[med-svn] r17770 - in trunk/packages/mapsembler2/trunk/debian: . patches

Olivier Sallou osallou at moszumanska.debian.org
Mon Aug 18 17:11:41 UTC 2014 

Author: osallou
Date: 2014-08-18 17:11:41 +0000 (Mon, 18 Aug 2014)
New Revision: 17770

Added:
   trunk/packages/mapsembler2/trunk/debian/patches/add_hardening
Modified:
   trunk/packages/mapsembler2/trunk/debian/copyright
   trunk/packages/mapsembler2/trunk/debian/docs
   trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
   trunk/packages/mapsembler2/trunk/debian/patches/series
   trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs
   trunk/packages/mapsembler2/trunk/debian/rules
Log:
add patch for debian hardening, update copyright

Modified: trunk/packages/mapsembler2/trunk/debian/copyright
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/copyright	2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/copyright	2014-08-18 17:11:41 UTC (rev 17770)
@@ -6,6 +6,7 @@
     results_visualization
     mapsembler2_extremities/thirdparty/gatb-core/thirdparty/boost
     mapsembler2_extremities/thirdparty/gatb-core/thirdparty/hdf5
+    mapsembler2_extremities/thirdparty/gatb-core/doc/design
 
 Files: mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/*
 Copyright: 2013 Giuseppe Ottaviano <giuott at gmail.com>
@@ -55,8 +56,26 @@
 Files: minia/*
 Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
            2012 Guillaume Rizk
-License: CeCILL
+License: AGPL-3+
 
+Files: mapsembler2_extremities/thirdparty/gatb-core/*
+Copyright: 2014 INRIA R.Chikhi, G.Rizk, E.Drezen
+Licence: AGPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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 Affero General Public License for more details.
+ You should have received a copy of the GNU Affero General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ .
+ The complete text of the GNU Affero General Public License
+ can be found in the file `/usr/share/doc/mapsembler2/LICENCE.md.gz'.
+
 Files: *
 Copyright: 2013 INRIA / IRISA
 License: AGPL-3+

Modified: trunk/packages/mapsembler2/trunk/debian/docs
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/docs	2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/docs	2014-08-18 17:11:41 UTC (rev 17770)
@@ -1 +0,0 @@
-LICENCE.md

Modified: trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages	2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages	2014-08-18 17:11:41 UTC (rev 17770)
@@ -1,5 +1,5 @@
 mapsembler2_extremities.1
-mapsembler2_extend.1
+mapsembler_extend.1
 kissreads.1
 kissreads_graph.1
 

Added: trunk/packages/mapsembler2/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/add_hardening	                        (rev 0)
+++ trunk/packages/mapsembler2/trunk/debian/patches/add_hardening	2014-08-18 17:11:41 UTC (rev 17770)
@@ -0,0 +1,67 @@
+Index: mapsembler2_pipeline/kissreads/Makefile
+===================================================================
+--- mapsembler2_pipeline.orig/kissreads/Makefile
++++ mapsembler2_pipeline/kissreads/Makefile
+@@ -20,11 +20,15 @@ CC		=gcc
+ # 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 #@!
+ CFLAGS+=$(MYFLAGS)
+ #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+ LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+ 
++CPPFLAGS += $(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
++
+ ## debug flags
+ 
+ 
+Index: mapsembler2_pipeline/kissreads_graph/makefile
+===================================================================
+--- mapsembler2_pipeline.orig/kissreads_graph/makefile
++++ mapsembler2_pipeline/kissreads_graph/makefile
+@@ -4,6 +4,9 @@ EXEC=kissreads_graph
+ #Loader.cpp CFLAGS=  -g -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER
+ #Loader.cpp 
+ CFLAGS=  -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+ #CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER
+ SRC=block_allocator.cpp  DeBruijnGraph.cpp  Fragment.cpp  json.cpp  read_coherence_mapsembler/libchash.cpp     read_coherence_mapsembler/couple.cpp  read_coherence_mapsembler/misc_tools.cpp  read_coherence_mapsembler/read_groups.cpp read_coherence_mapsembler/consensus_common.cpp  read_coherence_mapsembler/list.cpp    read_coherence_mapsembler/read_coherence.cpp  read_coherence_mapsembler/interface_libchash.cpp commons.cpp ../minia/Kmer.cpp ../minia/Bank.cpp Loader.cpp ReadMapper.cpp
+ OBJ= $(SRC:.cpp=.o) 
+@@ -48,7 +51,7 @@ endif
+ all: $(EXEC)
+ 
+ kissreads_graph:  $(OBJ) KissReadsGraph.cpp
+-	$(CC) -o $@ $^ $(CFLAGS)
++	$(CC) -o $@ $^ $(CFLAGS)  $(LDFLAGS)
+ 
+ %.o: %.cpp %.h
+ 	$(CC) -lz -o $@ -c $< $(CFLAGS)
+Index: mapsembler2_pipeline/mapsembler2_extend/makefile
+===================================================================
+--- mapsembler2_pipeline.orig/mapsembler2_extend/makefile
++++ mapsembler2_pipeline/mapsembler2_extend/makefile
+@@ -3,6 +3,9 @@ EXEC=mapsembler_extend
+ #CFLAGS=  -O4 -lz --std=gnu++0x
+ #CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER
+ CFLAGS=  -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+ #CFLAGS=  -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER
+ #CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER
+ 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 commons.cpp IterativeExtensions.cpp Fragment_Bank.cpp Fragment.cpp GraphOutput.cpp  
+@@ -49,7 +52,7 @@ all: $(EXEC)
+ 
+ mapsembler_extend:  $(OBJ) $(OBJ2) mapsembler_extend.cpp
+ #mapsembler:  $(OBJ) $(OBJ2) test.cpp
+-	$(CC) -o $@ $^ $(CFLAGS) 
++	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+ 
+ %.o: %.cpp %.h 
+ 	$(CC) -lz -o $@ -c $< $(CFLAGS)

Modified: trunk/packages/mapsembler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/series	2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/patches/series	2014-08-18 17:11:41 UTC (rev 17770)
@@ -1 +1,2 @@
 use_debian_libs
+add_hardening

Modified: trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs	2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs	2014-08-18 17:11:41 UTC (rev 17770)
@@ -1,3 +1,8 @@
+Subject: use HDF5 lib in Debian
+Description: use Debian libs instead of embedded one
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-08-18
+Forwarded: no
 Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
 ===================================================================
 --- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt

Modified: trunk/packages/mapsembler2/trunk/debian/rules
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/rules	2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/rules	2014-08-18 17:11:41 UTC (rev 17770)
@@ -26,14 +26,14 @@
 	cd kissreads && make clean
 
 	rm -f mapsembler2_extremities.1
-	rm -f mapsembler2_extend.1
+	rm -f mapsembler_extend.1
 	rm -f kissreads.1
 	rm -f kissreads_graph.1
 	dh_clean
 
 override_dh_install:
 	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extremities/build/mapsembler2_extremities > mapsembler2_extremities.1
-	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend > mapsembler2_extend.1
+	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend > mapsembler_extend.1
 	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads/kissreads > kissreads.1
 	help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads_graph/kissreads_graph > kissreads_graph.1
 	dh_install

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