[med-svn] r18264 - in trunk/packages/discosnp/trunk/debian: . patches

Sat Oct 11 09:07:05 UTC 2014

Author: tille
Date: 2014-10-11 09:07:05 +0000 (Sat, 11 Oct 2014)
New Revision: 18264

Modified:
   trunk/packages/discosnp/trunk/debian/changelog
   trunk/packages/discosnp/trunk/debian/control
   trunk/packages/discosnp/trunk/debian/copyright
   trunk/packages/discosnp/trunk/debian/patches/fix_build
Log:
New upstream version + some polishing


Modified: trunk/packages/discosnp/trunk/debian/changelog
===================================================================

--- trunk/packages/discosnp/trunk/debian/changelog	2014-10-11 07:10:51 UTC (rev 18263)
+++ trunk/packages/discosnp/trunk/debian/changelog	2014-10-11 09:07:05 UTC (rev 18264)
@@ -1,3 +1,11 @@
+discosnp (1.2.5-1) unstable; urgency=medium
+
+  * New upstream release
+  * cme fix dpkg-control
+  * Fix some DEP3 lintian issues
+
+ -- Andreas Tille <tille at debian.org>  Sat, 11 Oct 2014 10:41:32 +0200
+
 discosnp (1.2.3-1) unstable; urgency=medium
 
   * New upstream release

Modified: trunk/packages/discosnp/trunk/debian/control
===================================================================
--- trunk/packages/discosnp/trunk/debian/control	2014-10-11 07:10:51 UTC (rev 18263)
+++ trunk/packages/discosnp/trunk/debian/control	2014-10-11 09:07:05 UTC (rev 18264)
@@ -1,19 +1,25 @@
 Source: discosnp
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>,
+           Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
- bc, zlib1g-dev, help2man
-Standards-Version: 3.9.5
+               bc,
+               zlib1g-dev,
+               help2man
+Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/discosnp/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/discosnp/trunk/
 Homepage: http://colibread.inria.fr/discosnp/
 
 Package: discosnp
 Architecture: any
-Depends: ${misc:Depends}, ${shlibs:Depends},
-         zlib1g, bc, python
+Depends: ${misc:Depends},
+         ${shlibs:Depends},
+         zlib1g,
+         bc,
+         python
 Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads
  Software discoSnp is designed for discovering Single Nucleotide 
  Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation

Modified: trunk/packages/discosnp/trunk/debian/copyright
===================================================================
--- trunk/packages/discosnp/trunk/debian/copyright	2014-10-11 07:10:51 UTC (rev 18263)
+++ trunk/packages/discosnp/trunk/debian/copyright	2014-10-11 09:07:05 UTC (rev 18264)
@@ -497,10 +497,16 @@
  .
  .
 
-Files: kissreads/include/libchash.h kissreads/src/libchash.c
+Files: kissreads/include/libchash.h
 Copyright: 1998-2005, Google Inc
            1998-2005 Craig Silverstein
-License: BSD
+License: BSD-3-clause
+
+Files: minia/ttmath/*
+Copyright: Tomasz Sowa <t.sowa at ttmath.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are
  met:
@@ -527,35 +533,6 @@
  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-Files: minia/ttmath/*
-Copyright: Tomasz Sowa <t.sowa at ttmath.org>
-License: BSD
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
-  * Redistributions of source code must retain the above copyright notice,
-    this list of conditions and the following disclaimer.
- .
-  * Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
- .
-  * Neither the name Tomasz Sowa nor the names of contributors to this
-    project may be used to endorse or promote products derived
-    from this software without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
- THE POSSIBILITY OF SUCH DAMAGE.
-
 Files: minia/*
 Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
            2012 Guillaume Rizk
@@ -568,7 +545,7 @@
 
 Files: debian/*
 Copyright: 2013 Olivier Sallou <osallou at debian.org>
-License: GPLv2+
+License: GPLv-2
  The Debian packaging is licensed under the GPL which is available at
- `/usr/share/common-licenses/GPL'.
+ `/usr/share/common-licenses/GPL-2'.
 

Modified: trunk/packages/discosnp/trunk/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-10-11 07:10:51 UTC (rev 18263)
+++ trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-10-11 09:07:05 UTC (rev 18264)
@@ -4,8 +4,6 @@
 Forwarded: no
 Author: Olivier Sallou <osallou at debian.org>
 Last-Updated: 2014-02-01
-Index: discoSnp/kissnp2/makefile
-===================================================================
 --- discoSnp.orig/kissnp2/makefile
 +++ discoSnp/kissnp2/makefile
 @@ -33,7 +33,10 @@
@@ -20,7 +18,7 @@
  #CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -DDONTMARK
  SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp SNP.cpp filter.cpp IterativeExtensions.cpp commons.cpp
  EXEC=kissnp2
-@@ -41,7 +44,7 @@ OBJ= $(SRC:.cpp=.o)
+@@ -41,7 +44,7 @@
  all: $(EXEC)
  
  ifeq ($(prof),1)
@@ -29,7 +27,7 @@
  endif
  ifeq ($(deb),1)
   CFLAGS+=-O0 -DASSERTS -g -lz 
-@@ -79,7 +82,7 @@ endif
+@@ -79,7 +82,7 @@
  all: $(EXEC)
  
  kissnp2:  $(OBJ) kissnp2.cpp
@@ -38,27 +36,25 @@
  
  %.o: %.cpp %.h
  	$(CC) -o $@ -c $< $(CFLAGS)
-Index: discoSnp/kissreads/Makefile
-===================================================================
 --- discoSnp.orig/kissreads/Makefile
 +++ discoSnp/kissreads/Makefile
-@@ -20,10 +20,13 @@ CC		=gcc
+@@ -20,11 +20,13 @@
  # optimized flags
  
- #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§
--CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
-+#CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+ #CFLAGS=-Wall -O3 -L/../thirdparty/zlib/build/ -lz
+-CFLAGS= -O3  -L../thirdparty/zlib/build/ -lz
 +CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
++# CFLAGS= -O3  -L../thirdparty/zlib/build/ -lz
  CFLAGS+=$(MYFLAGS)
- #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
--LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
-+#LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
  
- ## debug flags
+ #LDFLAGS+=-Wall -lm -O3 -L../thirdparty/zlib/build/ -lz
+-LDFLAGS+= -O3 -lm  -L../thirdparty/zlib/build/ -lz
++#LDFLAGS+= -O3 -lm  -L../thirdparty/zlib/build/ -lz
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
  
-@@ -51,7 +54,7 @@ all: $(ALL)
+ ## debug flags
+ #CFLAGS		+=-Wall -g -lz -fopenmp
+@@ -54,7 +56,7 @@
  	@echo "#################"
  
  kissreads: $(OBJ) 
@@ -67,8 +63,6 @@
  
  
  kissReads.o: $(INCLDIR)coherence_algorithm.h  $(INCLDIR)couple.h $(INCLDIR)extension_algorithm.h $(INCLDIR)fragment_info.h  $(INCLDIR)libchash.h  $(INCLDIR)outputs.h $(INCLDIR)commons.h $(INCLDIR)extending_fragment.h $(INCLDIR)fragment_index.h $(INCLDIR)hash.h $(INCLDIR)list.h $(INCLDIR)tree.h
-Index: discoSnp/minia/makefile
-===================================================================
 --- discoSnp.orig/minia/makefile
 +++ discoSnp/minia/makefile
 @@ -1,4 +1,7 @@
@@ -80,7 +74,7 @@
  SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
  EXEC=minia
  OBJ= $(SRC:.cpp=.o)
-@@ -60,7 +63,7 @@ all:
+@@ -60,7 +63,7 @@
  	$(MAKE) $(EXEC)
  
  minia: $(OBJ) Minia.cpp


