[med-svn] r7336 - in trunk/packages/circos/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Tue Jul 26 11:04:24 UTC 2011
Author: osallou-guest
Date: 2011-07-26 11:04:24 +0000 (Tue, 26 Jul 2011)
New Revision: 7336
Removed:
trunk/packages/circos/trunk/debian/README.source
trunk/packages/circos/trunk/debian/circos-tutorials.install
trunk/packages/circos/trunk/debian/watch-tools
Modified:
trunk/packages/circos/trunk/debian/README.Debian
trunk/packages/circos/trunk/debian/changelog
trunk/packages/circos/trunk/debian/circos.1
trunk/packages/circos/trunk/debian/circos.install
trunk/packages/circos/trunk/debian/control
trunk/packages/circos/trunk/debian/copyright
trunk/packages/circos/trunk/debian/get-orig-source
trunk/packages/circos/trunk/debian/patches/configpath_add_etc
trunk/packages/circos/trunk/debian/patches/debianpackaging
trunk/packages/circos/trunk/debian/rules
trunk/packages/circos/trunk/debian/watch
Log:
add TODO to fix licensing issues
Modified: trunk/packages/circos/trunk/debian/README.Debian
===================================================================
--- trunk/packages/circos/trunk/debian/README.Debian 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/README.Debian 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,8 +1,8 @@
Circos for Debian
-----------------
- To test the installation of the package, install both circos and circos-tutorials. then go to the directory:
- cd /usr/share/circos/tutorials/2/10
+ To test the installation of the package, go to the directory:
+ cd /usr/share/circos/example
and execute:
circos -conf circos.conf
- An image will be generared in /tmp
+ An image will be generared
Deleted: trunk/packages/circos/trunk/debian/README.source
===================================================================
--- trunk/packages/circos/trunk/debian/README.source 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/README.source 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,15 +0,0 @@
-circos for Debian
------------------
-
-Remote upstream files (tar.gz) are delivered as full package when named
-xxx-dd.tar.gz, but patches named xxx-dd-pp.tar.gz contains only modified
-files.
-Major delivery should be downloaded, then latest patch should overwrite files.
-get-orig-source target takes this stuff in charge
-
-Example: Go to
- http://circos.ca/software/download/
-download and extract circos-0.54.tar.gz, then circos-0.54-1.tar.gz and
-move content to circos-0.54. Then download and extract
-circos-tools-0.15.tar.gz into circos-0.54 (to replace tools), then again
-with circos-tools-0.15-1.tar.gz
Modified: trunk/packages/circos/trunk/debian/changelog
===================================================================
--- trunk/packages/circos/trunk/debian/changelog 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/changelog 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,5 +1,6 @@
-circos (0.54-1-1) unstable; urgency=low
+circos (0.55-1) unstable; urgency=low
* First debian import (Closes: #632174)
+ - TODO fix licensing issues (missing files)
-- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 29 Jun 2011 12:04:57 +0200
Deleted: trunk/packages/circos/trunk/debian/circos-tutorials.install
===================================================================
--- trunk/packages/circos/trunk/debian/circos-tutorials.install 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/circos-tutorials.install 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1 +0,0 @@
-tutorials/* usr/share/circos/tutorials/
Modified: trunk/packages/circos/trunk/debian/circos.1
===================================================================
--- trunk/packages/circos/trunk/debian/circos.1 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/circos.1 2011-07-26 11:04:24 UTC (rev 7336)
@@ -144,7 +144,7 @@
All command line options listed below can be defined in the configuration file. Defining them on the command line is useful when using a configuration template for many images.
.SH QUICK STARTUP
.IX Header "QUICK STARTUP"
-For a quick start, it is possible to use the tutorials examples. To do so, it is needed to install the circos-tutorials package. Once this si done, go to directory /usr/share/circos/tutorials/2/10 (for example) and run "circos -conf circos.conf". An image will be generated in /tmp.
+For a quick start, it is possible to use the given example. To do so, go to /usr/share/circos/example and run "circos -conf circos.conf". An image will be generated.
.SH "OPTIONS"
.IX Header "OPTIONS"
.SS "Configuration"
Modified: trunk/packages/circos/trunk/debian/circos.install
===================================================================
--- trunk/packages/circos/trunk/debian/circos.install 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/circos.install 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,7 +1,6 @@
bin/circos usr/bin/
-data/* var/lib/circos/data/
etc/* etc/circos/
fonts/* usr/share/circos/fonts/
lib/* usr/share/perl5/
-svg/* usr/share/circos/svg/
tiles/* usr/share/circos/tiles/
+example/* usr/share/circos/example/
Modified: trunk/packages/circos/trunk/debian/control
===================================================================
--- trunk/packages/circos/trunk/debian/control 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/control 2011-07-26 11:04:24 UTC (rev 7336)
@@ -17,8 +17,8 @@
libdata-dumper-simple-perl, libgd-gd2-perl, libgetopt-simple-perl,
libmath-bezier-perl, libmath-round-perl, libparams-validate-perl, libreadonly-perl,
libset-intspan-perl, liblist-allutils-perl, libfile-basedir-perl,libfile-spec-perl,
- libmath-bigint-perl,libmath-vec-perl, libio-all-perl, libmath-vecstat-perl
-Suggests: circos-tutorials
+ libmath-bigint-perl,libmath-vec-perl, libio-all-perl, libmath-vecstat-perl, libgraphics-colorobject-perl
+Recommends: circos-tools
Description: Package for visualizing data and information
Circos visualizes data in a circular layout — this makes Circos
ideal for exploring relationships between objects or positions.
@@ -26,17 +26,3 @@
and illustrations with a high data-to-ink ratio, richly layered
data and pleasant symmetries. You have fine control each element
in the figure to tailor its focus points and detail to your audience.
-
-Package: circos-tutorials
-Architecture: any
-Depends: ${misc:Depends}
-Enhances: circos
-Description: Tutorials for circos - package for visualizing data and information
- Circos visualizes data in a circular layout — this makes Circos
- ideal for exploring relationships between objects or positions.
- Circos is ideal for creating publication-quality infographics
- and illustrations with a high data-to-ink ratio, richly layered
- data and pleasant symmetries. You have fine control each element
- in the figure to tailor its focus points and detail to your audience.
- .
- This package contains hints for usage and examples for Circos
Modified: trunk/packages/circos/trunk/debian/copyright
===================================================================
--- trunk/packages/circos/trunk/debian/copyright 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/copyright 2011-07-26 11:04:24 UTC (rev 7336)
@@ -2,6 +2,67 @@
Upstream-Name: circos
Source: http://circos.ca/
+Files: fonts/circles/*
+Copyright: 2003 Fonts & Things
+License:
+ Circle Things is a freeware truetype font from Fonts & Things.
+ You may use this for personal or commercial use free of charge.
+ You may freely distribute this font providing no fee whatsoever is charged and this text file is included.
+
+Files: fonts/shapes/*
+Copyright: 2001, Fonts & Things
+License:
+ Basic Shapes is a freeware truetype font from Fonts & Things. You may use this for personal or commercial use free of charge.
+ You may freely distribute this font providing no fee whatsoever is charged and this text file and character map (gif) are included.
+
+Files: fonts/distrobats/*
+Copyright: 2001 swordfish/PJ Ramsey
+License:
+ These fonts are offered for distribution as limited license 'freeware'. You are welcome to use them and distribute them in any way you wish, provided that NO MONEY CHANGES HANDS at any stage. A copy of this text file MUST accompany any and all fonts distributed in any manner. The font files themselves must not be modified, either by editing the outlines or by messing with the font's names, copyright or other notices.
+
+Files: fonts/modern/*
+Copyright: 2005, Andrey V. Panov
+License:
+ Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, and/or sell copies of the Software, and to permit persons to
+whom the Software is furnished to do so, provided that the above
+copyright notice(s) and this permission notice appear in all copies of
+the Software and that both the above copyright notice(s) and this
+permission notice appear in supporting documentation.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF
+THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS
+INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT
+OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
+OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THIS SOFTWARE.
+
+Except as contained in this notice, the name of a copyright holder shall
+not be used in advertising or otherwise to promote the sale, use or
+other dealings in this Software without prior written authorization of
+the copyright holder.
+
+As a special exception, if you create a document which uses these fonts,
+and embed these fonts or unaltered portions of these fonts into the
+document, these fonts does not by itself cause the resulting document to
+be covered by the X11 License. This exception does not however
+invalidate any other reasons why the document might be covered by the
+X11 License. If you modify these fonts, you may extend this exception to
+your version of the fonts, but you are not obligated to do so. If you do
+not wish to do so, delete this exception statement from your version.
+
+Files: fonts/pointers
+Copyright: 1995 Russ Rowlett <rowlettœemail.unc.edu>
+License:
+ This is freeware. It is not in the public domain. As an individual user, you have permission to make copies of Pointers for all your kith and kin, provided you follow two rules: (1) all documentation files must be copied along with the font suitcase, and (2) nothing whatsoever can be charged for copies of the font. All other rights reserved.
+
+
Files: etc/brewer.*
Copyright: Cynthia A. Brewer, Mark Harrower, Pennsylvania State University
License: Apache v2.0
Modified: trunk/packages/circos/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/circos/trunk/debian/get-orig-source 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/get-orig-source 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,95 +1,15 @@
#!/bin/bash
+set -e
-function downloadAndExtract {
-VERSIONMAIN=$1
-if [ -z $2 ]; then
-COMPONENT=""
-else
-COMPONENT="-$2"
-fi
-MAJOR=$(echo $VERSIONMAIN | cut -d"-" -f1)
-echo "Major: "$MAJOR
-wget http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}.tar.gz
-#echo "should download http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}.tar.gz"
-if [ $? -ne 0 ]; then
- wget http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}.tgz
- #echo "should download http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}.tgz"
- if [ $? -ne 0 ]; then
- echo "Failed to download main version"
- exit 1
- fi
- MAINFILE=circos${COMPONENT}-${MAJOR}.tgz
-else
-MAINFILE=circos${COMPONENT}-${MAJOR}.tar.gz
-fi
-
-echo "Main file: ${MAINFILE}"
-tar xzf ${MAINFILE}
-echo "Copy circos${COMPONENT}-${MAJOR}/* into ${WORKDIR}/"
-cp -R circos${COMPONENT}-${MAJOR}/* $WORKDIR/
-rm -rf circos${COMPONENT}-${MAJOR}
-rm -f ${MAINFILE}
-
-MINOR=$(echo $VERSIONMAIN | cut -d"-" -f2)
-echo "Minor: "$MINOR
-if [ "${MINOR}" == "${MAJOR}" ]; then
-echo "No patch to apply"
-else
-for (( MINORCOUNT=1; MINORCOUNT<=${MINOR}; MINORCOUNT++ ))
-do
- echo "download and extract ${MINORCOUNT}"
- wget http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}-${MINORCOUNT}.tar.gz
- #echo "Should download http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}-${MINORCOUNT}.tar.gz"
- if [ $? -ne 0 ]; then
- wget http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}-${MINORCOUNT}.tgz
- #echo "Should download http://circos.ca/distribution/circos${COMPONENT}-${MAJOR}-${MINORCOUNT}.tgz"
- if [ $? -ne 0 ]; then
- echo "Failed to download patch version ${MINORCOUNT}"
- exit 1
- fi
- MINORFILE=circos${COMPONENT}-${MAJOR}-${MINORCOUNT}.tgz
- else
- MINORFILE=circos${COMPONENT}-${MAJOR}-${MINORCOUNT}.tar.gz
- fi
- echo "Minor file: ${MINORFILE}"
- tar xfz ${MINORFILE}
- echo "Copy circos${COMPONENT}-${MAJOR}-${MINORCOUNT}/* into ${WORKDIR}/"
- cp -R circos${COMPONENT}-${MAJOR}-${MINORCOUNT}/* $WORKDIR/
- rm -rf circos${COMPONENT}-${MAJOR}-${MINORCOUNT}
- rm -f ${MINORFILE}
-done
-fi
-
-}
-
-
PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSIONMAIN=`uscan --rename --verbose --timeout 60 |
- grep "Newest version on remote site is .* local version is .*" |
- head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.\-]\+\),.*/\1/"`
+VERSION=`uscan --verbose --force-download |
+ grep "Newest version on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
-echo "Main: $VERSIONMAIN"
+mkdir -p ../tarballs
-VERSIONTOOLS=`uscan --watchfile debian/watch-tools --rename --verbose --timeout 60 |
- grep "Newest version on remote site is .* local version is .*" |
- head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.\-]\+\),.*/\1/"`
+UTAR="${PKG}_${VERSION}.orig.tgz"
+mv ../${PKG}-${VERSION}.tgz ../tarballs/${UTAR}
-
-VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }'`
-
-cd ../tarballs
-mkdir -p ${PKG}_${VERSIONMAIN}.orig
-export WORKDIR="${PKG}_${VERSIONMAIN}.orig"
-
-downloadAndExtract $VERSIONMAIN
-
-echo "Tools: $VERSIONTOOLS"
-
-downloadAndExtract $VERSIONTOOLS "tools"
-
-tar cvf ${WORKDIR}.tar ${WORKDIR}
-bzip2 ${WORKDIR}.tar
-rm -rf ${WORKDIR}
Modified: trunk/packages/circos/trunk/debian/patches/configpath_add_etc
===================================================================
--- trunk/packages/circos/trunk/debian/patches/configpath_add_etc 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/patches/configpath_add_etc 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,6 +1,6 @@
--- a/lib/Circos/Configuration.pm
+++ b/lib/Circos/Configuration.pm
-@@ -193,6 +193,7 @@
+@@ -370,6 +370,7 @@
#$OPT{configfile} = $file;
my @configpath = (
@@ -10,11 +10,11 @@
"$FindBin::RealBin/etc",
--- a/lib/Circos/Utils.pm
+++ b/lib/Circos/Utils.pm
-@@ -202,6 +202,7 @@
- } else {
- # look for the file elsewhere
- @dirs = (
-+ "/usr/share/circos",
- "$FindBin::RealBin/../",
- "$FindBin::RealBin/",
- "$FindBin::RealBin/etc",
+@@ -310,6 +310,7 @@
+ } else {
+ # look for the file elsewhere
+ @dirs = (
++ "/usr/share/circos",
+ "$FindBin::RealBin/../",
+ "$FindBin::RealBin/",
+ "$FindBin::RealBin/etc",
Modified: trunk/packages/circos/trunk/debian/patches/debianpackaging
===================================================================
--- trunk/packages/circos/trunk/debian/patches/debianpackaging 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/patches/debianpackaging 2011-07-26 11:04:24 UTC (rev 7336)
@@ -6,43 +6,3 @@
=pod
---- a/data/3/make_random_highlights
-+++ b/data/3/make_random_highlights
-@@ -1,4 +1,4 @@
--#!/home/martink/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Math::Random qw(random_normal);
---- a/data/6/hist.random.make
-+++ b/data/6/hist.random.make
-@@ -1,4 +1,4 @@
--#!/home/martink/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Math::VecStat qw(min max);
---- a/svg/textrotation
-+++ b/svg/textrotation
-@@ -1,4 +1,4 @@
--#!/home/martink/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- $\ = "\n";
---- a/data/8/17/bingenes
-+++ b/data/8/17/bingenes
-@@ -1,4 +1,4 @@
--#!/bin/env perl
-+#!/usr/bin/env perl
-
- =pod
-
---- a/tutorials/8/11/addidtolinks
-+++ b/tutorials/8/11/addidtolinks
-@@ -1,4 +1,4 @@
--#!/home/martink/bin/perl510
-+#!/usr/bin/perl
-
- use strict;
-
Modified: trunk/packages/circos/trunk/debian/rules
===================================================================
--- trunk/packages/circos/trunk/debian/rules 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/rules 2011-07-26 11:04:24 UTC (rev 7336)
@@ -12,19 +12,9 @@
override_dh_install:
dh_install
# Update circos relative path to absolute debian paths
- find debian/circos -type f | xargs sed -i \
- -e 's/include etc/include \/usr\/share\/circos\/etc/g' \
- -e 's/include fonts/include \/usr\/share\/circos\/fonts/g' \
- -e 's/include svg/include \/usr\/share\/circos\/svg/g' \
- -e 's/include tiles/include \/usr\/share\/circos\/tiles/g' \
- -e 's/include data/include \/var\/lib\/circos\/data/g'
- find debian/circos-tutorials -type f | xargs sed -i \
- -e 's/include etc/include \/usr\/share\/circos\/etc/g' \
- -e 's/include fonts/include \/usr\/share\/circos\/fonts/g' \
- -e 's/include svg/include \/usr\/share\/circos\/svg/g' \
- -e 's/include tiles/include \/usr\/share\/circos\/tiles/g' \
- -e 's/include data/include \/var\/lib\/circos\/data/g' \
- -e 's/= data/= \/var\/lib\/circos\/data/g'
+ find debian/circos -type f | xargs sed -i 's/include etc/include \/usr\/share\/circos\/etc/g'
+ find debian/circos -type f | xargs sed -i 's/include fonts/include \/usr\/share\/circos\/fonts/g'
+ find debian/circos -type f | xargs sed -i 's/include tiles/include \/usr\/share\/circos\/tiles/g'
override_dh_builddeb:
dh_builddeb -- -Z bzip2
Modified: trunk/packages/circos/trunk/debian/watch
===================================================================
--- trunk/packages/circos/trunk/debian/watch 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/watch 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,2 +1,2 @@
version=3
-http://circos.ca/software/download .*/distribution/circos-([-.\d]*).(?:tar(?:\.gz|\.bz2)?|tgz|zip)
+http://circos.ca/software/download .*/distribution/circos-([-.\d]*)\.tgz debian uupdate
Deleted: trunk/packages/circos/trunk/debian/watch-tools
===================================================================
--- trunk/packages/circos/trunk/debian/watch-tools 2011-07-26 11:02:10 UTC (rev 7335)
+++ trunk/packages/circos/trunk/debian/watch-tools 2011-07-26 11:04:24 UTC (rev 7336)
@@ -1,2 +0,0 @@
-version=3
-http://circos.ca/software/download .*/distribution/circos-tools-([-.\d]*).(?:tar(?:\.gz|\.bz2)?|tgz|zip)
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