[med-svn] r11328 - in trunk/packages/circos/trunk/debian: . patches

Olivier Sallou osallou at alioth.debian.org
Thu Jun 14 11:36:17 UTC 2012


Author: osallou
Date: 2012-06-14 11:36:16 +0000 (Thu, 14 Jun 2012)
New Revision: 11328

Added:
   trunk/packages/circos/trunk/debian/patches/fix_examples
Modified:
   trunk/packages/circos/trunk/debian/README.Debian
   trunk/packages/circos/trunk/debian/changelog
   trunk/packages/circos/trunk/debian/control
   trunk/packages/circos/trunk/debian/patches/configpath_add_etc
   trunk/packages/circos/trunk/debian/patches/series
   trunk/packages/circos/trunk/debian/patches/use_ttf_fonts
Log:
new upstream release

Modified: trunk/packages/circos/trunk/debian/README.Debian
===================================================================
--- trunk/packages/circos/trunk/debian/README.Debian	2012-06-13 18:16:09 UTC (rev 11327)
+++ trunk/packages/circos/trunk/debian/README.Debian	2012-06-14 11:36:16 UTC (rev 11328)
@@ -8,3 +8,8 @@
 
 The files ‘circos.svg’ and ‘circos.png’ will be regenerated, and can be
 compared to the originals.
+
+Warning: Many example files are compressed in /usr/share/doc/circos/examples/*.
+Running the example program will failed due to the compressed files. To execute
+ the sample program, you should first uncompress those files.
+

Modified: trunk/packages/circos/trunk/debian/changelog
===================================================================
--- trunk/packages/circos/trunk/debian/changelog	2012-06-13 18:16:09 UTC (rev 11327)
+++ trunk/packages/circos/trunk/debian/changelog	2012-06-14 11:36:16 UTC (rev 11328)
@@ -1,12 +1,15 @@
-circos (0.55-3) UNRELEASED; urgency=low
+circos (0.61-1) unstable; urgency=low
 
+  [ Olivier Sallou ]
+  * New upstream release
+
   [ Charles Plessy ]
   * renamed debian/upstream-metadata.yaml to debian/upstream
 
   [ Andreas Tille ]
-  * debian/upstream: enhanced citation information
+  * debian/upstream: enhanced citation information 
 
- -- Andreas Tille <tille at debian.org>  Sun, 01 Apr 2012 08:08:55 +0200
+ -- Olivier Sallou <osallou at debian.org>  Thu, 14 Jun 2012 12:56:33 +0200
 
 circos (0.55-2) unstable; urgency=low
 

Modified: trunk/packages/circos/trunk/debian/control
===================================================================
--- trunk/packages/circos/trunk/debian/control	2012-06-13 18:16:09 UTC (rev 11327)
+++ trunk/packages/circos/trunk/debian/control	2012-06-14 11:36:16 UTC (rev 11328)
@@ -18,7 +18,8 @@
  libdata-dumper-simple-perl, libgd-gd2-perl, libgetopt-simple-perl,
  libmath-bezier-perl, libmath-round-perl, libparams-validate-perl, libreadonly-perl,
  libset-intspan-perl (>= 1.16), liblist-allutils-perl, libfile-basedir-perl,libfile-spec-perl,
- libmath-bigint-perl,libmath-vec-perl, libio-all-perl, libmath-vecstat-perl, libgraphics-colorobject-perl
+ libmath-bigint-perl,libmath-vec-perl, libio-all-perl, libmath-vecstat-perl, libgraphics-colorobject-perl,
+ libtext-format-perl, libfont-ttf-perl
 Recommends: circos-tools
 Description: Package for visualizing data and information
  Circos visualizes data in a circular layout — this makes Circos 

Modified: trunk/packages/circos/trunk/debian/patches/configpath_add_etc
===================================================================
--- trunk/packages/circos/trunk/debian/patches/configpath_add_etc	2012-06-13 18:16:09 UTC (rev 11327)
+++ trunk/packages/circos/trunk/debian/patches/configpath_add_etc	2012-06-14 11:36:16 UTC (rev 11328)
@@ -3,26 +3,27 @@
 Last-Update: 2011-08-01
 --- a/lib/Circos/Configuration.pm
 +++ b/lib/Circos/Configuration.pm
-@@ -370,6 +370,7 @@
-   #$OPT{configfile} = $file;
-     
+@@ -569,6 +569,7 @@
+   }
+   
    my @configpath = (
-+                    "/etc/circos",
- 		    dirname($file),
- 		    dirname($file)."/etc",
- 		    "$FindBin::RealBin/etc", 
++                "/etc/circos",
+ 		dirname($file),
+ 		dirname($file)."/etc",
+ 		"$FindBin::RealBin/etc", 
 --- a/lib/Circos/Utils.pm
 +++ b/lib/Circos/Utils.pm
-@@ -310,6 +310,7 @@
-     } else {
- 	# look for the file elsewhere
- 	@dirs = (
-+            "/usr/share/circos",
- 	    "$FindBin::RealBin/../",
- 	    "$FindBin::RealBin/",       
- 	    "$FindBin::RealBin/etc",
---- a/etc/makehusteps
-+++ b/etc/makehusteps
+@@ -429,7 +429,7 @@
+ 	%params = @_;
+     }
+     # look for the file in various directories
+-    my @dir_1 = (getcwd,$FindBin::RealBin);
++    my @dir_1 = (getcwd,$FindBin::RealBin,"/usr/share/circos");
+     my @dir_2 = qw(. .. ../..);
+     my @dir_3 = qw(. etc data);
+ 
+--- a/etc/makehuesteps
++++ b/etc/makehuesteps
 @@ -1,4 +1,4 @@
 -#!/bin/env perl 
 +#!/usr/bin/env perl 

Added: trunk/packages/circos/trunk/debian/patches/fix_examples
===================================================================
--- trunk/packages/circos/trunk/debian/patches/fix_examples	                        (rev 0)
+++ trunk/packages/circos/trunk/debian/patches/fix_examples	2012-06-14 11:36:16 UTC (rev 11328)
@@ -0,0 +1,40 @@
+Subject: change path to conf file for examples
+Description: etc sub directory is hard coded 
+ in example conf files. In Debian conf files are
+ in /etc/circos. This path is already added to search
+ path.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 14/06/12
+--- a/example/etc/circos.conf
++++ b/example/etc/circos.conf
+@@ -246,16 +246,16 @@
+ <<include ticks.conf>>
+ 
+ <image>
+-<<include etc/image.conf>>
++<<include image.conf>>
+ </image>
+ 
+-# includes etc/colors.conf
+-#          etc/fonts.conf
+-#          etc/patterns.conf
+-<<include etc/colors_fonts_patterns.conf>>
++# includes colors.conf
++#          fonts.conf
++#          patterns.conf
++<<include colors_fonts_patterns.conf>>
+ 
+ # system and debug settings
+-<<include etc/housekeeping.conf>>
++<<include housekeeping.conf>>
+ 
+ anti_aliasing* = no
+ 
+--- a/example/run
++++ b/example/run
+@@ -1,4 +1,4 @@
+ #!/bin/bash
+ 
+-../bin/circos -conf etc/circos.conf -debug_group summary,timer,textplace > run.out
++circos -conf etc/circos.conf -debug_group summary,timer,textplace > run.out
+ 

Modified: trunk/packages/circos/trunk/debian/patches/series
===================================================================
--- trunk/packages/circos/trunk/debian/patches/series	2012-06-13 18:16:09 UTC (rev 11327)
+++ trunk/packages/circos/trunk/debian/patches/series	2012-06-14 11:36:16 UTC (rev 11328)
@@ -1,3 +1,4 @@
 use_ttf_fonts
 debianpackaging
 configpath_add_etc
+fix_examples

Modified: trunk/packages/circos/trunk/debian/patches/use_ttf_fonts
===================================================================
--- trunk/packages/circos/trunk/debian/patches/use_ttf_fonts	2012-06-13 18:16:09 UTC (rev 11327)
+++ trunk/packages/circos/trunk/debian/patches/use_ttf_fonts	2012-06-14 11:36:16 UTC (rev 11328)
@@ -3,44 +3,65 @@
 Last-Update: 2011-09-08
 --- a/etc/fonts.conf
 +++ b/etc/fonts.conf
-@@ -2,24 +2,24 @@
- # Helvetica has been replaced by Computer Modern
- # http://cm-unicode.sourceforge.net/
+@@ -27,18 +27,18 @@
+ # CMU Typewriter Regular, when rotated. For this reason, TTF versions
+ # of these fonts are used.
  
--serif_roman    = fonts/modern/cmunrm.otf
--serif_default  = fonts/modern/cmunrm.otf
--serif_normal   = fonts/modern/cmunrm.otf
--serif_bold     = fonts/modern/cmunbx.otf
--serif_italic   = fonts/modern/cmunui.otf
-+serif_roman    = fonts/modern/cmunrm.ttf
-+serif_default  = fonts/modern/cmunrm.ttf
-+serif_normal   = fonts/modern/cmunrm.ttf
-+serif_bold     = fonts/modern/cmunbx.ttf
-+serif_italic   = fonts/modern/cmunui.ttf
+-serif               = fonts/modern/cmunrm.otf # CMUSerif-Roman
+-serif_roman         = fonts/modern/cmunrm.otf # CMUSerif-Roman
+-serif_default       = fonts/modern/cmunrm.otf # CMUSerif-Roman
+-serif_normal        = fonts/modern/cmunrm.otf # CMUSerif-Roman
+-serif_light         = fonts/modern/cmunrm.otf # CMUSerif-Roman
+-serif_bold          = fonts/modern/cmunbx.otf # CMUSerif-Bold
+-serif_italic        = fonts/modern/cmunui.otf # CMUSerif-Italic
+-serif_bolditalic    = fonts/modern/cmunbi.otf # CMUSerif-BoldItalic
+-serif_italicbold    = fonts/modern/cmunbi.otf # CMUSerif-BoldItalic
+-serif_condensed     = fonts/modern/cmunssdc.otf # CMUSerif-DemiCondensed
+-serif_condensedbold = fonts/modern/cmunssdc.otf # CMUSerif-DemiCondensed
+-serif_boldcondensed = fonts/modern/cmunssdc.otf # CMUSerif-DemiCondensed
++serif               = fonts/modern/cmunrm.ttf # CMUSerif-Roman
++serif_roman         = fonts/modern/cmunrm.ttf # CMUSerif-Roman
++serif_default       = fonts/modern/cmunrm.ttf # CMUSerif-Roman
++serif_normal        = fonts/modern/cmunrm.ttf # CMUSerif-Roman
++serif_light         = fonts/modern/cmunrm.ttf # CMUSerif-Roman
++serif_bold          = fonts/modern/cmunbx.ttf # CMUSerif-Bold
++serif_italic        = fonts/modern/cmunui.ttf # CMUSerif-Italic
++serif_bolditalic    = fonts/modern/cmunbi.ttf # CMUSerif-BoldItalic
++serif_italicbold    = fonts/modern/cmunbi.ttf # CMUSerif-BoldItalic
++serif_condensed     = fonts/modern/cmunssdc.ttf # CMUSerif-DemiCondensed
++serif_condensedbold = fonts/modern/cmunssdc.ttf # CMUSerif-DemiCondensed
++serif_boldcondensed = fonts/modern/cmunssdc.ttf # CMUSerif-DemiCondensed
  
--light          = fonts/modern/cmunss.otf
--normal         = fonts/modern/cmunss.otf
--default        = fonts/modern/cmunss.otf
--condensed      = fonts/modern/cmunss.otf
--semibold       = fonts/modern/cmunbsr.otf
--condensedbold  = fonts/modern/cmunbsr.otf
--bold           = fonts/modern/cmunsx.otf
-+light          = fonts/modern/cmunss.ttf
-+normal         = fonts/modern/cmunss.ttf
-+default        = fonts/modern/cmunss.ttf
-+condensed      = fonts/modern/cmunss.ttf
-+semibold       = fonts/modern/cmunbsr.ttf
-+condensedbold  = fonts/modern/cmunbsr.ttf
-+bold           = fonts/modern/cmunsx.ttf
+ sans_serif     = fonts/modern/cmunbmr.ttf # CMUBright-Roman
+ sans           = fonts/modern/cmunbmr.ttf # CMUBright-Roman
+@@ -46,20 +46,20 @@
+ light          = fonts/modern/cmunbmr.ttf # CMUBright-Roman
+ normal         = fonts/modern/cmunbmr.ttf # CMUBright-Roman
+ default        = fonts/modern/cmunbmr.ttf # CMUBright-Roman
+-semibold       = fonts/modern/cmunbsr.otf # CMUBright-Semibold
+-bold           = fonts/modern/cmunbbx.otf # CMUBright-Bold
+-italic         = fonts/modern/cmunbmo.otf # CMUBright-Oblique
+-bolditalic     = fonts/modern/cmunbxo.otf # CMUBright-BoldOblique
+-italicbold     = fonts/modern/cmunbxo.otf # CMUBright-BoldOblique
++semibold       = fonts/modern/cmunbsr.ttf # CMUBright-Semibold
++bold           = fonts/modern/cmunbbx.ttf # CMUBright-Bold
++italic         = fonts/modern/cmunbmo.ttf # CMUBright-Oblique
++bolditalic     = fonts/modern/cmunbxo.ttf # CMUBright-BoldOblique
++italicbold     = fonts/modern/cmunbxo.ttf # CMUBright-BoldOblique
  
--mono           = fonts/modern/cmuntt.otf
--fixed          = fonts/modern/cmuntt.otf
--mono_light     = fonts/modern/cmunbtl.otf
--fixed_light    = fonts/modern/cmunbtl.otf
-+mono           = fonts/modern/cmuntt.ttf
-+fixed          = fonts/modern/cmuntt.ttf
-+mono_light     = fonts/modern/cmunbtl.ttf
-+fixed_light    = fonts/modern/cmunbtl.ttf
+-condensed      = fonts/modern/cmunssdc.otf # CMUSansSerif-DemiCondensed
+-condensedbold  = fonts/modern/cmunssdc.otf # CMUSansSerif-DemiCondensed
+-boldcondensed  = fonts/modern/cmunssdc.otf # CMUSansSerif-DemiCondensed
++condensed      = fonts/modern/cmunssdc.ttf # CMUSansSerif-DemiCondensed
++condensedbold  = fonts/modern/cmunssdc.ttf # CMUSansSerif-DemiCondensed
++boldcondensed  = fonts/modern/cmunssdc.ttf # CMUSansSerif-DemiCondensed
  
+ mono           = fonts/modern/cmuntt.ttf # CMUTypewriter-Regular
+ fixed          = fonts/modern/cmuntt.ttf # CMUTypewriter-Regular
+-mono_light     = fonts/modern/cmunbtl.otf # CMUTypewriter-Light
+-fixed_light    = fonts/modern/cmunbtl.otf # CMUTypewriter-Light
++mono_light     = fonts/modern/cmunbtl.ttf # CMUTypewriter-Light
++fixed_light    = fonts/modern/cmunbtl.ttf # CMUTypewriter-Light
+ 
  # All wingding and webding fonts have been replaced
  # by a GPL glyph font designed by Martin Krzywinski




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