deal.II build error

out.txt

[*] Setting-up deal.II...

-- This is CMake 3.5.2
CMake Warning (dev) in cmake/macros/macro_deal_ii_invoke_autopilot.cmake:
  Syntax Warning in cmake code at

    /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake:70:47

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMakeLists.txt:48 (INCLUDE)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in cmake/macros/macro_deal_ii_invoke_autopilot.cmake:
  Syntax Warning in cmake code at

    /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake:70:48

  Argument not separated from preceding token by whitespace.
Call Stack (most recent call first):
  CMakeLists.txt:48 (INCLUDE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- The CXX compiler identification is GNU 6.1.1
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The C compiler identification is GNU 6.1.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- The Fortran compiler identification is GNU 6.1.1
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- 
-- Performing Test DEAL_II_HAVE_USABLE_CXX_FLAGS
-- Performing Test DEAL_II_HAVE_USABLE_CXX_FLAGS - Success
-- 
-- Set up default compiler flags.
-- Performing Test DEAL_II_HAVE_FLAG_pedantic
-- Performing Test DEAL_II_HAVE_FLAG_pedantic - Success
-- Performing Test DEAL_II_HAVE_FLAG_fpic
-- Performing Test DEAL_II_HAVE_FLAG_fpic - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wl__as-needed
-- Performing Test DEAL_II_HAVE_FLAG_Wl__as-needed - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wall
-- Performing Test DEAL_II_HAVE_FLAG_Wall - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wpointer-arith
-- Performing Test DEAL_II_HAVE_FLAG_Wpointer-arith - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wwrite-strings
-- Performing Test DEAL_II_HAVE_FLAG_Wwrite-strings - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wsynth
-- Performing Test DEAL_II_HAVE_FLAG_Wsynth - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wsign-compare
-- Performing Test DEAL_II_HAVE_FLAG_Wsign-compare - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wswitch
-- Performing Test DEAL_II_HAVE_FLAG_Wswitch - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wno-unused-local-typedefs
-- Performing Test DEAL_II_HAVE_FLAG_Wno-unused-local-typedefs - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wno-deprecated
-- Performing Test DEAL_II_HAVE_FLAG_Wno-deprecated - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wno-deprecated-declarations
-- Performing Test DEAL_II_HAVE_FLAG_Wno-deprecated-declarations - Success
-- Performing Test DEAL_II_HAVE_FLAG_funroll-loops
-- Performing Test DEAL_II_HAVE_FLAG_funroll-loops - Success
-- Performing Test DEAL_II_HAVE_FLAG_funroll-all-loops
-- Performing Test DEAL_II_HAVE_FLAG_funroll-all-loops - Success
-- Performing Test DEAL_II_HAVE_FLAG_fstrict-aliasing
-- Performing Test DEAL_II_HAVE_FLAG_fstrict-aliasing - Success
-- Performing Test DEAL_II_HAVE_FLAG_felide-constructors
-- Performing Test DEAL_II_HAVE_FLAG_felide-constructors - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wno-unused
-- Performing Test DEAL_II_HAVE_FLAG_Wno-unused - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wno-sign-compare
-- Performing Test DEAL_II_HAVE_FLAG_Wno-sign-compare - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wno-write-strings
-- Performing Test DEAL_II_HAVE_FLAG_Wno-write-strings - Success
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/checks/check_01_compiler_features.cmake
-- Performing Test DEAL_II_COMPILER_USE_VECTOR_ARITHMETICS
-- Performing Test DEAL_II_COMPILER_USE_VECTOR_ARITHMETICS - Success
-- Performing Test DEAL_II_VECTOR_ITERATOR_IS_POINTER_OK
-- Performing Test DEAL_II_VECTOR_ITERATOR_IS_POINTER_OK - Success
-- Test successful, do not define DEAL_II_VECTOR_ITERATOR_IS_POINTER
-- Performing Test HAVE_BUILTIN_EXPECT
-- Performing Test HAVE_BUILTIN_EXPECT - Success
-- Performing Test HAVE_VERBOSE_TERMINATE
-- Performing Test HAVE_VERBOSE_TERMINATE - Success
-- Performing Test HAVE_GLIBC_STACKTRACE
-- Performing Test HAVE_GLIBC_STACKTRACE - Success
-- Performing Test DEAL_II_HAVE_FLAG_rdynamic
-- Performing Test DEAL_II_HAVE_FLAG_rdynamic - Success
-- Performing Test HAVE_LIBSTDCXX_DEMANGLER
-- Performing Test HAVE_LIBSTDCXX_DEMANGLER - Success
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_PRETTY_FUNCTION
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_PRETTY_FUNCTION - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wa__compress-debug-sections
-- Performing Test DEAL_II_HAVE_FLAG_Wa__compress-debug-sections - Success
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED - Success
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/checks/check_01_cpu_features.cmake
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Performing Test DEAL_II_HAVE_SSE2
-- Performing Test DEAL_II_HAVE_SSE2 - Success
-- Performing Test DEAL_II_HAVE_AVX
-- Performing Test DEAL_II_HAVE_AVX - Failed
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/checks/check_01_cxx_features.cmake
-- Performing Test DEAL_II_HAVE_CXX11_FLAG
-- Performing Test DEAL_II_HAVE_CXX11_FLAG - Success
-- Performing Test DEAL_II_HAVE_CXX11_ARRAY
-- Performing Test DEAL_II_HAVE_CXX11_ARRAY - Success
-- Performing Test DEAL_II_HAVE_CXX11_CONDITION_VARIABLE
-- Performing Test DEAL_II_HAVE_CXX11_CONDITION_VARIABLE - Success
-- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL
-- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL - Success
-- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_GCCBUG35569_OK
-- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_GCCBUG35569_OK - Success
-- Performing Test DEAL_II_HAVE_CXX11_SHARED_PTR
-- Performing Test DEAL_II_HAVE_CXX11_SHARED_PTR - Success
-- Performing Test DEAL_II_HAVE_CXX11_THREAD
-- Performing Test DEAL_II_HAVE_CXX11_THREAD - Success
-- Performing Test DEAL_II_HAVE_CXX11_MUTEX
-- Performing Test DEAL_II_HAVE_CXX11_MUTEX - Success
-- Performing Test DEAL_II_HAVE_CXX11_TUPLE
-- Performing Test DEAL_II_HAVE_CXX11_TUPLE - Success
-- Performing Test DEAL_II_HAVE_CXX11_TYPE_TRAITS
-- Performing Test DEAL_II_HAVE_CXX11_TYPE_TRAITS - Success
-- Sufficient C++11 support. Enabling -std=c++11.
-- Performing Test HAVE_ISNAN
-- Performing Test HAVE_ISNAN - Failed
-- Performing Test HAVE_UNDERSCORE_ISNAN
-- Performing Test HAVE_UNDERSCORE_ISNAN - Failed
-- Performing Test DEAL_II_HAVE_ISFINITE
-- Performing Test DEAL_II_HAVE_ISFINITE - Success
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/checks/check_02_system_features.cmake
-- Looking for C++ include sys/resource.h
-- Looking for C++ include sys/resource.h - found
-- Looking for C++ include sys/time.h
-- Looking for C++ include sys/time.h - found
-- Looking for C++ include sys/times.h
-- Looking for C++ include sys/times.h - found
-- Looking for times
-- Looking for times - found
-- Looking for C++ include unistd.h
-- Looking for C++ include unistd.h - found
-- Looking for gethostname
-- Looking for gethostname - found
-- Looking for getpid
-- Looking for getpid - found
-- Looking for rand_r
-- Looking for rand_r - found
-- Looking for jn
-- Looking for jn - found
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/checks/check_03_compiler_bugs.cmake
-- Performing Test DEAL_II_EXPLICIT_DESTRUCTOR_BUG_OK
-- Performing Test DEAL_II_EXPLICIT_DESTRUCTOR_BUG_OK - Success
-- Test successful, do not define DEAL_II_EXPLICIT_DESTRUCTOR_BUG
-- Performing Test DEAL_II_WRETURN_TYPE_CONST_QUALIFIER_BUG_OK
-- Performing Test DEAL_II_WRETURN_TYPE_CONST_QUALIFIER_BUG_OK - Success
-- Test successful, do not define DEAL_II_WRETURN_TYPE_CONST_QUALIFIER_BUG
-- Performing Test DEAL_II_TEMPL_SPEC_FRIEND_BUG_OK
-- Performing Test DEAL_II_TEMPL_SPEC_FRIEND_BUG_OK - Success
-- Test successful, do not define DEAL_II_TEMPL_SPEC_FRIEND_BUG
-- Performing Test DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG_OK
-- Performing Test DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG_OK - Success
-- Test successful, do not define DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG
-- Performing Test DEAL_II_MEMBER_VAR_SPECIALIZATION_BUG_OK
-- Performing Test DEAL_II_MEMBER_VAR_SPECIALIZATION_BUG_OK - Success
-- Test successful, do not define DEAL_II_MEMBER_VAR_SPECIALIZATION_BUG
-- Performing Test DEAL_II_EXPLICIT_CONSTRUCTOR_BUG
-- Performing Test DEAL_II_EXPLICIT_CONSTRUCTOR_BUG - Failed
-- Performing Test DEAL_II_CONST_MEMBER_DEDUCTION_BUG_OK
-- Performing Test DEAL_II_CONST_MEMBER_DEDUCTION_BUG_OK - Success
-- Test successful, do not define DEAL_II_CONST_MEMBER_DEDUCTION_BUG
-- Performing Test DEAL_II_TYPE_QUALIFIER_BUG_OK
-- Performing Test DEAL_II_TYPE_QUALIFIER_BUG_OK - Success
-- Test successful, do not define DEAL_II_TYPE_QUALIFIER_BUG
-- Performing Test DEAL_II_BOOST_BIND_COMPILER_BUG_OK
-- Performing Test DEAL_II_BOOST_BIND_COMPILER_BUG_OK - Failed
-- Test unsuccessful, define DEAL_II_BOOST_BIND_COMPILER_BUG
-- Performing Test DEAL_II_ICC_NUMERICLIMITS_BUG_OK
-- Performing Test DEAL_II_ICC_NUMERICLIMITS_BUG_OK - Success
-- Test successful, do not define DEAL_II_ICC_NUMERICLIMITS_BUG
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_1_lapack.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_1_mpi.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_1_threads.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_1_umfpack.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_2_metis.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_2_petsc.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_2_trilinos.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_arpack.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_boost.cmake
CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1315 (_Boost_MISSING_DEPENDENCIES)
  cmake/macros/macro_find_package.cmake:28 (_FIND_PACKAGE)
  cmake/configure/configure_boost.cmake:54 (FIND_PACKAGE)
  CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 (FEATURE_BOOST_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:72 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:241 (RUN_COMMAND)
  cmake/configure/configure_boost.cmake:121 (CONFIGURE_FEATURE)
  CMakeLists.txt:104 (INCLUDE)


CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1315 (_Boost_MISSING_DEPENDENCIES)
  cmake/macros/macro_find_package.cmake:28 (_FIND_PACKAGE)
  cmake/configure/configure_boost.cmake:54 (FIND_PACKAGE)
  CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 (FEATURE_BOOST_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:72 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:241 (RUN_COMMAND)
  cmake/configure/configure_boost.cmake:121 (CONFIGURE_FEATURE)
  CMakeLists.txt:104 (INCLUDE)


-- Could NOT find Boost
CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1315 (_Boost_MISSING_DEPENDENCIES)
  cmake/macros/macro_find_package.cmake:28 (_FIND_PACKAGE)
  cmake/configure/configure_boost.cmake:63 (FIND_PACKAGE)
  CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 (FEATURE_BOOST_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:72 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:241 (RUN_COMMAND)
  cmake/configure/configure_boost.cmake:121 (CONFIGURE_FEATURE)
  CMakeLists.txt:104 (INCLUDE)


CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1315 (_Boost_MISSING_DEPENDENCIES)
  cmake/macros/macro_find_package.cmake:28 (_FIND_PACKAGE)
  cmake/configure/configure_boost.cmake:63 (FIND_PACKAGE)
  CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 (FEATURE_BOOST_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:72 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:241 (RUN_COMMAND)
  cmake/configure/configure_boost.cmake:121 (CONFIGURE_FEATURE)
  CMakeLists.txt:104 (INCLUDE)


-- Could NOT find Boost
-- DEAL_II_WITH_BOOST has unmet external dependencies.
-- DEAL_II_WITH_BOOST successfully set up with bundled packages.
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_functionparser.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_hdf5.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_mumps.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_netcdf.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_p4est.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_slepc.cmake
-- 
-- Include /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/cmake/configure/configure_zlib.cmake
-- 
-- Configuring done. Proceed to target definitions now.
-- Found Perl: /usr/bin/perl (found version "5.24.0")
-- Could NOT find Doxygen (missing:  DOXYGEN_EXECUTABLE)
CMake Warning (dev) at cmake/config/CMakeLists.txt:74 (GET_TARGET_PROPERTY):
  Policy CMP0026 is not set: Disallow use of the LOCATION target property.
  Run "cmake --help-policy CMP0026" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The LOCATION property should not be read from target "deal_II-daetools".
  Use the target name directly with add_custom_command, or use the generator
  expression $<TARGET_FILE>, as appropriate.

This warning is for project developers.  Use -Wno-dev to suppress it.

###
#
#  deal.II-daetools configuration:
#        CMAKE_BUILD_TYPE:       Release
#        BUILD_SHARED_LIBS:      OFF
#        CMAKE_INSTALL_PREFIX:   /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II/build
#        CMAKE_SOURCE_DIR:       /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II (Version 8.0.0)
#        CMAKE_BINARY_DIR:       /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II
#        CMAKE_CXX_COMPILER:     GNU 6.1.1 on platform Linux x86_64
#                                /usr/bin/c++
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = OFF):
#      ( DEAL_II_WITH_64BIT_INDICES = OFF )
#      ( DEAL_II_WITH_ARPACK = OFF )
#        DEAL_II_WITH_BOOST set up with bundled packages
#      ( DEAL_II_WITH_FUNCTIONPARSER = OFF )
#      ( DEAL_II_WITH_HDF5 = OFF )
#      ( DEAL_II_WITH_LAPACK = OFF )
#      ( DEAL_II_WITH_METIS = OFF )
#      ( DEAL_II_WITH_MPI = OFF )
#      ( DEAL_II_WITH_MUMPS = OFF )
#      ( DEAL_II_WITH_NETCDF = OFF )
#      ( DEAL_II_WITH_P4EST = OFF )
#      ( DEAL_II_WITH_PETSC = OFF )
#      ( DEAL_II_WITH_SLEPC = OFF )
#      ( DEAL_II_WITH_THREADS = OFF )
#      ( DEAL_II_WITH_TRILINOS = OFF )
#      ( DEAL_II_WITH_UMFPACK = OFF )
#      ( DEAL_II_WITH_ZLIB = OFF )
#
#  Component configuration:
#        DEAL_II_COMPONENT_COMPAT_FILES
#      ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#      ( DEAL_II_COMPONENT_EXAMPLES = OFF )
#        DEAL_II_COMPONENT_MESH_CONVERTER
#      ( DEAL_II_COMPONENT_PARAMETER_GUI = OFF )
#
# Detailed information (compiler flags, feature configuration) can be found in detailed.log
#
###
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    DEAL_II_CMAKE_CXX_FLAGS
    DEAL_II_CMAKE_C_FLAGS


-- Build files have been written to: /home/raymond/builds/mine_python-daetools-svn/20160629/src/trunk/deal.II

[*] Done!


[*] Building deal.II...

make: *** No rule to make target 'expand_instantiations_exe'.  Stop.