[med-svn] r15189 - in trunk/packages/rostlab/disulfinder/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 21:50:56 UTC 2013
Author: tille
Date: 2013-11-20 21:50:56 +0000 (Wed, 20 Nov 2013)
New Revision: 15189
Added:
trunk/packages/rostlab/disulfinder/trunk/debian/docs
trunk/packages/rostlab/disulfinder/trunk/debian/patches/
trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch
trunk/packages/rostlab/disulfinder/trunk/debian/patches/series
Removed:
trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian
trunk/packages/rostlab/disulfinder/trunk/debian/patches/
Modified:
trunk/packages/rostlab/disulfinder/trunk/debian/changelog
trunk/packages/rostlab/disulfinder/trunk/debian/compat
trunk/packages/rostlab/disulfinder/trunk/debian/control
trunk/packages/rostlab/disulfinder/trunk/debian/copyright
trunk/packages/rostlab/disulfinder/trunk/debian/rules
Log:
Mass commit changes for 1.2.11-3
Deleted: trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian 2013-11-20 21:50:20 UTC (rev 15188)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian 2013-11-20 21:50:56 UTC (rev 15189)
@@ -1,34 +0,0 @@
-Disulfinder
-===========
-
-References
-----------
-* A. Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a
- Disulfide Bonding State and Cysteine Connectivity Prediction Server,
- Nucleic Acids Research, 34(Web Server issue):W177-W181, 2006.
-
-For the disulphide connectivity predictor see:
-
-* A. Vullo and P. Frasconi. Disulfide Connectivity Prediction using
- Recursive Neural Networks and Evolutionary Information, Bioinformatics,
- 20, 653-659, 2004.
-
-For the cystein bonding state predictor see:
-
-* P. Frasconi, A. Passerini, and A. Vullo. A Two-Stage SVM Architecture
- for Predicting the Disulfide Bonding State of Cysteines, Proc. IEEE
- Workshop on Neural Networks for Signal Processing, pp.25-34, 2002.
-
-* A.Ceroni, P.Frasconi, A.Passerini and A.Vullo. Predicting the Disulfide
- Bonding State of Cysteines with Combinations of Kernel Machines, Journal
- of VLSI Signal Processing, 35, 287-295, 2003.
-
-
-Upstream
---------
-
-The upstream package is maintained and made available by the Rost Lab
-instead of P. Frasconi et al. at this time (2011).
-
--- Laszlo Kajan <lkajan at rostlab.org> Sat, 09 Jul 2011 12:08:06 +0200
-
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/changelog 2013-11-20 21:50:20 UTC (rev 15188)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/changelog 2013-11-20 21:50:56 UTC (rev 15189)
@@ -1,8 +1,18 @@
-disulfinder (1.2.11-3) UNRELEASED; urgency=low
+disulfinder (1.2.11-3) unstable; urgency=low
* debian/upstream: Valid BibTeX syntax in author strings
+ * debian/control:
+ - cme fix dpkg-control
+ - Priority: s/extra/optional/
+ - canonical Vcs URLs
+ - debhelper 9
+ * debian/copyright: DEP5
+ * debian/patches/hardening.patch: Propagate hardening options
+ * debian/rules: use dh consequently
+ * README.Debian: references are now in debian/upstream - install this
+ instead into doc directory
- -- Andreas Tille <tille at debian.org> Mon, 07 May 2012 23:09:04 +0200
+ -- Andreas Tille <tille at debian.org> Sun, 17 Nov 2013 08:46:05 +0100
disulfinder (1.2.11-2) unstable; urgency=low
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/compat
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/compat 2013-11-20 21:50:20 UTC (rev 15188)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/compat 2013-11-20 21:50:56 UTC (rev 15189)
@@ -1 +1 @@
-7
+9
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/control 2013-11-20 21:50:20 UTC (rev 15188)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/control 2013-11-20 21:50:56 UTC (rev 15189)
@@ -1,18 +1,24 @@
Source: disulfinder
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Guy Yachdav <gyachdav at rostlab.org>,
+ Laszlo Kajan <lkajan at rostlab.org>,
+ Andreas Tille <tille at debian.org>
Section: science
-Priority: extra
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Guy Yachdav <gyachdav at rostlab.org>, Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 7.0.50~), libboost-dev, libboost-graph-dev, libf2c2-dev
-Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/disulfinder/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/disulfinder/trunk/
-DM-Upload-Allowed: yes
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libboost-dev,
+ libboost-graph-dev,
+ libf2c2-dev
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/disulfinder/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/disulfinder/trunk/
Homepage: http://disulfind.dsi.unifi.it/
Package: disulfinder
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, disulfinder-data
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ disulfinder-data
Description: cysteines disulfide bonding state and connectivity predictor
'disulfinder' is for predicting the disulfide bonding state of cysteines
and their disulfide connectivity starting from sequence alone. Disulfide
@@ -38,4 +44,3 @@
.
This package contains all data files to reduce the redundancy between
architectures in Debian.
-
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/copyright
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/copyright 2013-11-20 21:50:20 UTC (rev 15188)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/copyright 2013-11-20 21:50:56 UTC (rev 15189)
@@ -1,59 +1,48 @@
-This package was debianized by Laszlo Kajan <lkajan at rostlab.org> on
-Fri, 30 Oct 2009 12:12:21 +0100.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Laszlo Kajan <lkajan at rostlab.org>
+Source: ftp://rostlab.org/disulfinder/
-It was obtained from A. Passerini.
+Files: *
+Copyright: © 2011 Alessio Ceroni,
+ Andrea Passerini <passerini at disi.unitn.it>,
+ Alessandro Vullo,
+ Paolo Frasconi
+ © 2009 Laszlo Kajan <lkajan at rostlab.org>,
+ Technical University Munich (Munich, DE)
+License: GPL2+
-Upstream Authors:
+License: GPL2+
+ This suite of programs 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.
+ .
+ In other words, you are free to modify, copy, or redistribute this
+ source code and its documentation in any way you like, but you must
+ distribute all derivative versions as free software under the same
+ terms that I've provided my code to you (i.e. the GNU General Public
+ License). This precludes any use of the code in proprietary or
+ commercial software unless your source code is made freely available.
+ .
+ If you wish to use Disulfinder code under a different Open Source
+ license that's not compatible with the GPL (like the Artistic License,
+ BSD license, or the Netscape Public License), please contact me
+ (passerini at disi.unitn.it) for permission.
+ .
+ This software 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 Disulfinder release, in the file LICENSE; 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-2'.
- Alessio Ceroni
- Andreas Passerini <passerini at disi.unitn.it>
- Alessandro Vullo
- P. Frasconi
-
- Maintenance modifications to the source by:
-
- Laszlo Kajan <lkajan at rostlab.org>
-
-Copyright:
-
- Copyright (C) 2011 Alessio Ceroni,
- Andrea Passerini <passerini at disi.unitn.it>, Alessandro Vullo,
- Paolo Frasconi
-
- Copyright (C) 2009 Laszlo Kajan <lkajan at rostlab.org>
- Technical University Munich (Munich, DE)
-
-License:
-
- This suite of programs 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.
-
- In other words, you are free to modify, copy, or redistribute this
- source code and its documentation in any way you like, but you must
- distribute all derivative versions as free software under the same
- terms that I've provided my code to you (i.e. the GNU General Public
- License). This precludes any use of the code in proprietary or
- commercial software unless your source code is made freely available.
-
- If you wish to use Disulfinder code under a different Open Source
- license that's not compatible with the GPL (like the Artistic License,
- BSD license, or the Netscape Public License), please contact me
- (passerini at disi.unitn.it) for permission.
-
- This software 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 Disulfinder release, in the file LICENSE; 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'.
-
-The Debian packaging is (C) 2009, Laszlo Kajan <lkajan at rostlab.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+Files: debian/*
+Copyright: © 2009-2011 Laszlo Kajan <lkajan at rostlab.org>
+ © 2013 Andreas Tille <tille at debian.org>
+License: GPL2+
Added: trunk/packages/rostlab/disulfinder/trunk/debian/docs
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/docs (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/docs 2013-11-20 21:50:56 UTC (rev 15189)
@@ -0,0 +1 @@
+debian/upstream
Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/hardening.patch 2013-11-20 21:50:56 UTC (rev 15189)
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Sun, 17 Nov 2013 08:46:05 +0100
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -13,7 +13,7 @@ MAN1PAGES := disulfinder.1
+ prefix := /usr
+ docdir := $(prefix)/share/doc/$(PACKAGE)
+
+-CXXFLAGS := -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\"
++CXXFLAGS += -DDEFAULT_PKGDATADIR=\"$(prefix)/share/disulfinder\"
+ export CXXFLAGS
+
+ .PHONY: all
+--- a/disulfind/src/Makefile
++++ b/disulfind/src/Makefile
+@@ -1,5 +1,5 @@
+ LIBS=-lCommon
+-LDFLAGS=-LCommon/
++LDFLAGS+=-LCommon/
+ TARGETS=disulfinder disultrainer
+ ifndef CXX
+ CXX=g++
Added: trunk/packages/rostlab/disulfinder/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/patches/series (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/patches/series 2013-11-20 21:50:56 UTC (rev 15189)
@@ -0,0 +1 @@
+hardening.patch
Modified: trunk/packages/rostlab/disulfinder/trunk/debian/rules
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/rules 2013-11-20 21:50:20 UTC (rev 15188)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/rules 2013-11-20 21:50:56 UTC (rev 15189)
@@ -4,24 +4,16 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
+pkg := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+pkgdata := $(pkg)-data
+
%:
dh $@
-build-indep: build-stamp
- echo "Nothing extra to do for build-indep"
+override_dh_auto_install:
+ $(MAKE) DESTDIR=$(CURDIR)/debian/$(pkg) prefix=/usr install
-build build-arch: build-stamp
-build-stamp:
- dh_testdir
- $(MAKE) prefix=/usr
- #docbook-to-man debian/disulfinder.sgml > disulfinder.1
- touch $@
-
-override_dh_install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
- $(MAKE) DESTDIR=$(CURDIR)/debian/disulfinder prefix=/usr install
- mkdir -p $(CURDIR)/debian/disulfinder-data/usr/share/disulfinder
- mv $(CURDIR)/debian/disulfinder/usr/share/disulfinder/Models $(CURDIR)/debian/disulfinder-data/usr/share/disulfinder/
+override_dh_install:
+ dh_install
+ mkdir -p $(CURDIR)/debian/$(pkgdata)/usr/share/$(pkg)
+ mv $(CURDIR)/debian/$(pkg)/usr/share/$(pkg) $(CURDIR)/debian/$(pkgdata)/usr/share/
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