ScottishCovidResponse / SCRCIssueTracking

Central issue tracking repository for all repos in the consortium
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CMake fails on test directory #120

Closed peter-t-fox closed 4 years ago

peter-t-fox commented 4 years ago

On @thibaud-porphyre Mac environment, CMake 3.17 fails to configure build of the test directory. Works successfully on Linux using CMake 3.10.

Error messages to go here:

thibaud-porphyre commented 4 years ago

Error messages from Bash: mvm-ri-m18002:build tporphyr$ cmake .. -- APPLE=1 -- CMAKE_ADDR2LINE=CMAKE_ADDR2LINE-NOTFOUND -- CMAKE_AR=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar -- CMAKE_AR=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar -- CMAKE_AUTOGEN_ORIGIN_DEPENDS=ON -- CMAKE_AUTOMOC_COMPILER_PREDEFINES=ON -- CMAKE_AUTOMOC_MACRO_NAMES=Q_OBJECT;Q_GADGET;Q_NAMESPACE;Q_NAMESPACE_EXPORT -- CMAKE_AUTOMOC_PATH_PREFIX=ON -- CMAKE_BASE_NAME=c++ -- CMAKE_BINARY_DIR=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build -- CMAKE_BUILD_TOOL=/usr/bin/make -- CMAKE_BUILD_TYPE= -- CMAKE_CACHEFILE_DIR=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build -- CMAKE_CACHE_MAJOR_VERSION=3 -- CMAKE_CACHE_MINOR_VERSION=17 -- CMAKE_CACHE_PATCH_VERSION=1 -- CMAKE_CFG_INTDIR=. -- CMAKE_COLOR_MAKEFILE=ON -- CMAKE_COMMAND=/usr/local/Cellar/cmake/3.17.1/bin/cmake -- 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DARWIN_MAJOR_VERSION=18 -- DARWIN_MINOR_VERSION=7 -- FIND_PACKAGE_MESSAGE_DETAILS_GSL=[/usr/local/Cellar/gsl/2.6/include][/usr/local/Cellar/gsl/2.6/lib/libgsl.dylib][/usr/local/Cellar/gsl/2.6/lib/libgslcblas.dylib][v2.6()] -- FIND_PACKAGE_MESSAGE_DETAILS_PkgConfig=[/usr/local/bin/pkg-config][v0.29.2()] -- FIND_PACKAGE_MESSAGE_DETAILS_Threads=[TRUE][v()] -- GIT_EXECUTABLE=/usr/local/bin/git -- GMOCK_INCLUDE_DIRS=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googlemock/include -- GMOCK_LIBRARY=gmock -- GMOCK_LIBRARY_PATH=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest-build/lib/libgmock.a -- GMOCK_MAIN_LIBRARY=gmock_main -- GMOCK_MAIN_LIBRARY_PATH=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest-build/lib/libgmock_main.a -- GSL_CBLAS_LIBRARY=/usr/local/Cellar/gsl/2.6/lib/libgslcblas.dylib -- 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GSL_STATIC_INCLUDE_DIRS=/usr/local/Cellar/gsl/2.6/include -- GSL_STATIC_LDFLAGS=-L/usr/local/Cellar/gsl/2.6/lib;-lgsl;-lgslcblas;-lm -- GSL_STATIC_LDFLAGS_OTHER= -- GSL_STATIC_LIBDIR= -- GSL_STATIC_LIBRARIES=gsl;gslcblas;m -- GSL_STATIC_LIBRARY_DIRS=/usr/local/Cellar/gsl/2.6/lib -- GSL_STATIC_LIBS= -- GSL_STATIC_LIBS_L= -- GSL_STATIC_LIBS_OTHER= -- GSL_STATIC_LIBS_PATHS= -- GSL_USE_PKGCONFIG= -- GSL_VERSION=2.6 -- GSL_gsl_INCLUDEDIR= -- GSL_gsl_LIBDIR= -- GSL_gsl_PREFIX= -- GSL_gsl_VERSION= -- GTEST_INCLUDE_DIRS=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include -- GTEST_LIBRARY=gtest -- GTEST_LIBRARY_PATH=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest-build/lib/libgtest.a -- GTEST_MAIN_LIBRARY=gtest_main -- GTEST_MAIN_LIBRARY_PATH=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest-build/lib/libgtest_main.a -- HAVE_FLAG_SEARCH_PATHS_FIRST=1 -- OSX_DEVELOPER_ROOT=/Applications/Xcode.app/Contents/Developer -- PKG_CONFIG_EXECUTABLE=/usr/local/bin/pkg-config -- PROJECT_BINARY_DIR=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build -- PROJECT_DESCRIPTION= -- PROJECT_HOMEPAGE_URL= -- PROJECT_NAME=Covid19EERAModel -- PROJECT_SOURCE_DIR=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel -- PROJECT_VERSION=0.0.0 -- PROJECT_VERSION_MAJOR=0 -- PROJECT_VERSION_MINOR=0 -- PROJECT_VERSION_PATCH=0 -- PROJECT_VERSION_TWEAK= -- PTHREAD_C_CXX_TEST_SOURCE=#include

void test_func(void data) { return data; }

int main(void) { pthread_t thread; pthread_create(&thread, NULL, test_func, NULL); pthread_detach(thread); pthread_cancel(thread); pthread_join(thread, NULL); pthread_atfork(NULL, NULL, NULL); pthread_exit(NULL);

return 0; }

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pch_header_OBJCXX=objective-c++-header -- __pkg_config_arguments_GSL=QUIET;gsl -- pkg_config_checked_GSL=1 -- __ranlib=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib -- _abolute_path=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/Library/Frameworks -- _apps=/Applications/Xcode.app/Contents/Developer/Applications -- _ep_documentation_line_count=936 -- _ep_func=ExternalProject_Add_StepDependencies -- _ep_hash_algos=MD5|SHA1|SHA224|SHA256|SHA384|SHA512|SHA3_224|SHA3_256|SHA3_384|SHA3_512 -- _ep_hash_regex=^(MD5|SHA1|SHA224|SHA256|SHA384|SHA512|SHA3_224|SHA3_256|SHA3_384|SHA3_512)=([0-9A-Fa-f]+)$ -- _ep_key=USES_TERMINAL -- 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ExternalProject_Add_StepDependencies -- pkgcfg_lib_GSL_gsl=/usr/local/Cellar/gsl/2.6/lib/libgsl.dylib -- pkgcfg_lib_GSL_gslcblas=/usr/local/Cellar/gsl/2.6/lib/libgslcblas.dylib -- pkgcfg_lib_GSL_m=/usr/lib/libm.dylib -- prefix_result=/usr/local/Cellar/gsl/2.6/lib -- source_dir=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest -- type= -- v= CMake Error at test/CMakeLists.txt:36 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at test/CMakeLists.txt:39 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at test/CMakeLists.txt:42 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at test/CMakeLists.txt:45 (set_target_properties): set_target_properties called with incorrect number of arguments.

-- Configuring incomplete, errors occurred! See also "/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/CMakeFiles/CMakeOutput.log". mvm-ri-m18002:build tporphyr$ cmake .. |grep GTEST -- GTEST_INCLUDE_DIRS=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include -- GTEST_LIBRARY=gtest -- GTEST_LIBRARY_PATH=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest-build/lib/libgtest.a -- GTEST_MAIN_LIBRARY=gtest_main -- GTEST_MAIN_LIBRARY_PATH=/Users/tporphyr/Documents/GitHub/Covid19_EERAModel/build/test/googletest-prefix/src/googletest-build/lib/libgtest_main.a CMake Error at test/CMakeLists.txt:36 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at test/CMakeLists.txt:39 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at test/CMakeLists.txt:42 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at test/CMakeLists.txt:45 (set_target_properties): set_target_properties called with incorrect number of arguments.

kzscisoft commented 4 years ago

I have narrowed this down to CMAKE_THREAD_LIBS_INIT is an empty variable which explains why the number of arguments is incorrect, the variable is stated but it is not given a value. As to why this happens only on Mac OS, I do not know yet

kzscisoft commented 4 years ago

Quote from https://gitlab.kitware.com/cmake/cmake/issues/19823:

"The CMAKE_THREAD_LIBS_INIT variable and corresponding Threads::Threads INTERFACE_LINK_LIBRARIES target property is the empty string for the case when the (Posix) threads functions are provided by the C library. According to a second-hand report I received this case happens on Mac OS X (at least for MacPorts). Therefore, please document this expected result for that important use case."

kzscisoft commented 4 years ago

Fixed using:

# assume built-in pthreads on MacOS
IF(APPLE)
    set(CMAKE_THREAD_LIBS_INIT "-lpthread")
    set(CMAKE_HAVE_THREADS_LIBRARY 1)
    set(CMAKE_USE_WIN32_THREADS_INIT 0)
    set(CMAKE_USE_PTHREADS_INIT 1)
    set(THREADS_PREFER_PTHREAD_FLAG ON)
ENDIF()

from https://stackoverflow.com/questions/54587052/cmake-on-mac-could-not-find-threads-missing-threads-found, however now have new build issues with GoogleTest when building on Mac:

/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:844:12: error: 
      no member named 'make_tuple' in namespace 'std'
using std::make_tuple;
      ~~~~~^
/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:845:12: error: 
      no member named 'tuple' in namespace 'std'
using std::tuple;
      ~~~~~^
/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:965:3: error: 
      deleted function definitions are a C++11 extension [-Werror,-Wc++11-extensions]
  GTEST_DISALLOW_COPY_AND_ASSIGN_(GTestLog);
  ^
/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:684:23: note: 
      expanded from macro 'GTEST_DISALLOW_COPY_AND_ASSIGN_'
  type(type const&) = delete;                 \
                      ^
/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:965:3: error: 
      deleted function definitions are a C++11 extension [-Werror,-Wc++11-extensions]
/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:685:34: note: 
      expanded from macro 'GTEST_DISALLOW_COPY_AND_ASSIGN_'
  type& operator=(type const&) = delete
                                 ^
/Users/krizar/Covid19_EERAModel/build/test/googletest-prefix/src/googletest/googletest/include/gtest/internal/gtest-port.h:1209:3: error: 
      deleted function definitions are a C++11 extension [-Werror,-Wc++11-extensions]
  GTEST_DISALLOW_COPY_AND_ASSIGN_(Notification);
...
kzscisoft commented 4 years ago

Someone has opened a pull request on Google Test to fix this, maybe we can clone the repository and build GoogleTest that way and merge this in?

https://github.com/google/googletest/pull/2736/files

kzscisoft commented 4 years ago

I can confirm using the above fix on Google Test everything works under Mac OS 10.14

kzscisoft commented 4 years ago

@thibaud-porphyre it should work now on your Mac. I think we can close this issue @peter-t-fox? (see https://github.com/ScottishCovidResponse/Covid19_EERAModel/commit/7dd23219a1ded5bc474e052174db607639366a93)

peter-t-fox commented 4 years ago

@thibaud-porphyre If you uncomment the line add_subdirectory(test) from the top-level CMakeLists.txt file, and re-run the cmake .. and make commands in the build directory, everything should work. If you can confirm this, we can then close the issue.