[med-svn] [Git][med-team/mustang][master] 6 commits: use standard variable for the c++ compiler
Andreas Tille
gitlab at salsa.debian.org
Mon Apr 9 20:42:46 BST 2018
Andreas Tille pushed to branch master at Debian Med / mustang
Commits:
f8160baa by Andreas Tille at 2018-04-09T21:29:47+02:00
use standard variable for the c++ compiler
- - - - -
a44f8294 by Andreas Tille at 2018-04-09T21:32:25+02:00
s/CPPFLAGS/CXXFLAGS/
- - - - -
cb5e5e3c by Andreas Tille at 2018-04-09T21:33:00+02:00
Standards-Version: 4.1.4
- - - - -
b0450cee by Andreas Tille at 2018-04-09T21:33:32+02:00
Point Vcs URLs to Salsa
- - - - -
377cad2f by Andreas Tille at 2018-04-09T21:33:53+02:00
debhelper 11
- - - - -
9428c2f9 by Andreas Tille at 2018-04-09T21:42:02+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/compat
- debian/control
- + debian/patches/cross.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,16 @@
+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 at 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/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,10 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at 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
=====================================
--- /dev/null
+++ b/debian/patches/cross.patch
@@ -0,0 +1,135 @@
+Author: Helmut Grohne <helmut at 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
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
03-test_zf-cchh.patch
gcc-4.7.patch
hardening.patch
+cross.patch
View it on GitLab: https://salsa.debian.org/med-team/mustang/compare/ea64524dc9edbc72ca2fb2c1297f80a3a1593d7c...9428c2f93e27609ace6bd220071e459c15acc586
---
View it on GitLab: https://salsa.debian.org/med-team/mustang/compare/ea64524dc9edbc72ca2fb2c1297f80a3a1593d7c...9428c2f93e27609ace6bd220071e459c15acc586
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