diff -Nru gff2aplot-2.0/debian/changelog gff2aplot-2.0/debian/changelog --- gff2aplot-2.0/debian/changelog 2011-01-25 13:10:18.000000000 +0000 +++ gff2aplot-2.0/debian/changelog 2012-05-02 08:24:27.000000000 +0000 @@ -1,3 +1,17 @@ +gff2aplot (2.0-7) unstable; urgency=low + + * debian/upstream: Added citation information + * debian/control: + - Standards-Version: 3.9.3 (no changes needed) + - Fixed Vcs-Svn + - Removed cdbs+quilt from Build-Depends + * debian/copyright: Rewritten to DEP5 + * debian/patches/use-dpkg-buildflags.patch: Use build flags from environment + to enable hardening + * debhelper 9 (control+compat) + + -- Andreas Tille Tue, 01 May 2012 22:37:01 +0200 + gff2aplot (2.0-6) unstable; urgency=low * debian/control diff -Nru gff2aplot-2.0/debian/compat gff2aplot-2.0/debian/compat --- gff2aplot-2.0/debian/compat 2011-01-25 12:34:06.000000000 +0000 +++ gff2aplot-2.0/debian/compat 2012-05-02 08:10:43.000000000 +0000 @@ -1 +1 @@ -7 +9 diff -Nru gff2aplot-2.0/debian/control gff2aplot-2.0/debian/control --- gff2aplot-2.0/debian/control 2011-01-25 13:00:53.000000000 +0000 +++ gff2aplot-2.0/debian/control 2012-05-02 08:10:52.000000000 +0000 @@ -5,10 +5,10 @@ DM-Upload-Allowed: yes Uploaders: Nelson A. de Oliveira , Andreas Tille -Build-Depends: cdbs, debhelper (>= 7.1), quilt (>= 0.47) -Standards-Version: 3.9.1 +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gff2aplot/trunk/ -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gff2aplot/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gff2aplot/trunk/ Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Package: gff2aplot diff -Nru gff2aplot-2.0/debian/copyright gff2aplot-2.0/debian/copyright --- gff2aplot-2.0/debian/copyright 2008-11-17 06:38:37.000000000 +0000 +++ gff2aplot-2.0/debian/copyright 2012-05-02 08:07:03.000000000 +0000 @@ -1,29 +1,34 @@ -This package was debianized by Nelson A. de Oliveira on -Mon, 21 Mar 2005 20:30:45 -0300. - -It was downloaded from http://genome.imim.es/software/gfftools/GFF2APLOT.html - -Copyright © 1999-2003 Josep Francesc ABRIL FERRANDO - Thomas WIEHE - Roderic GUIGO SERRA - -Upstream Author: Josep Francesc ABRIL FERRANDO - -License: +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: GFF2APLOT +Upstream-Contact: Josep Francesc ABRIL FERRANDO +Source: http://genome.imim.es/software/gfftools/GFF2APLOT.html + +Files: * +Copyright: 1999-2003 Josep Francesc ABRIL FERRANDO + Thomas WIEHE + Roderic GUIGO SERRA +License: GPL-2+ + +Files: debian/* +Copyright: 2005-2008 Nelson A. de Oliveira + 2011-2012 Andreas Tille +License: GPL-2+ +License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.. - + . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. - + . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + . + On Debian systems, the complete text of the GNU General + Public License can be found in `/usr/share/common-licenses/GPL'. -On Debian systems, the complete text of the GNU General -Public License can be found in `/usr/share/common-licenses/GPL'. diff -Nru gff2aplot-2.0/debian/patches/02-blat2gff.diff gff2aplot-2.0/debian/patches/02-blat2gff.diff --- gff2aplot-2.0/debian/patches/02-blat2gff.diff 2011-01-25 12:38:39.000000000 +0000 +++ gff2aplot-2.0/debian/patches/02-blat2gff.diff 2012-05-02 08:13:22.000000000 +0000 @@ -1,7 +1,7 @@ Author: Nelson A. de Oliveira Date: 2005-03-21 22:46:49 -0300 ---- gff2aplot-2.0.orig.orig/src/blat2gff.pl -+++ gff2aplot-2.0.orig/src/blat2gff.pl +--- gff2aplot-2.0.orig/src/blat2gff.pl ++++ gff2aplot-2.0/src/blat2gff.pl @@ -82,7 +82,7 @@ my @f = (); next unless /^\d/o; diff -Nru gff2aplot-2.0/debian/patches/03-parseblast.diff gff2aplot-2.0/debian/patches/03-parseblast.diff --- gff2aplot-2.0/debian/patches/03-parseblast.diff 2011-01-25 12:39:33.000000000 +0000 +++ gff2aplot-2.0/debian/patches/03-parseblast.diff 2012-05-02 08:13:13.000000000 +0000 @@ -1,7 +1,7 @@ Author: Nelson A. de Oliveira Date: 2005-03-22 18:39:54 -0300 ---- gff2aplot-2.0.orig.orig/src/parseblast.pl -+++ gff2aplot-2.0.orig/src/parseblast.pl +--- gff2aplot-2.0.orig/src/parseblast.pl ++++ gff2aplot-2.0/src/parseblast.pl @@ -827,7 +827,7 @@ }; }; # $prt diff -Nru gff2aplot-2.0/debian/patches/series gff2aplot-2.0/debian/patches/series --- gff2aplot-2.0/debian/patches/series 2011-01-25 13:00:00.000000000 +0000 +++ gff2aplot-2.0/debian/patches/series 2012-05-02 08:17:00.000000000 +0000 @@ -1,2 +1,3 @@ 02-blat2gff.diff 03-parseblast.diff +use-dpkg-buildflags.patch diff -Nru gff2aplot-2.0/debian/patches/use-dpkg-buildflags.patch gff2aplot-2.0/debian/patches/use-dpkg-buildflags.patch --- gff2aplot-2.0/debian/patches/use-dpkg-buildflags.patch 1970-01-01 00:00:00.000000000 +0000 +++ gff2aplot-2.0/debian/patches/use-dpkg-buildflags.patch 2012-05-02 08:20:26.000000000 +0000 @@ -0,0 +1,15 @@ +Description: Use build flags from environment (dpkg-buildflags). + Necessary for hardening flags. +Author: Andreas Tille +Date: Wed, 02 May 2012 10:20:01 +0200 +--- gff2aplot-2.0.orig/src/ali2gff/Makefile ++++ gff2aplot-2.0/src/ali2gff/Makefile +@@ -22,7 +22,7 @@ + all : ali2gff + + ali2gff : ali2gff.c ali2gff.h Makefile +- @$(CC) -o ali2gff ali2gff.c; ++ @$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o ali2gff ali2gff.c; + @chmod 755 ali2gff + + clean : diff -Nru gff2aplot-2.0/debian/rules gff2aplot-2.0/debian/rules --- gff2aplot-2.0/debian/rules 2011-01-25 13:03:04.000000000 +0000 +++ gff2aplot-2.0/debian/rules 2012-05-02 08:01:00.000000000 +0000 @@ -4,7 +4,7 @@ # GPL %: - dh $@ --with quilt + dh $@ # Upstream is missing to clean some files override_dh_auto_clean: diff -Nru gff2aplot-2.0/debian/upstream gff2aplot-2.0/debian/upstream --- gff2aplot-2.0/debian/upstream 1970-01-01 00:00:00.000000000 +0000 +++ gff2aplot-2.0/debian/upstream 2012-05-01 20:36:36.000000000 +0000 @@ -0,0 +1,12 @@ +Reference: + Author: J. F. Abril and R. Guigó and T. Wiehe + Title: "gff2aplot: Plotting sequence comparisons" + Journal: Bioinformatics + Year: 2003 + Volume: 19 + Number: 18 + Pages: 2477-2479 + DOI: 10.1093/bioinformatics/btg334 + PMID: 4668236 + URL: http://bioinformatics.oxfordjournals.org/content/19/18/2477.abstract + eprint: http://bioinformatics.oxfordjournals.org/content/19/18/2477.full.pdf+html