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

[shu-gong]

No description provided.

[shu-gong]

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 to pthread_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 <pthread.h>

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]

Hi developers,

Can someone tell me how to solve it?

thanks,

shu

[olevs]

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