[Debian-med-packaging] Bug#667293: mustang: ftbfs with GCC-4.7

[Matthias Klose]

Package: mustang
Version: 3.2.1-1
Severity: important
Tags: sid wheezy
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-4.7

The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.

./src/superpose_on_core_2.cpp:578:9: error: 'sleep' was not declared in this scope

The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/mustang_3.2.1-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.

Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html

To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

[...]
g++  -traditional -Wall -O3  -c ./src/pdb_ripper_2.cpp -o ./obj/pdb_ripper.o
./src/pdb_ripper_2.cpp: In function 'int CHECK_NCHAINS_IN_PDB(char*)':
./src/pdb_ripper_2.cpp:53:6: warning: variable 'chain_id' set but not used [-Wunused-but-set-variable]
g++  -traditional -Wall -O3  -c ./src/merge_global_local_libs.cpp -o ./obj/merge_global_local_libs.o
g++  -traditional -Wall -O3  -c ./src/ew_2.cpp -o ./obj/ew.o
./src/ew_2.cpp: In function 'void CALCULATE_EDGE_WEIGHTS(int, int, float***)':
./src/ew_2.cpp:217:29: warning: variable 'prev_ROTMAT' set but not used [-Wunused-but-set-variable]
./src/ew_2.cpp:218:51: warning: variable 'prev_CM_S' set but not used [-Wunused-but-set-variable]
./src/ew_2.cpp:218:67: warning: variable 'prev_CM_M' set but not used [-Wunused-but-set-variable]
g++  -traditional -Wall -O3  -c ./src/refine_pairalgn_2.cpp -o ./obj/refine_pairalgn.o
g++  -traditional -Wall -O3  -c ./src/superpose_weightedRMS.cpp -o ./obj/superpose_weightedRMS.o
g++  -traditional -Wall -O3  -c ./src/superpose_2.cpp -o ./obj/superpose_2.o
g++  -traditional -Wall -O3  -c ./src/jacobi.cpp -o ./obj/jacobi.o
g++  -traditional -Wall -O3  -c ./src/3D_manip_functions.cpp -o ./obj/3D_manip_functions.o
./src/3D_manip_functions.cpp: In function 'void coordinate_transformer(float (*)[500], float (*)[500], int, int, int, int)':
./src/3D_manip_functions.cpp:210:9: warning: variable 'AX' set but not used [-Wunused-but-set-variable]
g++  -traditional -Wall -O3  -c ./src/extended_lib_gen_3.cpp -o ./obj/extended_lib_gen.o
./src/extended_lib_gen_3.cpp: In function 'void EXTENDED_LIBRARY_GENERATION()':
./src/extended_lib_gen_3.cpp:219:20: warning: variable 'AAA' set but not used [-Wunused-but-set-variable]
g++  -traditional -Wall -O3  -c ./src/progress_align_3.cpp -o ./obj/progress_align.o
g++  -traditional -Wall -O3  -c ./src/neighbour_joining.cpp -o ./obj/neighbour_joining.o
g++  -traditional -Wall -O3  -c ./src/upgma.cpp -o ./obj/upgma.o
g++  -traditional -Wall -O3  -c ./src/superpose_on_core_2.cpp -o ./obj/superpose_on_core.o
./src/superpose_on_core_2.cpp: In function 'void SUPERPOSE_ON_CORE(char**)':
./src/superpose_on_core_2.cpp:578:9: error: 'sleep' was not declared in this scope
make[1]: *** [obj/superpose_on_core.o] Error 1
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build: make -j1 returned exit code 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2