Your message dated Mon, 09 Apr 2018 21:43:48 +0000
with message-id <e1f5ezo-0005uj...@fasolo.debian.org>
and subject line Bug#895299: fixed in mustang 3.2.3-3
has caused the Debian Bug report #895299,
regarding mustang FTCBFS: uses a non-standard variable for the c++ compiler
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
895299: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895299
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: mustang
Version: 3.2.3-2
Tags: patch upstream
User: helm...@debian.org
Usertags: rebootstrap
mustang uses the CPP variable for storing the C++ compiler. This
variable is usually used for the C preprocessor. Thus dh_auto_build
doesn't supply a cross compiler there. After renaming it to the more
common CXX, mustang cross builds successfully. Please consider also
renaming CPPFLAGS to CXXFLAGS in addition to applying the attached
patch.
Helmut
Index: mustang-3.2.3/Makefile
===================================================================
--- mustang-3.2.3.orig/Makefile
+++ mustang-3.2.3/Makefile
@@ -11,11 +11,11 @@
BIN = $(MUSTANG)/bin
#compiler options
-CPP = g++
+CXX = g++
CPPFLAGS = -traditional -Wall -O3
LDFLAGS := $(LDFLAGS)
.cpp.o:
- $(CPP) $(CPPFLAGS) -c -o $@ $<
+ $(CXX) $(CPPFLAGS) -c -o $@ $<
#macros
OBJECTS = $(OBJ)/globals.o $(OBJ)/CmdLineParser.o $(OBJ)/distmat.o $(OBJ)/sse_RK.o \
@@ -36,86 +36,86 @@
#------------------------------------------------------------------------------
$(BIN)/mustang-3.2.3: $(OBJECTS)
- $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS)
+ $(CXX) $(CPPFLAGS) $(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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -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) $(CPPFLAGS) -c $(SRC)/main.cpp -o $(OBJ)/main.o
#------------------------------------------------------------------------------
clean:
--- End Message ---
--- Begin Message ---
Source: mustang
Source-Version: 3.2.3-3
We believe that the bug you reported is fixed in the latest version of
mustang, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 895...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated mustang package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 09 Apr 2018 21:33:59 +0200
Source: mustang
Binary: mustang mustang-testdata
Architecture: source
Version: 3.2.3-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
mustang - multiple structural alignment of proteins
mustang-testdata - multiple structural alignment of proteins, test data
Closes: 895299
Changes:
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
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