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 <[email protected]> Sun, 01 Apr 2012 08:08:55 +0200 + -- Olivier Sallou <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
