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debian/changelog
View file @ 9428c2f9
mustang (3.2.3-3) unstable; urgency=medium
[ Helmut Grohne ]
* use standard variable for the c++ compiler
Closes: #895299
[ Andreas Tille ]
* Standards-Version: 4.1.4
* Point Vcs URLs to Salsa
* debhelper 11
-- Andreas Tille <tille@debian.org> Mon, 09 Apr 2018 21:33:59 +0200
mustang (3.2.3-2) unstable; urgency=medium
* Moved packaging from SVN to Git
......
debian/control
View file @ 9428c2f9
......@@ -3,10 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10)
Standards-Version: 4.1.1
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mustang.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/mustang.git
Build-Depends: debhelper (>= 11~)
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/mustang
Vcs-Git: https://salsa.debian.org/med-team/mustang.git
Homepage: http://lcb.infotech.monash.edu.au/mustang/
Package: mustang
......
debian/patches/cross.patch 0 → 100644
View file @ 9428c2f9
Author: Helmut Grohne <helmut@subdivi.de>
Last-Update: Mon, 9 Apr 2018 16:07:04 +0200
Bug-Debian: https://bugs.debian.org/895299
Description: use standard variable for the c++ compiler
.
As advises in the bug log the patch includes the suggested
s/CPPFLAGS/CXXFLAGS/
--- a/Makefile
+++ b/Makefile
@@ -11,11 +11,11 @@ OBJ = $(MUSTANG)/obj
BIN = $(MUSTANG)/bin
#compiler options
-CPP = g++
+CXX = g++
CPPFLAGS = -traditional -Wall -O3
LDFLAGS := $(LDFLAGS)
.cpp.o:
- $(CPP) $(CPPFLAGS) -c -o $@ $<
+ $(CXX) $(CXXFLAGS) -c -o $@ $<
#macros
OBJECTS = $(OBJ)/globals.o $(OBJ)/CmdLineParser.o $(OBJ)/distmat.o $(OBJ)/sse_RK.o \
@@ -36,86 +36,86 @@ all: $(ALL)
#------------------------------------------------------------------------------
$(BIN)/mustang-3.2.3: $(OBJECTS)
- $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS)
$(OBJ)/globals.o: $(SRC)/globals.h $(SRC)/macros.h $(SRC)/globals.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/globals.cpp -o $(OBJ)/globals.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/globals.cpp -o $(OBJ)/globals.o
$(OBJ)/CmdLineParser.o: $(SRC)/CmdLineParser.h $(SRC)/macros.h $(SRC)/globals.h $(SRC)/de_alloc_routines.h $(SRC)/CmdLineParser_2.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/CmdLineParser_2.cpp -o $(OBJ)/CmdLineParser.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/CmdLineParser_2.cpp -o $(OBJ)/CmdLineParser.o
$(OBJ)/pdb_ripper.o: $(SRC)/pdb_ripper.h $(SRC)/macros.h $(SRC)/globals.h $(SRC)/alloc_routines.h $(SRC)/init_routines.h $(SRC)/pdb_ripper_2.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/pdb_ripper_2.cpp -o $(OBJ)/pdb_ripper.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/pdb_ripper_2.cpp -o $(OBJ)/pdb_ripper.o
$(OBJ)/read_structures.o: $(SRC)/read_structures.h $(SRC)/macros.h $(SRC)/globals.h $(SRC)/pdb_ripper.h $(SRC)/alloc_routines.h $(SRC)/init_routines.h $(SRC)/de_alloc_routines.h $(SRC)/read_structures.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/read_structures.cpp -o $(OBJ)/read_structures.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/read_structures.cpp -o $(OBJ)/read_structures.o
$(OBJ)/3D_manip_functions.o: $(SRC)/3D_manip_functions.h $(SRC)/3D_manip_functions.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/3D_manip_functions.cpp -o $(OBJ)/3D_manip_functions.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/3D_manip_functions.cpp -o $(OBJ)/3D_manip_functions.o
$(OBJ)/distmat.o: $(SRC)/macros.h $(SRC)/globals.h $(SRC)/distmat.h $(SRC)/distmat.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/distmat.cpp -o $(OBJ)/distmat.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/distmat.cpp -o $(OBJ)/distmat.o
$(OBJ)/sse_RK.o: $(SRC)/macros.h $(SRC)/globals.h $(SRC)/sse_RK.h $(SRC)/sse_RK.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/sse_RK.cpp -o $(OBJ)/sse_RK.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/sse_RK.cpp -o $(OBJ)/sse_RK.o
$(OBJ)/primary_lib_gen.o: $(SRC)/macros.h $(SRC)/primary_lib_gen.h $(SRC)/globals.h \
$(SRC)/pairwise_global_structalgn.h $(SRC)/primary_lib_gen.cpp \
$(SRC)/merge_global_local_libs.h
- $(CPP) $(CPPFLAGS) -c $(SRC)/primary_lib_gen.cpp -o $(OBJ)/primary_lib_gen.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/primary_lib_gen.cpp -o $(OBJ)/primary_lib_gen.o
$(OBJ)/pairwise_global_structalgn.o: $(SRC)/macros.h $(SRC)/globals.h $(SRC)/pairwise_global_structalgn.h \
$(SRC)/ew.h $(SRC)/refine_pairalgn.h \
$(SRC)/pairwise_global_structalgn.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/pairwise_global_structalgn.cpp -o $(OBJ)/pairwise_global_structalgn.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/pairwise_global_structalgn.cpp -o $(OBJ)/pairwise_global_structalgn.o
$(OBJ)/refine_pairalgn.o: $(SRC)/macros.h $(SRC)/globals.h $(SRC)/refine_pairalgn.h \
$(SRC)/de_alloc_routines.h $(SRC)/superpose_2.h \
$(SRC)/refine_pairalgn_2.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/refine_pairalgn_2.cpp -o $(OBJ)/refine_pairalgn.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/refine_pairalgn_2.cpp -o $(OBJ)/refine_pairalgn.o
$(OBJ)/superpose_2.o: $(SRC)/jacobi.h $(SRC)/macros.h $(SRC)/superpose_2.h $(SRC)/superpose_2.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/superpose_2.cpp -o $(OBJ)/superpose_2.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/superpose_2.cpp -o $(OBJ)/superpose_2.o
$(OBJ)/superpose_weightedRMS.o: $(SRC)/jacobi.h $(SRC)/macros.h $(SRC)/superpose_weightedRMS.h $(SRC)/superpose_weightedRMS.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/superpose_weightedRMS.cpp -o $(OBJ)/superpose_weightedRMS.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/superpose_weightedRMS.cpp -o $(OBJ)/superpose_weightedRMS.o
$(OBJ)/jacobi.o: $(SRC)/jacobi.h $(SRC)/jacobi.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/jacobi.cpp -o $(OBJ)/jacobi.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/jacobi.cpp -o $(OBJ)/jacobi.o
$(OBJ)/ew.o: $(SRC)/globals.h $(SRC)/ew.h $(SRC)/superpose_2.h $(SRC)/superpose_weightedRMS.h \
$(SRC)/ew_2.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/ew_2.cpp -o $(OBJ)/ew.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/ew_2.cpp -o $(OBJ)/ew.o
$(OBJ)/merge_global_local_libs.o: $(SRC)/merge_global_local_libs.h $(SRC)/macros.h $(SRC)/globals.h \
$(SRC)/merge_global_local_libs.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/merge_global_local_libs.cpp -o $(OBJ)/merge_global_local_libs.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/merge_global_local_libs.cpp -o $(OBJ)/merge_global_local_libs.o
$(OBJ)/extended_lib_gen.o: $(SRC)/extended_lib_gen.h $(SRC)/globals.h $(SRC)/macros.h $(SRC)/extended_lib_gen_3.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/extended_lib_gen_3.cpp -o $(OBJ)/extended_lib_gen.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/extended_lib_gen_3.cpp -o $(OBJ)/extended_lib_gen.o
$(OBJ)/progress_align.o: $(SRC)/progress_align.h $(SRC)/globals.h $(SRC)/macros.h \
$(SRC)/neighbour_joining.h $(SRC)/progress_align_3.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/progress_align_3.cpp -o $(OBJ)/progress_align.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/progress_align_3.cpp -o $(OBJ)/progress_align.o
$(OBJ)/neighbour_joining.o: $(SRC)/globals.h $(SRC)/neighbour_joining.h $(SRC)/neighbour_joining.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/neighbour_joining.cpp -o $(OBJ)/neighbour_joining.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/neighbour_joining.cpp -o $(OBJ)/neighbour_joining.o
$(OBJ)/upgma.o: $(SRC)/globals.h $(SRC)/upgma.h $(SRC)/upgma.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/upgma.cpp -o $(OBJ)/upgma.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/upgma.cpp -o $(OBJ)/upgma.o
$(OBJ)/superpose_on_core.o: $(SRC)/superpose_on_core.h $(SRC)/superpose_2.h $(SRC)/macros.h $(SRC)/globals.h $(SRC)/alloc_routines.h $(SRC)/init_routines.h $(SRC)/de_alloc_routines.h $(SRC)/read_structures.h $(SRC)/superpose_on_core_2.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/superpose_on_core_2.cpp -o $(OBJ)/superpose_on_core.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/superpose_on_core_2.cpp -o $(OBJ)/superpose_on_core.o
$(OBJ)/multiple_superposition.o: $(SRC)/multiple_superposition.h $(SRC)/jacobi.h $(SRC)/alloc_routines.h $(SRC)/multiple_superposition.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/multiple_superposition.cpp -o $(OBJ)/multiple_superposition.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/multiple_superposition.cpp -o $(OBJ)/multiple_superposition.o
$(OBJ)/output_algn.o: $(SRC)/output_algn.h $(SRC)/macros.h $(SRC)/globals.h $(SRC)/output_algn.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/output_algn.cpp -o $(OBJ)/output_algn.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/output_algn.cpp -o $(OBJ)/output_algn.o
$(OBJ)/main.o: $(SRC)/macros.h $(SRC)/globals.h $(SRC)/distmat.h $(SRC)/sse_RK.h $(SRC)/primary_lib_gen.h $(SRC)/main.cpp
- $(CPP) $(CPPFLAGS) -c $(SRC)/main.cpp -o $(OBJ)/main.o
+ $(CXX) $(CXXFLAGS) -c $(SRC)/main.cpp -o $(OBJ)/main.o
#------------------------------------------------------------------------------
clean:
debian/patches/series
View file @ 9428c2f9
03-test_zf-cchh.patch
gcc-4.7.patch
hardening.patch
cross.patch