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SINTEFMedtek / Fraxinus

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Build Failed: Makefile:126: recipe for target 'cmTC_ce5c1/fast' failed #4

Open shu-gong opened 2 years ago

shu-gong commented 2 years ago

Hi developers,

I build Fraxinus using the following commend.

mkdir dev mkdir dev/fx cd dev/fx git clone git@github.com:SINTEFMedTek/Fraxinus.git FX/FX cd FX/FX git checkout develop ./FX/FX/script/cxFraxinusInstaller.py --full --all -t Release

But it failed when configure CustusX.

----Below is commend output----

==================== configure CustusX =============================== 4665.1s = CX_CMAKE_CXX_FLAGS:STRING is now set to -DEIGEN_DONT_ALIGN CX_CMAKE_CXX_FLAGS:STRING was set to -DEIGEN_DONT_ALIGN CX_CMAKE_CXX_FLAGS:STRING is now set to -DEIGEN_DONT_ALIGN -Wno-deprecated -Wno-unknown-warning-option -Wno-inconsistent-missing-override -Wno-self-assign-field *** CMake Options: CMAKE_BUILD_TYPE:STRING = Release CX_EXTERNAL_PLUGIN_Fraxinus = /home/shu/dev/fx/FX/FX/org.custusx.fraxinus CX_EXTERNAL_PLUGIN_org_custusx_fraxinus_widgets = /home/shu/dev/fx/FX/FX/org.custusx.fraxinus.widgets IGSTK_DIR:PATH = /home/shu/dev/fx/IGSTK/build_Release CX_BUILD_USER_DOCUMENTATION:BOOL = False OpenIGTLink_DIR:PATH = /home/shu/dev/fx/OpenIGTLink/build_Release CX_CMAKE_CXX_FLAGS:STRING = -DEIGEN_DONT_ALIGN -Wno-deprecated -Wno-unknown-warning-option -Wno-inconsistent-missing-override -Wno-self-assign-field CX_SYSTEM_BASE_NAME:STRING = Fraxinus OpenCLUtilityLibrary_DIR:PATH = /home/shu/dev/fx/OpenCLUtilityLibrary/build_Release CX_PLUGIN_org.custusx.core.state = OFF VTK_DIR:PATH = /home/shu/dev/fx/VTK/build_Release CMAKE_ECLIPSE_GENERATE_LINKED_RESOURCES = False BUILD_DOCUMENTATION:BOOL = False CX_PLUGIN_org.custusx.filter.airways:BOOL = False BUILD_SHARED_LIBS:BOOL = True CTK_SOURCE_DIR:PATH = /home/shu/dev/fx/CTK/CTK CX_APP_CustusX:BOOL = OFF CMAKE_ECLIPSE_VERSION = 3.6 EIGEN_INCLUDE_DIR:PATH = /home/shu/dev/fx/eigen/eigen CTK_DIR:PATH = /home/shu/dev/fx/CTK/build_Release ITK_DIR:PATH = /home/shu/dev/fx/ITK/build_Release CX_SYSTEM_DEFAULT_APPLICATION:STRING = Fraxinus SSC_USE_GCOV:BOOL = False CX_APP_Fraxinus:BOOL = ON OpenCV_DIR:PATH = /home/shu/dev/fx/OpenCV/build_Release qhttpserver_DIR:PATH = /home/shu/dev/fx/QHttpServer/build_Release CX_EXTERNAL_PLUGIN_org.custusx.anglecorrection = /home/shu/dev/fx/CX/CX/source/plugins/org.custusx.anglecorrection CX_EXTERNAL_PLUGIN_org_custusx_fraxinus_core_state = /home/shu/dev/fx/FX/FX/org.custusx.fraxinus.core.state CX_OPTIONAL_CONFIG_ROOT:PATH = /home/shu/dev/fx/FX/FX/config OpenIGTLinkIO_DIR:PATH = /home/shu/dev/fx/OpenIGTLinkIO/build_Release BUILD_OPEN_IGTLINK_SERVER:BOOL = ON BUILD_TESTING:BOOL = True CMAKE_PREFIX_PATH:PATH = /opt/local/libexec/qt5-mac

[shell cmd] cd /home/shu/dev/fx/CX/build_Release [shell cmd] cmake -G"Eclipse CDT4 - Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING="Release" -DCX_EXTERNAL_PLUGIN_Fraxinus="/home/shu/dev/fx/FX/FX/org.custusx.fraxinus" -DCX_EXTERNAL_PLUGIN_org_custusx_fraxinus_widgets="/home/shu/dev/fx/FX/FX/org.custusx.fraxinus.widgets" -DIGSTK_DIR:PATH="/home/shu/dev/fx/IGSTK/build_Release" -DCX_BUILD_USER_DOCUMENTATION:BOOL="False" -DOpenIGTLink_DIR:PATH="/home/shu/dev/fx/OpenIGTLink/build_Release" -DCX_CMAKE_CXX_FLAGS:STRING="-DEIGEN_DONT_ALIGN -Wno-deprecated -Wno-unknown-warning-option -Wno-inconsistent-missing-override -Wno-self-assign-field" -DCX_SYSTEM_BASE_NAME:STRING="Fraxinus" -DOpenCLUtilityLibrary_DIR:PATH="/home/shu/dev/fx/OpenCLUtilityLibrary/build_Release" -DCX_PLUGIN_org.custusx.core.state="OFF" -DVTK_DIR:PATH="/home/shu/dev/fx/VTK/build_Release" -DCMAKE_ECLIPSE_GENERATE_LINKED_RESOURCES="False" -DBUILD_DOCUMENTATION:BOOL="False" -DCX_PLUGIN_org.custusx.filter.airways:BOOL="False" -DBUILD_SHARED_LIBS:BOOL="True" -DCTK_SOURCE_DIR:PATH="/home/shu/dev/fx/CTK/CTK" -DCX_APP_CustusX:BOOL="OFF" -DCMAKE_ECLIPSE_VERSION="3.6" -DEIGEN_INCLUDE_DIR:PATH="/home/shu/dev/fx/eigen/eigen" -DCTK_DIR:PATH="/home/shu/dev/fx/CTK/build_Release" -DITK_DIR:PATH="/home/shu/dev/fx/ITK/build_Release" -DCX_SYSTEM_DEFAULT_APPLICATION:STRING="Fraxinus" -DSSC_USE_GCOV:BOOL="False" -DCX_APP_Fraxinus:BOOL="ON" -DOpenCV_DIR:PATH="/home/shu/dev/fx/OpenCV/build_Release" -Dqhttpserver_DIR:PATH="/home/shu/dev/fx/QHttpServer/build_Release" -DCX_EXTERNAL_PLUGIN_org.custusx.anglecorrection="/home/shu/dev/fx/CX/CX/source/plugins/org.custusx.anglecorrection" -DCX_EXTERNAL_PLUGIN_org_custusx_fraxinus_core_state="/home/shu/dev/fx/FX/FX/org.custusx.fraxinus.core.state" -DCX_OPTIONAL_CONFIG_ROOT:PATH="/home/shu/dev/fx/FX/FX/config" -DOpenIGTLinkIO_DIR:PATH="/home/shu/dev/fx/OpenIGTLinkIO/build_Release" -DBUILD_OPEN_IGTLINK_SERVER:BOOL="ON" -DBUILD_TESTING:BOOL="True" -DCMAKE_PREFIX_PATH:PATH="/opt/local/libexec/qt5-mac" /home/shu/dev/fx/CX/CX -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Eclipse version is set to 3.6. Adjust CMAKE_ECLIPSE_VERSION if this is wrong. -- 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 -- 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 -- 'BeforeCMAKE_CXX_FLAGS' -- 'CX_CMAKE_CXX_FLAGS'-DEIGEN_DONT_ALIGN -Wno-deprecated -Wno-unknown-warning-option -Wno-inconsistent-missing-override -Wno-self-assign-field -- '_ITER'-DEIGEN_DONT_ALIGN -Wno-deprecated -Wno-unknown-warning-option -Wno-inconsistent-missing-override -Wno-self-assign-field -- 'AfterCMAKE_CXX_FLAGS' -- DirDefs: -- The Unix Makefiles was used. -- Setting CX_SYSTEM_BASE_NAME=[Fraxinus] -- Setting CX_SYSTEM_DEFAULT_APPLICATION=[Fraxinus] -- Found Git: /usr/bin/git (found version "2.7.4") fatal: no tag exactly matches 'a06e4699bc1e7232948a4d90ee5ad109a7446832' -- CustusX Alpha Version: 2022.04.20-dev+develop.a06e4 -----------------CX_INSTALL_ROOT_DIR: Fraxinus -----------------CX_INSTALL_BINARY_DIR: Fraxinus/bin -----------------CX_INSTALL_CONFIG_DIR: Fraxinus/config -----------------CX_BUNDLE_NAME: Fraxinus -- Boost version: 1.58.0 -- Found Eigen: /home/shu/dev/fx/eigen/eigen (Required is at least version "2.91.0") -- Trying to find DCMTK expecting DCMTKConfig.cmake -- Trying to find DCMTK expecting DCMTKConfig.cmake - failed -- Trying to find DCMTK relying on FindDCMTK.cmake -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Found DCMTK: /home/shu/dev/fx/CTK/build_Release/DCMTK-build/config/include/dcmtk/config
-- Performing Test DCMTK_HAVE_CONFIG_H_OPTIONAL -- Performing Test DCMTK_HAVE_CONFIG_H_OPTIONAL - Success -- Trying to find DCMTK relying on FindDCMTK.cmake - ok -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found GLEW: /usr/include
Found new plugin org.custusx.webserver, adding option OFF. -- Generated: /home/shu/dev/fx/CX/build_Release/source/plugins/DGraphInput-alldep-withext.txt -- Checking to see if CXX compiler accepts flag -fvisibility=hidden -- Checking to see if CXX compiler accepts flag -fvisibility=hidden - yes -- Checking to see if CXX compiler accepts flag -fvisibility-inlines-hidden -- Checking to see if CXX compiler accepts flag -fvisibility-inlines-hidden - yes -- Configuring plugin org.custusx.fraxinus... -- Configuring application Fraxinus... CMake Error at /home/shu/dev/fx/CTK/CTK/CMake/ctkMacroSetupPlugins.cmake:211 (add_subdirectory): The binary directory

/home/shu/dev/fx/CX/build_Release/source/plugins/private_plugins/org.custusx.fraxinus

is already used to build a source directory. It cannot be used to build source directory

/home/shu/dev/fx/FX/FX/org.custusx.fraxinus

Specify a unique binary directory name. Call Stack (most recent call first): source/plugins/CMakeLists.txt:85 (ctkMacroSetupPlugins)

-- Performing Test SUPPORTS_STD_CXX11 -- Performing Test SUPPORTS_STD_CXX11 - Success -- Performing Test SUPPORTS_STD_CXX01 -- Performing Test SUPPORTS_STD_CXX01 - Success CMake Error at /home/shu/dev/fx/CTK/CTK/CMake/ctkMacroSetupPlugins.cmake:211 (add_subdirectory): The binary directory

/home/shu/dev/fx/CX/build_Release/source/plugins/private_plugins/org.custusx.fraxinus.core.state

is already used to build a source directory. It cannot be used to build source directory

/home/shu/dev/fx/FX/FX/org.custusx.fraxinus.core.state

Specify a unique binary directory name. Call Stack (most recent call first): source/plugins/CMakeLists.txt:85 (ctkMacroSetupPlugins)

CMake Error at /home/shu/dev/fx/CTK/CTK/CMake/ctkMacroSetupPlugins.cmake:211 (add_subdirectory): The binary directory

/home/shu/dev/fx/CX/build_Release/source/plugins/private_plugins/org.custusx.fraxinus.widgets

is already used to build a source directory. It cannot be used to build source directory

/home/shu/dev/fx/FX/FX/org.custusx.fraxinus.widgets

Specify a unique binary directory name. Call Stack (most recent call first): source/plugins/CMakeLists.txt:85 (ctkMacroSetupPlugins)

-- Generating master Catch exe. -- Adding tests from: -- cxtestResource -- cxtestResourceUsReconstructionTypes -- cxtestResourceVisualization -- cxtestOpenIGTLinkUtilities -- cxtestUtilities -- cxtestResourceWidgets -- cxtestGrabber -- cxtestFilter -- cxtestLogicManager -- cxtestGui -- cxtest_org_custusx_core_patientmodel -- cxtest_org_custusx_core_view -- cxtest_org_custusx_core_tracking -- cxtest_org_custusx_core_tracking_igstk -- cxtest_org_custusx_core_openigtlink3 -- cxtest_org_custusx_core_video -- cxtest_org_custusx_core_filemanager -- cxtest_org_custusx_usreconstruction_vnncl -- cxtest_org_custusx_usreconstruction_pnn -- cxtest_org_custusx_registration -- cxtest_org_custusx_registration_method_manual -- cxtest_org_custusx_registration_method_landmark -- cxtest_org_custusx_registration_method_bronchoscopy -- cxtest_org_custusx_registration_method_centerline -- cxtest_org_custusx_registration_method_commandline -- cxtest_org_custusx_usreconstruction -- cxtest_org_custusx_acquisition -- cxtest_org_custusx_calibration -- cxtest_org_custusx_help -- cxtest_org_custusx_filter_accusurf -- cxtest_org_custusx_ceetron -- cxtest_org_custusx_filter_airwaysfromcenterline -- cxtest_org_custusx_example -- cxtest_org_custusx_fraxinus_core_state -- cxtest_org_custusx_anglecorrection -- cxtest_org_custusx_anglecorrection_gui -- Qt5 plugin directory:/usr/lib/x86_64-linux-gnu/qt5/plugins -- Qt5 qml directory:/usr/lib/x86_64-linux-gnu/qt5/qml -- QT_PLUGINS_DIR: /usr/lib/x86_64-linux-gnu/qt5/plugins -- QT_LIBS_DIR: /usr/lib/x86_64-linux-gnu -- QT_QML_DIR: /usr/lib/x86_64-linux-gnu/qt5/qml -- PATTERN=Fraxinus/bin/.so -- PATTERN=Fraxinus/bin/plugins/.so -- PATTERN=Fraxinus/bin/*.so -- Found OpenCV: /home/shu/dev/fx/OpenCV/build_Release (found version "3.3.0") -- Configuration for Fraxinus 2022.04.20-dev+develop.a06e4

Build Settings:
    System Base Name: Fraxinus
    Built on system: Linux-4.15.0-142-generic  x86_64
    Build type: Release
    Shared Libraries: 
    Coverage: False
    Dev docs: False
    User docs: False

Libraries:
    Qt Version 5.5.1
    VTK Version: 7.1.0
    ITK Version: 4.12.0
    CTK Version: 0.1.0
    OpenCV Version: 3.3.0
    CMake Version: 3.5.1
    IGSTK Version: 5.2.0
    OpenIGTLink Version: 3.1.0
    Boost Version: 1.58.0
    OpenCL Version: 
    OpenGL Version:  4.5.0 NVIDIA 384.130

    Eigen Version: 3.3.5

    OpenCL Utility Library: ON

Plugins:
    /home/shu/dev/fx/FX/FX/org.custusx.fraxinus ON
    /home/shu/dev/fx/FX/FX/org.custusx.fraxinus.core.state ON
    /home/shu/dev/fx/FX/FX/org.custusx.fraxinus.widgets ON
    org.custusx.acquisition ON
    org.custusx.anglecorrection ON
    org.custusx.bronchoscopynavigation ON
    org.custusx.calibration ON
    org.custusx.ceetron ON
    org.custusx.core.filemanager ON
    org.custusx.core.openigtlink3 ON
    org.custusx.core.patientmodel ON
    org.custusx.core.state OFF
    org.custusx.core.tracking ON
    org.custusx.core.tracking.system.igstk ON
    org.custusx.core.video ON
    org.custusx.core.view ON
    org.custusx.dicom OFF
    org.custusx.example ON
    org.custusx.filter.accusurf ON
    org.custusx.filter.airways False
    org.custusx.filter.airwaysfromcenterline ON
    org.custusx.filter.routetotarget ON
    org.custusx.help ON
    org.custusx.registration ON
    org.custusx.registration.gui ON
    org.custusx.registration.method.bronchoscopy ON
    org.custusx.registration.method.centerline ON
    org.custusx.registration.method.commandline ON
    org.custusx.registration.method.landmark ON
    org.custusx.registration.method.manual ON
    org.custusx.registration.method.plate ON
    org.custusx.registration.method.pointcloud ON
    org.custusx.registration.method.vessel ON
    org.custusx.training ON
    org.custusx.usreconstruction ON
    org.custusx.usreconstruction.pnn ON
    org.custusx.usreconstruction.vnncl ON
    org.custusx.virtualbronchoscopy ON
    org.custusx.webserver OFF

-- Configuring incomplete, errors occurred! See also "/home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeOutput.log". See also "/home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeError.log". [shell info] Terminating: shell command exited with a nonzero return value [1] Terminating: shell command exited with a nonzero return value [1]

----Below is ~/dev/fx/CX/build_Release/CMakeFiles/CMakeError.log----

Determining if the pthread_create exist failed with the following output: Change Dir: /home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_ce5c1/fast" /usr/bin/make -f CMakeFiles/cmTC_ce5c1.dir/build.make CMakeFiles/cmTC_ce5c1.dir/build make[1]: Entering directory '/home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_ce5c1.dir/CheckSymbolExists.c.o /usr/bin/cc -w -fno-tree-vectorize -w -fno-tree-vectorize -o CMakeFiles/cmTC_ce5c1.dir/CheckSymbolExists.c.o -c /home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp/CheckSymbolExists.c Linking C executable cmTC_ce5c1 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_ce5c1.dir/link.txt --verbose=1 /usr/bin/cc -w -fno-tree-vectorize -w -fno-tree-vectorize CMakeFiles/cmTC_ce5c1.dir/CheckSymbolExists.c.o -o cmTC_ce5c1 -rdynamic CMakeFiles/cmTC_ce5c1.dir/CheckSymbolExists.c.o: In function main': CheckSymbolExists.c:(.text+0x16): undefined reference topthread_create' collect2: error: ld returned 1 exit status CMakeFiles/cmTC_ce5c1.dir/build.make:97: recipe for target 'cmTC_ce5c1' failed make[1]: [cmTC_ce5c1] Error 1 make[1]: Leaving directory '/home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp' Makefile:126: recipe for target 'cmTC_ce5c1/fast' failed make: [cmTC_ce5c1/fast] Error 2

File /home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp/CheckSymbolExists.c: / /

include

int main(int argc, char** argv) { (void)argv;

ifndef pthread_create

return ((int*)(&pthread_create))[argc];

else

(void)argc; return 0;

endif

}

Determining if the function pthread_create exists in the pthreads failed with the following output: Change Dir: /home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_2b20d/fast" /usr/bin/make -f CMakeFiles/cmTC_2b20d.dir/build.make CMakeFiles/cmTC_2b20d.dir/build make[1]: Entering directory '/home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_2b20d.dir/CheckFunctionExists.c.o /usr/bin/cc -w -fno-tree-vectorize -w -fno-tree-vectorize -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_2b20d.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.5/Modules/CheckFunctionExists.c Linking C executable cmTC_2b20d /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2b20d.dir/link.txt --verbose=1 /usr/bin/cc -w -fno-tree-vectorize -w -fno-tree-vectorize -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_2b20d.dir/CheckFunctionExists.c.o -o cmTC_2b20d -rdynamic -lpthreads /usr/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status CMakeFiles/cmTC_2b20d.dir/build.make:97: recipe for target 'cmTC_2b20d' failed make[1]: [cmTC_2b20d] Error 1 make[1]: Leaving directory '/home/shu/dev/fx/CX/build_Release/CMakeFiles/CMakeTmp' Makefile:126: recipe for target 'cmTC_2b20d/fast' failed make: [cmTC_2b20d/fast] Error 2

shu-gong commented 2 years ago

Hi developers,

Can someone tell me how to solve it?

thanks,

shu

olevs commented 2 years ago

Hi Shu,

You get some errors saying that some of the Fraxinus plugin directories have been used for another build. Do you have files from another build in your fx tree? Like from the CustusX installer script? You could try to delete the fx/CX/build_Release folder and run the Fraxinus installer script again, or delete everything and start from scratch.

I just tried running the same command in a fresh folder, and it seems to run ok for me. I'm currently using Ubuntu 20.04, but it should work for Ubuntu 16.04 as well.

PS: If the build time is very long you could try to install ninja before running the script in a fresh folder. Installing ninja should be something like: apt-get install ninja-build You may have to make sure that ninja is in the path for the Fraxinus installer script to find it.

Best, Ole Vegard