[med-svn] r3328 - trunk/packages/sigma-align/trunk/debian

Charles Plessy plessy at alioth.debian.org
Mon Apr 27 12:05:06 UTC 2009 

Author: plessy
Date: 2009-04-27 12:05:05 +0000 (Mon, 27 Apr 2009)
New Revision: 3328

Added:
   trunk/packages/sigma-align/trunk/debian/docs
   trunk/packages/sigma-align/trunk/debian/manpages
   trunk/packages/sigma-align/trunk/debian/reference
Modified:
   trunk/packages/sigma-align/trunk/debian/changelog
   trunk/packages/sigma-align/trunk/debian/compat
   trunk/packages/sigma-align/trunk/debian/control
   trunk/packages/sigma-align/trunk/debian/copyright
   trunk/packages/sigma-align/trunk/debian/rules
Log:
New upstream release, and a lot of package refreshing including a conversion to CDBS to easily update config.guess and config.sub.

  * Converted the packaging to CDBS.
    - debian/rules is much shorter.
    - CDBS will take care of updating config.guess and config.sub.
    - Created debian/docs and debian/manpages.
  * debian/control:
    - Updated my email address.
    - Incremented Standards-Version to reflect conformance with Policy 3.8.1 (no
      changes needed).
    - Depend on debhelper 7, cdbs and autotools-dev
    - Moved bibliographic information to debian/reference.
    - Use nice Unicode English quotes in the long descriptions.
  * debian/copyright:
    - Updated to latest version of the machine-readable format.
    - Incremented years and updated my email address.
  * Using debhelper 7 (debian/compat).


Modified: trunk/packages/sigma-align/trunk/debian/changelog
===================================================================
--- trunk/packages/sigma-align/trunk/debian/changelog	2009-04-27 05:17:22 UTC (rev 3327)
+++ trunk/packages/sigma-align/trunk/debian/changelog	2009-04-27 12:05:05 UTC (rev 3328)
@@ -1,8 +1,23 @@
-sigma-align (1.1.1-4) UNRELEASED; urgency=low
+sigma-align (1.1.3-1) unstable; urgency=low
 
-  * Updated my email address.
+  * New upstream release.
+  * Converted the packaging to CDBS.
+    - debian/rules is much shorter.
+    - CDBS will take care of updating config.guess and config.sub.
+    - Created debian/docs and debian/manpages.
+  * debian/control:
+    - Updated my email address.
+    - Incremented Standards-Version to reflect conformance with Policy 3.8.1 (no
+      changes needed).
+    - Depend on debhelper 7, cdbs and autotools-dev
+    - Moved bibliographic information to debian/reference.
+    - Use nice Unicode English quotes in the long descriptions.
+  * debian/copyright:
+    - Updated to latest version of the machine-readable format.
+    - Incremented years and updated my email address.
+  * Using debhelper 7 (debian/compat).
 
- -- Charles Plessy <plessy at debian.org>  Sun, 27 Apr 2008 16:55:41 +0900
+ -- Charles Plessy <plessy at debian.org>  Mon, 27 Apr 2009 20:49:06 +0900
 
 sigma-align (1.1.1-3) unstable; urgency=low
 
@@ -28,7 +43,7 @@
 
   * Removed obsolete manpage in the debian directory.
   * Not rebuilding the manpage, and dropping corresponding
-    build-depencancies.
+    build-dependencies.
 
  -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu, 26 Jul 2007 23:02:07 +0900
 

Modified: trunk/packages/sigma-align/trunk/debian/compat
===================================================================
--- trunk/packages/sigma-align/trunk/debian/compat	2009-04-27 05:17:22 UTC (rev 3327)
+++ trunk/packages/sigma-align/trunk/debian/compat	2009-04-27 12:05:05 UTC (rev 3328)
@@ -1 +1 @@
-5
+7

Modified: trunk/packages/sigma-align/trunk/debian/control
===================================================================
--- trunk/packages/sigma-align/trunk/debian/control	2009-04-27 05:17:22 UTC (rev 3327)
+++ trunk/packages/sigma-align/trunk/debian/control	2009-04-27 12:05:05 UTC (rev 3328)
@@ -5,8 +5,8 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>,
  Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 5), libglib2.0-dev
-Standards-Version: 3.7.3
+Build-Depends: autotools-dev, cdbs, debhelper (>= 7), libglib2.0-dev
+Standards-Version: 3.8.1
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sigma-align/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/sigma-align/trunk/
 Homepage: http://www.imsc.res.in/~rsidd/sigma/
@@ -15,12 +15,10 @@
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: Simple greedy multiple alignment of non-coding DNA sequences
- Sigma ("Simple greedy multiple alignment") is an alignment program with a new
- algorithm and scoring scheme designed specifically for non-coding DNA
+ Sigma (“Simple greedy multiple alignment”) is an alignment program with a
+ new algorithm and scoring scheme designed specifically for non-coding DNA
  sequence. It uses a strategy of seeking the best possible gapless local
  alignments, at each step making the best possible alignment consistent with
- existing alignments, and scores the significance of the alignment based on the
- lengths of the aligned fragments and a background model which may be supplied
- or estimated from an auxiliary file of intergenic DNA.
- .
- Sigma has been published in BMC Bioinformatics. 2006 Mar 16;7:143.
+ existing alignments, and scores the significance of the alignment based on
+ the lengths of the aligned fragments and a background model which may be
+ supplied or estimated from an auxiliary file of intergenic DNA.

Modified: trunk/packages/sigma-align/trunk/debian/copyright
===================================================================
--- trunk/packages/sigma-align/trunk/debian/copyright	2009-04-27 05:17:22 UTC (rev 3327)
+++ trunk/packages/sigma-align/trunk/debian/copyright	2009-04-27 12:05:05 UTC (rev 3328)
@@ -1,27 +1,30 @@
-This package was debianized by Charles Plessy
-<charles-debian-nospam at plessy.org> on Tue,  5 Sep 2006 23:14:46 +0900. The
-packaging work is hereby placed in the public domain unless stated otherwise.
+Name: Sigma
+Source: http://www.imsc.res.in/~rsidd/sigma/source/sigma-1.1.3.tar.gz
+Contact: Rahul Siddharthan
 
-Sigma was downloaded from <http://www.imsc.res.in/~rsidd/sigma/>
-
-Copyright (C) Rahul Siddharthan, 2006-2007
-
-License:
-
+Copyright: Rahul Siddharthan, 2006-2009
+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
+Comment:
+ On Debian systems, the complete text of the GNU General Public License version
+ 2 can be found in `/usr/share/common-licenses/GPL-2'.
 
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
+Files: debian/*
+Copyright: 2006–2009  Charles Plessy                <plessy at debian.org>
+              2008    Andreas Tille                  <tille at debian.org>
+              2008    Nelson Antônio de Oliveira    <naoliv at debian.org>
+              2008    David Paleino              <d.paleino at gmail.com>
+License: PD
+ Please treat this work as if it were under public domain.

Added: trunk/packages/sigma-align/trunk/debian/docs
===================================================================
--- trunk/packages/sigma-align/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/docs	2009-04-27 12:05:05 UTC (rev 3328)
@@ -0,0 +1 @@
+README NOTES

Added: trunk/packages/sigma-align/trunk/debian/manpages
===================================================================
--- trunk/packages/sigma-align/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/manpages	2009-04-27 12:05:05 UTC (rev 3328)
@@ -0,0 +1 @@
+sigma.1

Added: trunk/packages/sigma-align/trunk/debian/reference
===================================================================
--- trunk/packages/sigma-align/trunk/debian/reference	                        (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/reference	2009-04-27 12:05:05 UTC (rev 3328)
@@ -0,0 +1,13 @@
+ at Article{16542424,
+AUTHOR = {Siddharthan, Rahul},
+TITLE = {Sigma: multiple alignment of weakly-conserved non-coding DNA sequence},
+JOURNAL = {BMC Bioinformatics},
+VOLUME = {7},
+YEAR = {2006},
+NUMBER = {1},
+PAGES = {143},
+URL = {http://www.biomedcentral.com/1471-2105/7/143},
+DOI = {10.1186/1471-2105-7-143},
+PubMedID = {16542424},
+ISSN = {1471-2105},
+}

Modified: trunk/packages/sigma-align/trunk/debian/rules
===================================================================
--- trunk/packages/sigma-align/trunk/debian/rules	2009-04-27 05:17:22 UTC (rev 3327)
+++ trunk/packages/sigma-align/trunk/debian/rules	2009-04-27 12:05:05 UTC (rev 3328)
@@ -1,59 +1,4 @@
 #!/usr/bin/make -f
-# -*- makefile -*-
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-# Modifications by Charles Plessy during the years 2006-2007
-# are hereby released as if they were in the public domain.
 
-configure: configure-stamp
-configure-stamp:
-	./configure --prefix=$(CURDIR)/debian/sigma-align/usr
-	touch $@
-
-build: configure src/sigma
-
-src/sigma: configure
-	$(MAKE)
-
-# To use the following rule, you need to install the xsltproc, docbook-xml and docbook-xsl packages.
-manpage:
-	xsltproc --nonet \
-		--param man.charmap.use.subset "0" \
-		--param make.year.ranges "1" \
-		--param make.single.year.ranges "1" \
-		sigma.1.xml
-
-clean: configure-stamp
-	dh_testdir
-	dh_testroot
-	[ -f ! Makefile ] || $(MAKE) distclean
-	dh_clean configure-stamp
-
-install: build
-	dh_testdir
-	dh_testroot
-	dh_clean -k 
-	dh_installdirs /usr/bin
-	$(MAKE) install
-
-binary-indep:
-binary-arch: install
-	dh_testdir
-	dh_testroot
-	dh_installchangelogs ChangeLog
-	dh_installdocs README NOTES
-	dh_installexamples Background
-	dh_installman sigma.1
-	dh_link
-	dh_strip
-	dh_compress
-	dh_fixperms
-	dh_installdeb
-	dh_shlibdeps
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
-
-binary: binary-indep binary-arch
-
-.PHONY: build clean binary-indep binary-arch binary install configure
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/debhelper.mk

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