Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1032 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0e5b89e0ea0d69ebfdb74ba3bbf29518f7ce5ce8

14 files changed, 116 insertions, 186 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 93e72dd2..dc6de64d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,66 +2,78 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHIdev)
 
 include(CMakeGUDHIVersion.txt)
-
-if (NOT CMAKE_BUILD_TYPE)
- # Set default build type to Release
- set(CMAKE_BUILD_TYPE "Release")
-endif()
-
-enable_testing()
-
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}")
-
 # Generate GUDHI official version file
 configure_file(GUDHIVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIVersion.cmake" @ONLY)
 
 find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer program_options thread REQUIRED)
 
-if(MSVC)
-  # Turn off some VC++ warnings
-  SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
+if(NOT Boost_FOUND)
+  message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
 else()
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O1")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
-endif()
 
-set(Boost_USE_STATIC_LIBS        ON)
-set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME    OFF)
+  set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
+  set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
+  message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}")
+  message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}")
 
-find_package(GMP)
-if(GMP_FOUND)
-	find_package(GMPXX)
-endif()
+  enable_testing()
 
-find_package(CGAL)
+  find_package(GMP)
+  if(GMP_FOUND)
+    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+    find_package(GMPXX)
+    if(GMPXX_FOUND)
+      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+    endif()
+  endif()
 
-# Find TBB package for parallel sort - not mandatory, just optional.
-set(TBB_FIND_QUIETLY ON)
-find_package(TBB)
+  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
+  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+  # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
+  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+  # but it implies to use cmake version 3.1 at least.
+  find_package(CGAL)
+  if(CGAL_FOUND)
+    include( ${CGAL_USE_FILE} )
+  endif()
+  
+  if(MSVC)
+    # Turn off some VC++ warnings
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
+  else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -Wpedantic -Wsign-compare")
+  endif()
 
-# Required programs for unitary tests purpose
-FIND_PROGRAM( GCOVR_PATH gcovr )
-if (GCOVR_PATH)
-  message("gcovr found in ${GCOVR_PATH}")
-endif()
-# Required programs for unitary tests purpose
-FIND_PROGRAM( GPROF_PATH gprof )
-if (GPROF_PATH)
-  message("gprof found in ${GPROF_PATH}")
-endif()
+  if(CMAKE_BUILD_TYPE MATCHES Debug)
+    message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+  else()
+    message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+  endif()
 
+  set(Boost_USE_STATIC_LIBS        ON)
+  set(Boost_USE_MULTITHREADED      ON)
+  set(Boost_USE_STATIC_RUNTIME    OFF)
+
+  # Find TBB package for parallel sort - not mandatory, just optional.
+  set(TBB_FIND_QUIETLY ON)
+  find_package(TBB)
+
+  # Required programs for unitary tests purpose
+  FIND_PROGRAM( GCOVR_PATH gcovr )
+  if (GCOVR_PATH)
+    message("gcovr found in ${GCOVR_PATH}")
+  endif()
+  # Required programs for unitary tests purpose
+  FIND_PROGRAM( GPROF_PATH gprof )
+  if (GPROF_PATH)
+    message("gprof found in ${GPROF_PATH}")
+  endif()
 FIND_PROGRAM( DIFF_PATH diff )
 if (DIFF_PATH)
   message("diff found in ${DIFF_PATH}")
 endif()
 
-
-if(NOT Boost_FOUND)
-  message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
-else()
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
   # BOOST ISSUE with Libraries name resolution under Windows
diff --git a/data/points/generator/CMakeLists.txt b/data/points/generator/CMakeLists.txt
index 26b44446..c01a380d 100644
--- a/data/points/generator/CMakeLists.txt
+++ b/data/points/generator/CMakeLists.txt
@@ -5,22 +5,6 @@ if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
     message(STATUS "CGAL version: ${CGAL_VERSION}.")
 
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
-
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
       include( ${EIGEN3_USE_FILE} )
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index d93dd436..e904133b 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -7,22 +7,6 @@ if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     message(STATUS "CGAL version: ${CGAL_VERSION}.")
 
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
- 
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
       message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index 52ec0a78..2e5d6c3d 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -1,28 +1,21 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIAlphaComplexTest)
 
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
 # need CGAL 4.7
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
     message(STATUS "CGAL version: ${CGAL_VERSION}.")
 
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
- 
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
       message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt
index 3dfd80cd..ad63c080 100644
--- a/src/Bottleneck/test/CMakeLists.txt
+++ b/src/Bottleneck/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIBottleneckUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( BottleneckUT bottleneck_unit_test.cpp )
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 962afeb2..21554729 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -3,41 +3,57 @@ project(GUDHI)
 
 include("CMakeGUDHIVersion.txt")
 
-if (NOT CMAKE_BUILD_TYPE)
- # Set default build type to Release
- set(CMAKE_BUILD_TYPE "Release")
-endif()
-
 enable_testing()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
 find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer REQUIRED)
 
-if(MSVC)
-  SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
+if(NOT Boost_FOUND)
+  message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
 else()
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-endif()
 
-set(Boost_USE_STATIC_LIBS        ON)
-set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME    OFF)
+  find_package(GMP)
+  if(GMP_FOUND)
+    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+    find_package(GMPXX)
+    if(GMPXX_FOUND)
+      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+    endif()
+  endif()
 
-find_package(GMP)
-if(GMP_FOUND)
-  find_package(GMPXX)
-endif()
+  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
+  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+  # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
+  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+  # but it implies to use cmake version 3.1 at least.
+  find_package(CGAL)
+  if(CGAL_FOUND)
+    include( ${CGAL_USE_FILE} )
+  endif()
+  
+  if(MSVC)
+    # Turn off some VC++ warnings
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
+  else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -Wpedantic -Wsign-compare")
+  endif()
 
-find_package(CGAL)
+  if(CMAKE_BUILD_TYPE MATCHES Debug)
+    message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+  else()
+    message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+  endif()
 
-# Find TBB package for parallel sort - not mandatory, just optional.
-set(TBB_FIND_QUIETLY ON)
-find_package(TBB)
+  set(Boost_USE_STATIC_LIBS        ON)
+  set(Boost_USE_MULTITHREADED      ON)
+  set(Boost_USE_STATIC_RUNTIME    OFF)
+
+  # Find TBB package for parallel sort - not mandatory, just optional.
+  set(TBB_FIND_QUIETLY ON)
+  find_package(TBB)
 
-if(NOT Boost_FOUND)
-  message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
-else()
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
   # BOOST ISSUE with Libraries name resolution under Windows
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 24cb0be1..d58d0bd4 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,7 +1,6 @@
 cmake_minimum_required(VERSION 2.8)
 project(GudhUI)
 
-find_package(CGAL  COMPONENTS Qt4)
 find_package(Qt4)
 find_package(QGLViewer)
 find_package(OpenGL)
@@ -14,27 +13,8 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   SET(Boost_USE_STATIC_LIBS ON)
   SET(Boost_USE_MULTITHREAD OFF)
 
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-  
   include(${QT_USE_FILE})
 
-  include(${CGAL_USE_FILE})
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to add "-std=c++11" again.
-  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-  # but it implies to use cmake version 3.1 at least.
-  if(NOT MSVC)
-    include(CheckCXXCompilerFlag)
-    CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-    if(COMPILER_SUPPORTS_CXX11)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    endif()
-  endif()
-  # - End of workaround
-
   include_directories (${QGLVIEWER_INCLUDE_DIR})
   include_directories(.)	
  
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index ed63a6ac..d16be5be 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIPersistentCohomologyUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index c70cfe35..200161a6 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -14,11 +14,7 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
-   message("CGAL_lib = ${CGAL_LIBRARIES_DIR}")
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-   INCLUDE_DIRECTORIES(${CGAL_INCLUDE_DIRS})
-   add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
-   target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-   add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
+  add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
+  target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+  add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
 endif()
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index c9eae163..1f2f7d33 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHISimplexTreeUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt
index 8b6fb672..5e063845 100644
--- a/src/Skeleton_blocker/test/CMakeLists.txt
+++ b/src/Skeleton_blocker/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIskbl)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable(TestSkeletonBlockerComplex TestSkeletonBlockerComplex.cpp)
diff --git a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
index b8b1a0d1..2a3f0501 100644
--- a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
+++ b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
@@ -601,7 +601,7 @@ bool test_link4() {
 }
 
 bool test_link5() {
-  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+  Complex complex(0);
   // Build the complexes
   build_complete(4, complex);
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
@@ -621,7 +621,7 @@ bool test_link5() {
 }
 
 bool test_link6() {
-  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+  Complex complex(0);
   // Build the complexes
   build_complete(4, complex);
   complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
@@ -642,7 +642,7 @@ bool test_link6() {
 }
 
 bool test_link7() {
-  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+  Complex complex(0);
   // Build the complexes
   build_complete(6, complex);
   complex.add_vertex();
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index d29e31e7..6c2e7669 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -4,24 +4,6 @@ project(GUDHIDelaunayTriangulationOffFileReadWrite)
 # need CGAL 4.6
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
- 
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
       message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
index a395338e..50655a93 100644
--- a/src/common/test/CMakeLists.txt
+++ b/src/common/test/CMakeLists.txt
@@ -1,19 +1,18 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIDelaunayTriangulationOffFileReadWriteUT)
 
-if(NOT MSVC)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage")
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
 # need CGAL 4.6
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
- 
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
       message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")