Catkin_make Error with liorf : Undefined References

[sribru]

I ham having trouble while trying to catkin_make the repo by installing the correct versions of gtsam (4.0.2) and cmake(3.7.2) based on the the suggested solutions from LIOSAM and liorf issues

I have attached output log file below.
ase path: /root/catkin_ws
Source space: /root/catkin_ws/src
Build space: /root/catkin_ws/build
Devel space: /root/catkin_ws/devel
Install space: /root/catkin_ws/install

Running command: "cmake /root/catkin_ws/src -DCATKIN_DEVEL_PREFIX=/root/catkin_ws/devel -DCMAKE_INSTALL_PREFIX=/root/catkin_ws/install -G Unix Makefiles" in "/root/catkin_ws/build"

-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- Using CATKIN_DEVEL_PREFIX: /root/catkin_ws/devel
-- Using CMAKE_PREFIX_PATH: /opt/ros/kinetic
-- This workspace overlays: /opt/ros/kinetic
-- Found PythonInterp: /usr/bin/python2 (found suitable version "2.7.12", minimum required is "2")
-- Using PYTHON_EXECUTABLE: /usr/bin/python2
-- Using Debian Python package layout
-- Using empy: /usr/bin/empy
-- Using CATKIN_ENABLE_TESTING: ON
-- Call enable_testing()
-- Using CATKIN_TEST_RESULTS_DIR: /root/catkin_ws/build/test_results
-- Found gtest sources under '/usr/src/gmock': gtests will be built
-- Found gmock sources under '/usr/src/gmock': gmock will be built
-- Found PythonInterp: /usr/bin/python2 (found version "2.7.12")
-- 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
-- Using Python nosetests: /usr/bin/nosetests-2.7
-- catkin 0.7.29
-- BUILD_SHARED_LIBS is on
-- BUILD_SHARED_LIBS is on
-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- ~~ traversing 1 packages in topological order:
-- ~~ - liorf
-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- +++ processing catkin package: 'liorf'
-- ==> add_subdirectory(liorf)
-- Using these message generators: gencpp;geneus;genlisp;gennodejs;genpy
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Checking for module 'eigen3'
-- Found eigen3, version 3.2.92
-- Found eigen: /usr/include/eigen3
-- Checking for module 'flann'
-- Found flann, version 1.8.4
-- Found Flann: /usr/lib/x86_64-linux-gnu/libflann_cpp_s.a
-- Checking for module 'libopenni'
-- Found libopenni, version 1.5.4.0
-- Found openni: /usr/lib/libOpenNI.so
-- Checking for module 'libopenni2'
-- No package 'libopenni2' found
-- Could NOT find OpenNI2 (missing: OPENNI2_LIBRARY OPENNI2_INCLUDE_DIRS)
-- The imported target "vtkRenderingPythonTkWidgets" references the file
"/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist. Possible reasons include:

• The file was deleted, renamed, or moved to another location.
• An install or uninstall procedure did not complete successfully.
• The installation package was faulty and contained
  "/usr/lib/cmake/vtk-6.2/VTKTargets.cmake"
  but not all the files it references.

-- The imported target "vtk" references the file
"/usr/bin/vtk"
but this file does not exist. Possible reasons include:

• The file was deleted, renamed, or moved to another location.
• An install or uninstall procedure did not complete successfully.
• The installation package was faulty and contained
  "/usr/lib/cmake/vtk-6.2/VTKTargets.cmake"
  but not all the files it references.

-- LIBUSB_1_LIBRARY (missing: LIBUSB_1_INCLUDE_DIR)
-- Checking for module 'libopenni2'
-- No package 'libopenni2' found
-- Could NOT find OpenNI2 (missing: OPENNI2_LIBRARY OPENNI2_INCLUDE_DIRS)
-- Found qhull: /usr/lib/x86_64-linux-gnu/libqhull.so
-- Found PCL_COMMON: /usr/lib/x86_64-linux-gnu/libpcl_common.so
-- Found PCL_KDTREE: /usr/lib/x86_64-linux-gnu/libpcl_kdtree.so
-- Found PCL_OCTREE: /usr/lib/x86_64-linux-gnu/libpcl_octree.so
-- Found PCL_SEARCH: /usr/lib/x86_64-linux-gnu/libpcl_search.so
-- Found PCL_SAMPLE_CONSENSUS: /usr/lib/x86_64-linux-gnu/libpcl_sample_consensus.so
-- Found PCL_FILTERS: /usr/lib/x86_64-linux-gnu/libpcl_filters.so
-- Found PCL_FEATURES: /usr/lib/x86_64-linux-gnu/libpcl_features.so
-- Found PCL_KEYPOINTS: /usr/lib/x86_64-linux-gnu/libpcl_keypoints.so
-- Found PCL_IO: /usr/lib/x86_64-linux-gnu/libpcl_io.so
-- Found PCL_GEOMETRY: /usr/include/pcl-1.7
-- Found PCL_VISUALIZATION: /usr/lib/x86_64-linux-gnu/libpcl_visualization.so
-- Found PCL_SEGMENTATION: /usr/lib/x86_64-linux-gnu/libpcl_segmentation.so
-- Found PCL_PEOPLE: /usr/lib/x86_64-linux-gnu/libpcl_people.so
-- Found PCL_SURFACE: /usr/lib/x86_64-linux-gnu/libpcl_surface.so
-- Found PCL_REGISTRATION: /usr/lib/x86_64-linux-gnu/libpcl_registration.so
-- Found PCL_TRACKING: /usr/lib/x86_64-linux-gnu/libpcl_tracking.so
-- Found PCL_RECOGNITION: /usr/lib/x86_64-linux-gnu/libpcl_recognition.so
-- Could NOT find PCL_APPS (missing: PCL_APPS_LIBRARY)
-- Found PCL_IN_HAND_SCANNER: /usr/include/pcl-1.7
-- Found PCL_MODELER: /usr/include/pcl-1.7
-- Found PCL_POINT_CLOUD_EDITOR: /usr/include/pcl-1.7
-- Found PCL_OUTOFCORE: /usr/lib/x86_64-linux-gnu/libpcl_outofcore.so
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- serialization
-- system
-- filesystem
-- thread
-- program_options
-- date_time
-- timer
-- chrono
-- regex
-- atomic
-- GTSAM include directory: /usr/local/lib/cmake/GTSAM/../../../include
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- timer
-- chrono
-- system
-- Reading /home/linuxbrew/.linuxbrew/lib/cmake/GeographicLib/geographiclib-config.cmake
-- GeographicLib configuration, version 2.3
-- ${{GeographicLib_LIBRARIES}} set to shared library
-- liorf: 1 messages, 1 services
CMake Warning at /opt/ros/kinetic/share/catkin/cmake/catkin_package.cmake:166 (message):
catkin_package() DEPENDS on 'GTSAM' but neither 'GTSAM_INCLUDE_DIRS' nor
'GTSAM_LIBRARIES' is defined.
Call Stack (most recent call first):
/opt/ros/kinetic/share/catkin/cmake/catkin_package.cmake:102 (_catkin_package)
liorf/CMakeLists.txt:54 (catkin_package)

-- Configuring done
CMake Warning at liorf/CMakeLists.txt:99 (add_executable):
Cannot generate a safe runtime search path for target liorf_mapOptmization
because files in some directories may conflict with libraries in implicit
directories:

runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
  /home/linuxbrew/.linuxbrew/lib

Some of these libraries may not be found correctly.

-- Generating done
-- Build files have been written to: /root/catkin_ws/build

Running command: "make -j32 -l32" in "/root/catkin_ws/build"

Scanning dependencies of target tf2_msgs_generate_messages_py
Scanning dependencies of target _liorf_generate_messages_check_deps_save_map
Scanning dependencies of target nav_msgs_generate_messages_cpp
Scanning dependencies of target geometry_msgs_generate_messages_cpp
Scanning dependencies of target sensor_msgs_generate_messages_cpp
Scanning dependencies of target _liorf_generate_messages_check_deps_cloud_info
Scanning dependencies of target liorf_imuPreintegration
Scanning dependencies of target std_msgs_generate_messages_cpp
Scanning dependencies of target visualization_msgs_generate_messages_nodejs
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Scanning dependencies of target tf_generate_messages_lisp
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Scanning dependencies of target tf_generate_messages_py
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Scanning dependencies of target std_msgs_generate_messages_nodejs
Scanning dependencies of target geometry_msgs_generate_messages_eus
Scanning dependencies of target actionlib_msgs_generate_messages_py
Scanning dependencies of target roscpp_generate_messages_py
Scanning dependencies of target tf_generate_messages_nodejs
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Scanning dependencies of target sensor_msgs_generate_messages_nodejs
Scanning dependencies of target nav_msgs_generate_messages_py
Scanning dependencies of target geometry_msgs_generate_messages_nodejs
Scanning dependencies of target rosgraph_msgs_generate_messages_nodejs
Scanning dependencies of target tf2_msgs_generate_messages_lisp
Scanning dependencies of target sensor_msgs_generate_messages_lisp
Scanning dependencies of target sensor_msgs_generate_messages_py
Scanning dependencies of target actionlib_generate_messages_cpp
Scanning dependencies of target sensor_msgs_generate_messages_eus
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[ 0%] Built target std_msgs_generate_messages_lisp
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Scanning dependencies of target actionlib_generate_messages_py
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Scanning dependencies of target actionlib_msgs_generate_messages_lisp
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Scanning dependencies of target visualization_msgs_generate_messages_eus
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[ 0%] Built target nav_msgs_generate_messages_py
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Scanning dependencies of target tf2_msgs_generate_messages_eus
Scanning dependencies of target _catkin_empty_exported_target
Scanning dependencies of target actionlib_msgs_generate_messages_nodejs
[ 0%] Built target _liorf_generate_messages_check_deps_save_map
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[ 0%] Built target _liorf_generate_messages_check_deps_cloud_info
[ 0%] Built target _catkin_empty_exported_target
[ 0%] Built target actionlib_msgs_generate_messages_nodejs
Scanning dependencies of target liorf_generate_messages_cpp
Scanning dependencies of target liorf_generate_messages_lisp
Scanning dependencies of target liorf_generate_messages_nodejs
Scanning dependencies of target liorf_generate_messages_py
Scanning dependencies of target liorf_generate_messages_eus
[ 4%] Generating Lisp code from liorf/cloud_info.msg
[ 13%] Generating Lisp code from liorf/save_map.srv
[ 13%] Generating C++ code from liorf/save_map.srv
[ 17%] Generating Javascript code from liorf/cloud_info.msg
[ 21%] Generating Python from MSG liorf/cloud_info
[ 26%] Generating C++ code from liorf/cloud_info.msg
[ 30%] Generating EusLisp code from liorf/cloud_info.msg
[ 34%] Generating Javascript code from liorf/save_map.srv
[ 39%] Generating Python code from SRV liorf/save_map
[ 43%] Generating EusLisp code from liorf/save_map.srv
[ 47%] Generating EusLisp manifest code for liorf
[ 47%] Built target liorf_generate_messages_nodejs
[ 47%] Built target liorf_generate_messages_lisp
[ 56%] Generating Python srv init.py for liorf
[ 56%] Generating Python msg init.py for liorf
[ 60%] Building CXX object liorf/CMakeFiles/liorf_imuPreintegration.dir/src/imuPreintegration.cpp.o
[ 65%] Building CXX object liorf/CMakeFiles/liorf_imuPreintegration.dir/lib/common_lib.cpp.o
[ 65%] Built target liorf_generate_messages_cpp
Scanning dependencies of target liorf_imageProjection
Scanning dependencies of target liorf_mapOptmization
:0:15: warning: ISO C++11 requires whitespace after the macro name
:0:15: warning: ISO C++11 requires whitespace after the macro name
[ 65%] Built target liorf_generate_messages_py
[ 73%] Building CXX object liorf/CMakeFiles/liorf_imageProjection.dir/src/imageProjection.cpp.o
[ 73%] Building CXX object liorf/CMakeFiles/liorf_imageProjection.dir/lib/common_lib.cpp.o
:0:15: warning: ISO C++11 requires whitespace after the macro name
:0:15: warning: ISO C++11 requires whitespace after the macro name
[ 82%] Building CXX object liorf/CMakeFiles/liorf_mapOptmization.dir/lib/common_lib.cpp.o
[ 82%] Building CXX object liorf/CMakeFiles/liorf_mapOptmization.dir/src/mapOptmization.cpp.o
[ 86%] Building CXX object liorf/CMakeFiles/liorf_mapOptmization.dir/include/Scancontext.cpp.o
:0:15: warning: ISO C++11 requires whitespace after the macro name
:0:15: warning: ISO C++11 requires whitespace after the macro name
:0:15: warning: ISO C++11 requires whitespace after the macro name
[ 86%] Built target liorf_generate_messages_eus
Scanning dependencies of target liorf_generate_messages
[ 86%] Built target liorf_generate_messages
/root/catkin_ws/src/liorf/include/Scancontext.cpp: In function ‘float xy2theta(const float&, const float&)’:
/root/catkin_ws/src/liorf/include/Scancontext.cpp:36:1: warning: control reaches end of non-void function [-Wreturn-type]
} // xy2theta
^
/root/catkin_ws/src/liorf/src/mapOptmization.cpp: In member function ‘bool mapOptimization::saveMapService(liorf::save_mapRequest&, liorf::save_mapResponse&)’:
/root/catkin_ws/src/liorf/src/mapOptmization.cpp:389:11: warning: variable ‘unused’ set but not used [-Wunused-but-set-variable]
int unused = system((std::string("exec rm -r ") + saveMapDirectory).c_str());
^
/root/catkin_ws/src/liorf/src/mapOptmization.cpp: In member function ‘void mapOptimization::performSCLoopClosure()’:
/root/catkin_ws/src/liorf/src/mapOptmization.cpp:639:15: warning: unused variable ‘yawDiffRad’ [-Wunused-variable]
float yawDiffRad = detectResult.second; // not use for v1 (because pcl icp withi initial somthing wrong...)
^
/root/catkin_ws/src/liorf/src/mapOptmization.cpp: In member function ‘void mapOptimization::publishFrames()’:
/root/catkin_ws/src/liorf/src/mapOptmization.cpp:1768:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (lastSLAMInfoPubSize != cloudKeyPoses6D->size())
^
[ 91%] Linking CXX executable /root/catkin_ws/devel/lib/liorf/liorf_imageProjection
[ 91%] Built target liorf_imageProjection
[ 95%] Linking CXX executable /root/catkin_ws/devel/lib/liorf/liorf_imuPreintegration
[ 95%] Built target liorf_imuPreintegration
[100%] Linking CXX executable /root/catkin_ws/devel/lib/liorf/liorf_mapOptmization
/home/linuxbrew/.linuxbrew/lib/liblzma.so.5: undefined reference to pthread_condattr_setclock@GLIBC_2.34' /home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to hypot@GLIBC_2.35'
/home/linuxbrew/.linuxbrew/lib/liblzma.so.5: undefined reference to pthread_create@GLIBC_2.34' /home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to __libc_single_threaded@GLIBC_2.32'
/home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to log2@GLIBC_2.29' /home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to pow@GLIBC_2.29'
/home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to exp2@GLIBC_2.29' /home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to exp@GLIBC_2.29'
/home/linuxbrew/.linuxbrew/lib/liblzma.so.5: undefined reference to pthread_sigmask@GLIBC_2.32' /home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to hypotf@GLIBC_2.35'
/home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to std::__throw_bad_array_new_length()@GLIBCXX_3.4.29' /home/linuxbrew/.linuxbrew/lib/libuuid.so.1: undefined reference to getrandom@GLIBC_2.25'
/home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to log@GLIBC_2.29' /home/linuxbrew/.linuxbrew/lib/liblzma.so.5: undefined reference to pthread_join@GLIBC_2.34'
/home/linuxbrew/.linuxbrew/lib/libGeographicLib.so.26.0.0: undefined reference to `expf@GLIBC_2.27'
collect2: error: ld returned 1 exit status
liorf/CMakeFiles/liorf_mapOptmization.dir/build.make:506: recipe for target '/root/catkin_ws/devel/lib/liorf/liorf_mapOptmization' failed
make[2]: *** [/root/catkin_ws/devel/lib/liorf/liorf_mapOptmization] Error 1
CMakeFiles/Makefile2:589: recipe for target 'liorf/CMakeFiles/liorf_mapOptmization.dir/all' failed
make[1]: *** [liorf/CMakeFiles/liorf_mapOptmization.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
Invoking "make -j32 -l32" failed

[YJZLuckyBoy]

I'm sorry, I haven't encountered this problem