149*** 39,55 ****
150
151 use Carp qw( carp confess croak );
152 use Data::Dumper;
153- use FindBin;
154 use Params::Validate qw(:all);
155 use Math::Round;
156 use Math::VecStat qw(average);
157 use List::Util qw(min max);
158 use Text::Balanced qw(extract_bracketed);
159
160- use lib "$FindBin::RealBin";
161- use lib "$FindBin::RealBin/../lib";
162- use lib "$FindBin::RealBin/lib";
163-
164 use Circos::Configuration;
165 use Circos::Constants;
166 use Circos::Debug;
167--- 39,50 ----
168diff -crB circos-0.69-6/lib/Circos/Font.pm circos-0.69-6-new/lib/Circos/Font.pm
169*** circos-0.69-6/lib/Circos/Font.pm 2014-05-12 18:20:19.000000000 +0200
170--- circos-0.69-6-new/lib/Circos/Font.pm 2018-01-12 10:12:51.657320357 +0100
171***************
172*** 45,59 ****
173 );
174
175 use Carp qw( carp confess croak );
176- use FindBin;
177 use GD::Image;
178 use Font::TTF::Font;
179 use Params::Validate qw(:all);
180
181- use lib "$FindBin::RealBin";
182- use lib "$FindBin::RealBin/../lib";
183- use lib "$FindBin::RealBin/lib";
184-
185 use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
186 use Circos::Constants;
187 use Circos::Colors;
188--- 45,54 ----
189diff -crB circos-0.69-6/lib/Circos/Geometry.pm circos-0.69-6-new/lib/Circos/Geometry.pm
190*** circos-0.69-6/lib/Circos/Geometry.pm 2014-05-12 18:20:19.000000000 +0200
191--- circos-0.69-6-new/lib/Circos/Geometry.pm 2018-01-12 10:12:58.961452282 +0100
192***************
193*** 41,54 ****
194 );
195
196 use Carp qw( carp confess croak );
197- use FindBin;
198 use GD::Image;
199 use Params::Validate qw(:all);
200
201- use lib "$FindBin::RealBin";
202- use lib "$FindBin::RealBin/../lib";
203- use lib "$FindBin::RealBin/lib";
204-
205 use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
206 use Circos::Constants;
207 use Circos::Debug;
208--- 41,49 ----
209diff -crB circos-0.69-6/lib/Circos/Heatmap.pm circos-0.69-6-new/lib/Circos/Heatmap.pm
210*** circos-0.69-6/lib/Circos/Heatmap.pm 2016-03-30 22:08:12.000000000 +0200
211--- circos-0.69-6-new/lib/Circos/Heatmap.pm 2018-01-12 10:13:09.953649538 +0100
212***************
213*** 24,40 ****
214 use Carp qw( carp confess croak );
215 use Clone;
216 use Data::Dumper;
217- use FindBin;
218 use GD::Image;
219 use Math::VecStat qw(min max);
220 use Params::Validate qw(:all);
221 use List::MoreUtils qw(uniq);
222 use Regexp::Common qw(number);
223
224- use lib "$FindBin::RealBin";
225- use lib "$FindBin::RealBin/../lib";
226- use lib "$FindBin::RealBin/lib";
227-
228 use Circos::Configuration;
229 use Circos::Constants;
230 use Circos::Colors;
231--- 24,35 ----
232diff -crB circos-0.69-6/lib/Circos/Ideogram.pm circos-0.69-6-new/lib/Circos/Ideogram.pm
233*** circos-0.69-6/lib/Circos/Ideogram.pm 2015-11-17 01:18:53.000000000 +0100
234--- circos-0.69-6-new/lib/Circos/Ideogram.pm 2018-01-12 10:13:22.045864798 +0100
235***************
236*** 40,46 ****
237
238 use Carp qw( carp confess croak );
239 use Cwd;
240- use FindBin;
241 use File::Spec::Functions;
242 use Math::Round;
243 use Math::VecStat qw(max);
244--- 40,45 ----
245***************
246*** 50,59 ****
247
248 use POSIX qw(floor ceil);
249
250- use lib "$FindBin::RealBin";
251- use lib "$FindBin::RealBin/../lib";
252- use lib "$FindBin::RealBin/lib";
253-
254 use Circos::Configuration;
255 use Circos::Constants;
256 use Circos::Debug;
257--- 49,54 ----
258diff -crB circos-0.69-6/lib/Circos/Image.pm circos-0.69-6-new/lib/Circos/Image.pm
259*** circos-0.69-6/lib/Circos/Image.pm 2014-05-12 18:20:19.000000000 +0200
260--- circos-0.69-6-new/lib/Circos/Image.pm 2018-01-12 10:13:31.094024696 +0100
261***************
262*** 45,58 ****
263 );
264
265 use Carp qw( carp confess croak );
266- use FindBin;
267 use GD::Image;
268 use Params::Validate qw(:all);
269
270- use lib "$FindBin::RealBin";
271- use lib "$FindBin::RealBin/../lib";
272- use lib "$FindBin::RealBin/lib";
273-
274 use Circos::Configuration;
275 use Circos::Colors;
276 use Circos::Constants;
277--- 45,53 ----
278diff -crB circos-0.69-6/lib/Circos/IO.pm circos-0.69-6-new/lib/Circos/IO.pm
279*** circos-0.69-6/lib/Circos/IO.pm 2015-12-03 05:51:11.000000000 +0100
280--- circos-0.69-6-new/lib/Circos/IO.pm 2018-01-12 10:13:41.686210640 +0100
281***************
282*** 39,45 ****
283 use Carp qw( carp confess croak );
284 use Storable qw(dclone);
285 use Cwd;
286- use FindBin;
287 use Data::Dumper;
288 use File::Spec::Functions;
289 use Math::Round;
290--- 39,44 ----
291***************
292*** 49,58 ****
293
294 use POSIX qw(floor ceil);
295
296- use lib "$FindBin::RealBin";
297- use lib "$FindBin::RealBin/../lib";
298- use lib "$FindBin::RealBin/lib";
299-
300 use Circos::Constants;
301 use Circos::Colors;
302 use Circos::Configuration;
303--- 48,53 ----
304diff -crB circos-0.69-6/lib/Circos/Karyotype.pm circos-0.69-6-new/lib/Circos/Karyotype.pm
305*** circos-0.69-6/lib/Circos/Karyotype.pm 2014-09-09 00:15:58.000000000 +0200
306--- circos-0.69-6-new/lib/Circos/Karyotype.pm 2018-01-12 10:13:53.318413330 +0100
307***************
308*** 38,44 ****
309
310 use Carp qw( carp confess croak );
311 use Cwd;
312- use FindBin;
313 use Math::Round;
314 use Math::VecStat qw(max);
315 use Params::Validate qw(:all);
316--- 38,43 ----
317***************
318*** 48,57 ****
319 #use Regexp::Common qw(number);
320 #use POSIX qw(floor ceil);
321
322- use lib "$FindBin::RealBin";
323- use lib "$FindBin::RealBin/../lib";
324- use lib "$FindBin::RealBin/lib";
325-
326 use Circos::Configuration;
327 use Circos::Constants;
328 use Circos::Debug;
329--- 47,52 ----
330diff -crB circos-0.69-6/lib/Circos/PNG.pm circos-0.69-6-new/lib/Circos/PNG.pm
331*** circos-0.69-6/lib/Circos/PNG.pm 2014-09-17 05:33:06.000000000 +0200
332--- circos-0.69-6-new/lib/Circos/PNG.pm 2018-01-12 10:14:31.011059637 +0100
333***************
334*** 37,51 ****
335 our @EXPORT = qw();
336
337 use Carp qw( carp confess croak );
338- use FindBin;
339 use GD;
340 use Math::VecStat qw(min max);
341 use Params::Validate qw(:all);
342
343- use lib "$FindBin::RealBin";
344- use lib "$FindBin::RealBin/../lib";
345- use lib "$FindBin::RealBin/lib";
346-
347 use Circos::Configuration;
348 use Circos::Colors;
349 use Circos::Constants;
350--- 37,46 ----
351diff -crB circos-0.69-6/lib/Circos/Rule.pm circos-0.69-6-new/lib/Circos/Rule.pm
352*** circos-0.69-6/lib/Circos/Rule.pm 2014-10-02 01:14:25.000000000 +0200
353--- circos-0.69-6-new/lib/Circos/Rule.pm 2018-01-12 10:14:38.195181067 +0100
354***************
355*** 38,51 ****
356
357 use Carp qw( carp confess croak );
358 use Data::Dumper;
359- use FindBin;
360 use GD::Image;
361 use Params::Validate qw(:all);
362
363- use lib "$FindBin::RealBin";
364- use lib "$FindBin::RealBin/../lib";
365- use lib "$FindBin::RealBin/lib";
366-
367 use Circos::Configuration; # qw(%CONF $DIMS);
368 use Circos::Constants;
369 use Circos::DataPoint;
370--- 38,46 ----
371diff -crB circos-0.69-6/lib/Circos/SVG.pm circos-0.69-6-new/lib/Circos/SVG.pm
372*** circos-0.69-6/lib/Circos/SVG.pm 2015-11-30 23:23:52.000000000 +0100
373--- circos-0.69-6-new/lib/Circos/SVG.pm 2018-01-12 10:14:47.803342631 +0100
374***************
375*** 26,39 ****
376 );
377
378 use Carp qw( carp confess croak );
379- use FindBin;
380 use GD::Image;
381 use Params::Validate qw(:all);
382
383- use lib "$FindBin::RealBin";
384- use lib "$FindBin::RealBin/../lib";
385- use lib "$FindBin::RealBin/lib";
386-
387 use Circos::Configuration;
388 use Circos::Colors;
389 use Circos::Constants;
390--- 26,34 ----
391diff -crB circos-0.69-6/lib/Circos/Text.pm circos-0.69-6-new/lib/Circos/Text.pm
392*** circos-0.69-6/lib/Circos/Text.pm 2014-05-12 18:20:19.000000000 +0200
393--- circos-0.69-6-new/lib/Circos/Text.pm 2018-01-12 10:14:57.083497772 +0100
394***************
395*** 42,55 ****
396 );
397
398 use Carp qw( carp confess croak );
399- use FindBin;
400 use GD::Image;
401 use Params::Validate qw(:all);
402
403- use lib "$FindBin::RealBin";
404- use lib "$FindBin::RealBin/../lib";
405- use lib "$FindBin::RealBin/lib";
406-
407 use Circos::Configuration; # qw(%CONF $DIMS);
408 use Circos::Constants;
409 use Circos::Colors;
410--- 42,50 ----
411diff -crB circos-0.69-6/lib/Circos/Track/Highlight.pm circos-0.69-6-new/lib/Circos/Track/Highlight.pm
412*** circos-0.69-6/lib/Circos/Track/Highlight.pm 2014-10-01 00:43:27.000000000 +0200
413--- circos-0.69-6-new/lib/Circos/Track/Highlight.pm 2018-01-12 10:15:06.795659206 +0100
414***************
415*** 37,50 ****
416 our @EXPORT = qw();
417
418 use Carp qw( carp confess croak );
419- use FindBin;
420 use GD::Image;
421 use Params::Validate qw(:all);
422
423- use lib "$FindBin::RealBin";
424- use lib "$FindBin::RealBin/../lib";
425- use lib "$FindBin::RealBin/lib";
426-
427 use Circos::Configuration; # qw(%CONF $DIMS);
428 use Circos::Constants;
429 #use Circos::Colors;
430--- 37,45 ----
431diff -crB circos-0.69-6/lib/Circos/Track/Link.pm circos-0.69-6-new/lib/Circos/Track/Link.pm
432*** circos-0.69-6/lib/Circos/Track/Link.pm 2014-05-12 18:20:19.000000000 +0200
433--- circos-0.69-6-new/lib/Circos/Track/Link.pm 2018-01-12 10:15:17.387834198 +0100
434***************
435*** 37,50 ****
436 our @EXPORT = qw();
437
438 use Carp qw( carp confess croak );
439- use FindBin;
440 use GD::Image;
441 use Params::Validate qw(:all);
442
443- use lib "$FindBin::RealBin";
444- use lib "$FindBin::RealBin/../lib";
445- use lib "$FindBin::RealBin/lib";
446-
447 use Circos::Configuration; # qw(%CONF $DIMS);
448 use Circos::Constants;
449 #use Circos::Colors;
450--- 37,45 ----
451diff -crB circos-0.69-6/lib/Circos/Track.pm circos-0.69-6-new/lib/Circos/Track.pm
452*** circos-0.69-6/lib/Circos/Track.pm 2014-09-16 05:31:46.000000000 +0200
453--- circos-0.69-6-new/lib/Circos/Track.pm 2018-01-12 10:15:29.628035063 +0100
454***************
455*** 41,56 ****
456
457 use Carp qw( carp confess croak );
458 use Data::Dumper;
459- use FindBin;
460 use GD::Image;
461 use List::MoreUtils qw(uniq);
462 use Math::VecStat qw(min max);
463 use Params::Validate qw(:all);
464 use Regexp::Common;
465 use Statistics::Basic qw(average stddev);
466- use lib "$FindBin::RealBin";
467- use lib "$FindBin::RealBin/../lib";
468- use lib "$FindBin::RealBin/lib";
469
470 use Circos::Configuration; # qw(%CONF $DIMS);
471 use Circos::Constants;
472--- 41,52 ----
473diff -crB circos-0.69-6/lib/Circos/Unit.pm circos-0.69-6-new/lib/Circos/Unit.pm
474*** circos-0.69-6/lib/Circos/Unit.pm 2014-05-12 18:20:19.000000000 +0200
475--- circos-0.69-6-new/lib/Circos/Unit.pm 2018-01-12 10:15:37.892169871 +0100
476***************
477*** 46,60 ****
478 );
479
480 use Carp qw( carp confess croak );
481- use FindBin;
482 use Data::Dumper;
483 use Params::Validate qw(:all);
484 use Regexp::Common qw(number);
485
486- use lib "$FindBin::RealBin";
487- use lib "$FindBin::RealBin/../lib";
488- use lib "$FindBin::RealBin/lib";
489-
490 use Circos::Configuration qw(%CONF $DIMS);
491 use Circos::Constants;
492 use Circos::Debug;
493--- 46,55 ----
494diff -crB circos-0.69-6/lib/Circos/URL.pm circos-0.69-6-new/lib/Circos/URL.pm
495*** circos-0.69-6/lib/Circos/URL.pm 2014-05-12 18:20:19.000000000 +0200
496--- circos-0.69-6-new/lib/Circos/URL.pm 2018-01-12 10:15:46.092303006 +0100
497***************
498*** 39,52 ****
499 );
500
501 use Carp qw( carp confess croak );
502- use FindBin;
503 use GD;
504 use Params::Validate qw(:all);
505
506- use lib "$FindBin::RealBin";
507- use lib "$FindBin::RealBin/../lib";
508- use lib "$FindBin::RealBin/lib";
509-
510 use Circos::Configuration;
511 #use Circos::Colors;
512 use Circos::Constants;
513--- 39,47 ----
514diff -crB circos-0.69-6/lib/Circos/Utils.pm circos-0.69-6-new/lib/Circos/Utils.pm
515*** circos-0.69-6/lib/Circos/Utils.pm 2014-10-01 21:36:19.000000000 +0200
516--- circos-0.69-6-new/lib/Circos/Utils.pm 2018-01-12 10:16:11.576712858 +0100
517***************
518*** 105,114 ****
519
520 use POSIX qw(floor ceil);
521
522- use lib "$FindBin::RealBin";
523- use lib "$FindBin::RealBin/../lib";
524- use lib "$FindBin::RealBin/lib";
525-
526 use Circos::Constants;
527 use Circos::Debug;
528 use Circos::Error;
529--- 105,110 ----
530diff -crB circos-0.69-6/lib/Circos.pm circos-0.69-6-new/lib/Circos.pm
531*** circos-0.69-6/lib/Circos.pm 2016-06-25 00:19:27.000000000 +0200
532--- circos-0.69-6-new/lib/Circos.pm 2018-01-12 10:16:35.801097176 +0100
533***************
534*** 49,57 ****
535
536 use strict;
537 use warnings;
538- use lib "$FindBin::RealBin";
539- use lib "$FindBin::RealBin/../lib";
540- use lib "$FindBin::RealBin/lib";
541
542 BEGIN {
543 require Circos::Modules;
544--- 49,54 ----