[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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