[med-svn] r15221 - in trunk/packages/dialign-t/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 22:08:55 UTC 2013
Author: tille
Date: 2013-11-20 22:08:55 +0000 (Wed, 20 Nov 2013)
New Revision: 15221
Added:
trunk/packages/dialign-t/trunk/debian/patches/
trunk/packages/dialign-t/trunk/debian/patches/hardening.patch
trunk/packages/dialign-t/trunk/debian/patches/prevent_enforcing_arch.patch
trunk/packages/dialign-t/trunk/debian/patches/series
Modified:
trunk/packages/dialign-t/trunk/debian/changelog
trunk/packages/dialign-t/trunk/debian/compat
trunk/packages/dialign-t/trunk/debian/control
trunk/packages/dialign-t/trunk/debian/copyright
trunk/packages/dialign-t/trunk/debian/rules
Log:
Mass commit for 1.0.2-3
Modified: trunk/packages/dialign-t/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign-t/trunk/debian/changelog 2013-11-20 22:08:30 UTC (rev 15220)
+++ trunk/packages/dialign-t/trunk/debian/changelog 2013-11-20 22:08:55 UTC (rev 15221)
@@ -1,4 +1,4 @@
-dialign-t (1.0.2-3) UNRELEASED; urgency=low
+dialign-t (1.0.2-3) unstable; urgency=low
[ Charles Plessy ]
* debian/upstream: renamed from upstream-metadata.yaml
@@ -7,8 +7,18 @@
* debian/upstream:
- Removed duplicate of DOI
- Moved PMID to References
+ * debian/control:
+ - cme fix dpkg-control
+ - removed Conflicts/Provides/Replaces: dialign-t,dialign-t-doc
+ since this is not even in oldstable any more
+ - canonical Vcs URLs
+ - debhelper 9
+ * debian/patches/prevent_enforcing_arch.patch: Do not enforce specific
+ architecture
+ * debian/patches/hardening.patch: Propagate hardening options
+ * debian/copyright: DEP5
- -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 16:36:42 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 13 Nov 2013 14:12:59 +0100
dialign-t (1.0.2-2) unstable; urgency=low
Modified: trunk/packages/dialign-t/trunk/debian/compat
===================================================================
--- trunk/packages/dialign-t/trunk/debian/compat 2013-11-20 22:08:30 UTC (rev 15220)
+++ trunk/packages/dialign-t/trunk/debian/compat 2013-11-20 22:08:55 UTC (rev 15221)
@@ -1 +1 @@
-7
+9
Modified: trunk/packages/dialign-t/trunk/debian/control
===================================================================
--- trunk/packages/dialign-t/trunk/debian/control 2013-11-20 22:08:30 UTC (rev 15220)
+++ trunk/packages/dialign-t/trunk/debian/control 2013-11-20 22:08:55 UTC (rev 15221)
@@ -1,22 +1,20 @@
Source: dialign-t
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7), cdbs
-Standards-Version: 3.9.1
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dialign-t/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dialign-t/trunk/
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/dialign-t/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/dialign-t/trunk/
Homepage: http://dialign-tx.gobics.de/
Package: dialign-tx
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, dialign-tx-data (= ${source:Version})
-Conflicts: dialign-t, dialign-t-doc
-Replaces: dialign-t, dialign-t-doc
-Provides: dialign-t, dialign-t-doc
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ dialign-tx-data (= ${source:Version})
Enhances: t-coffee
Description: Segment-based multiple sequence alignment
DIALIGN-TX is a command line tool to perform multiple alignment of protein or
@@ -31,7 +29,16 @@
Package: dialign-tx-data
Architecture: all
Depends: ${misc:Depends}
-Recommends: dialign-tx (= ${binary:Version})
-Description: Common data files for dialign-tx
+Enhances: dialign-tx
+Description: Segment-based multiple sequence alignment (data files)
+ DIALIGN-TX is a command line tool to perform multiple alignment of protein or
+ DNA sequences. It is a complete reimplementation of the segment-base approach
+ including several new improvements and heuristics that significantly enhance
+ the quality of the output alignments compared to DIALIGN 2.2 and DIALIGN-T.
+ For pairwise alignment, DIALIGN-TX uses a fragment-chaining algorithm that
+ favours chains of low-scoring local alignments over isolated high-scoring
+ fragments. For multiple alignment, DIALIGN-TX uses an improved greedy
+ procedure that is less sensitive to spurious local sequence similarities.
+ .
This package contain the score matrices and probability distribution files
that DIALIGN-TX needs to align peptidic and nucleic sequences.
Modified: trunk/packages/dialign-t/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign-t/trunk/debian/copyright 2013-11-20 22:08:30 UTC (rev 15220)
+++ trunk/packages/dialign-t/trunk/debian/copyright 2013-11-20 22:08:55 UTC (rev 15221)
@@ -1,14 +1,15 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
-Upstream-Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
-X-Packaged-By: Charles Plessy <plessy at debian.org>
-X-Packaged-Date: Tue, 9 Oct 2007 23:17:04 +0900
-Original-Source-Location: http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: DIALIGN-TX
+Upstream-Contact: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+Source: http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
Files: *
Copyright: © 2004-2008 Amarendran R. Subramanian
© 2004 Volker Menrad
© 2004 Dorothea Emig
License: LGPL-2.1+
+
+License: LGPL-2.1+
This package is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@@ -22,11 +23,12 @@
You should have received a copy of the GNU Lesser 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
-X-Comment: On Debian systems, the complete text of the GNU Lesser General
+ .
+ On Debian systems, the complete text of the GNU Lesser General
Public License can be found in `/usr/share/common-licenses/LGPL'.
Files: debian/*
Copyright: © 2007-2008 Charles Plessy <plessy at debian.org>
© 2008 David Paleino <d.paleino at gmail.com>
+ © 2011-2013 Andreas Tille <tille at debian.org>
License: LGPL-2.1+
- The Debian packaging is licensed under the same terms as DIALIGN-TX itself.
Added: trunk/packages/dialign-t/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/dialign-t/trunk/debian/patches/hardening.patch (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/patches/hardening.patch 2013-11-20 22:08:55 UTC (rev 15221)
@@ -0,0 +1,13 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Wed, 13 Nov 2013 14:12:59 +0100
+Description: Propagate hardening options
+
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -35,5 +35,5 @@ museq: $(OBJ)
+ rm -f $(TARGET)/$@
+ $(CC) -o $(TARGET)/$@ \
+ $(OBJ) \
+- -pipe -Wall -lm
++ -pipe -Wall -lm $(LDFLAGS)
+ mv museq dialign-tx
Added: trunk/packages/dialign-t/trunk/debian/patches/prevent_enforcing_arch.patch
===================================================================
--- trunk/packages/dialign-t/trunk/debian/patches/prevent_enforcing_arch.patch (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/patches/prevent_enforcing_arch.patch 2013-11-20 22:08:55 UTC (rev 15221)
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Wed, 13 Nov 2013 14:12:59 +0100
+Description: Do not enforce i686 architecture
+
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -8,7 +8,7 @@ CC=gcc
+ # THIS IS FOR THE OPTIMIZED ONE
+ #CPPFLAGS=-g
+ #CPPFLAGS=-O3 -march=i686 -funroll-loops
+-CPPFLAGS=-O3 -funroll-loops -march=i686 -mfpmath=sse -msse -mmmx
++CPPFLAGS=-O3 -funroll-loops -mfpmath=sse -msse -mmmx
+ #CPPFLAGS=-march=athlon-mp -g -O0 -Wall -D_USE_XOPEN -D__unix__
+
+ OBJ_DIR=.
Added: trunk/packages/dialign-t/trunk/debian/patches/series
===================================================================
--- trunk/packages/dialign-t/trunk/debian/patches/series (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/patches/series 2013-11-20 22:08:55 UTC (rev 15221)
@@ -0,0 +1,2 @@
+prevent_enforcing_arch.patch
+hardening.patch
Modified: trunk/packages/dialign-t/trunk/debian/rules
===================================================================
--- trunk/packages/dialign-t/trunk/debian/rules 2013-11-20 22:08:30 UTC (rev 15220)
+++ trunk/packages/dialign-t/trunk/debian/rules 2013-11-20 22:08:55 UTC (rev 15221)
@@ -1,9 +1,10 @@
#!/usr/bin/make -f
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
+SRCDIR=$(CURDIR)/source
-DEB_SRCDIR = $(CURDIR)/source
+%:
+ dh $@ --sourcedirectory=$(SRCDIR) --parallel
-binary-fixup/dialign-tx-data::
+override_dh_fixperms:
+ dh_fixperms
chmod 644 $(CURDIR)/debian/dialign-tx-data/usr/share/dialign-tx/*
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