LINK : fatal error LNK1181: cannot open input file '\machine:x64.obj' - c++

Question

I am porting a C++ project I have been working on for 2 years, to Windows, and I am facing this link issue, that I haven't seen on any google-referenced posts... :/
It is a CMake-generated project, and I get these CMake entries set by default to "\machine:x64"
CMAKE_EXE_LINKER_FLAGS
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_STATIC_LINKER_FLAGS
I tried removing the flag, which has no effect on any of the 3 last entries, but CMAKE_EXE_LINKER_FLAGS without this value gives me about 85 unresolved externals spread in my libraries.
ALL my projects / project dependencies are compiled with MSVC2015 in x64.
Linking fails both in debug & release mode (not that it matters..)
I should also probably mention that I have 6 projects in this solution, 4 libraries, 2 executables. 4 of these projects are compiling fine (1 executable & 4 libs), only the 2 last ones are failing (with the same link error for both).
The only difference in terms of dependencies are a dependency to the Point Cloud Library (pcl), and to Qt5 (Core GUI, XML, and OpenGL)
Did anyone already encountered this specific linker error?
Hope you can help =)
EDIT: Here are the 2 main CMakelists files (the one at the root of the project and the one that compiles both failing projects). I removed everything that didn't seem pertinent for this issue.
Root CMakeLists.txt:
project(SofaOR)
cmake_minimum_required(VERSION 2.4)
if (COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
include_directories(${CMAKE_SOURCE_DIR})
#Reading local file for the non automatically detected dependencies
if(EXISTS "${CMAKE_CURRENT_LIST_DIR}/cmake/dependencies.cmake")
message("Adding custom file")
include(${CMAKE_CURRENT_LIST_DIR}/cmake/dependencies.cmake)
endif()
include(CheckCXXCompilerFlag)
CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
CHECK_CXX_COMPILER_FLAG("-std=c++0x" COMPILER_SUPPORTS_CXX0X)
if(COMPILER_SUPPORTS_CXX11)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
elseif(COMPILER_SUPPORTS_CXX0X)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
else()
message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
endif()
set(SOFA_ALL_LIBS SofaHelper SofaDefaultType)
set(SOFA_INCLUDE_DIRS ${SOFA_DIR}/include)
set(SOFA_LIBRARY_DIRS ${SOFA_DIR}/lib)
add_subdirectory(${CMAKE_SOURCE_DIR}/processOR)
the CMakelists included by the last add_subdirectory:
project(processOR)
cmake_minimum_required(VERSION 3.0.2)
if (COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)
set(PROCESSOR_EXEC_NAME processOR)
set(PROCESSOR_LIB_NAME processOR_lib)
set(CMAKE_INCLUDE_CURRENT_DIR ON)
find_package(OpenCV COMPONENTS core imgproc xfeatures2d calib3d REQUIRED )
find_package(Qt5 COMPONENTS Core Gui Xml OpenGL REQUIRED )
find_package(PCL COMPONENTS common io kdtree REQUIRED )
find_package(Boost COMPONENTS program_options chrono thread REQUIRED)
find_package(OpenIGTLink REQUIRED )
set(CMAKE_AUTOMOC ON)
set(CMAKE_AUTOUIC ON)
set(PROCESSOR_INCLUDES ${CMAKE_CURRENT_SOURCE_DIR}/src/ PARENT_SCOPE)
set(PROCESSOR_SRC ${CMAKE_CURRENT_SOURCE_DIR}/src/)
include_directories(${PCL_INCLUDE_DIRS})
include_directories(${COMMON_INCLUDE_DIRS})
include_directories(${OpenIGTLink_INCLUDE_DIRS})
include_directories(${OpenCV_INCLUDE_DIRS})
include_directories(${QGLVIEWER_DIR})
include_directories(${Boost_INCLUDE_DIRS})
include_directories(${SOFA_INCLUDE_DIRS})
link_directories(${PCL_LIBRARY_DIRS})
link_directories(${COMMON_LIBRARY_DIRS})
link_directories(${OpenIGTLink_LIBRARY_DIRS})
link_directories(${OpenCV_LIBRARY_DIRS})
link_directories(${QGLVIEWER_DIR})
link_directories(${SOFA_LIBRARY_DIRS})
link_directories(${Boost_LIBRARY_DIRS})
include_directories(${PROCESSOR_SRC})
set(PROCESSOR_ALL_LIBS
${PCL_LIBRARIES}
${COMMON_LIBRARIES}
OpenIGTLink
${OpenCV_LIBS}
QGLViewer
${Boost_LIBRARIES}
${SOFA_ALL_LIBS}
)
set (HEADER_FILES
${PROCESSOR_SRC}/util/Calibration.h
${PROCESSOR_SRC}/fetchers/VideoFetcher.h
[…]
${PROCESSOR_SRC}/filters/PointCloudTriangulator.h
${PROCESSOR_SRC}/filters/PointCloudSmootherMLS.h
${PROCESSOR_SRC}/filters/PointCloudSegmenter.h
${PROCESSOR_SRC}/filters/PointCloudDownSampler.h
)
set (SOURCE_FILES
${PROCESSOR_SRC}/Registrator.cpp
${PROCESSOR_SRC}/tinyxml2.cpp
[…]
${PROCESSOR_SRC}/filters/PointCloudSegmenter.cpp
${PROCESSOR_SRC}/filters/PointCloudDownSampler.cpp
)
# Library
add_library(${PROCESSOR_LIB_NAME} SHARED ${HEADER_FILES} ${SOURCE_FILES})
target_link_libraries(${PROCESSOR_LIB_NAME} ${PROCESSOR_ALL_LIBS} ${CMAKE_EXE_LINKER_FLAGS} ${ADDITIONAL_LIBRARIES})
QT5_USE_MODULES(${PROCESSOR_LIB_NAME} Widgets Gui OpenGL Xml)
set(PROCESSOR_LIB ${PROCESSOR_LIB_NAME} PARENT_SCOPE)
# Main executable
set (SOURCE_FILES
${PROCESSOR_SRC}/mainRegistration.cpp
)
add_executable(${PROCESSOR_EXEC_NAME} ${HEADER_FILES} ${SOURCE_FILES})
target_link_libraries(${PROCESSOR_EXEC_NAME} ${PROCESSOR_LIB} ${Boost_LIBRARIES} ${PROCESSOR_LIB_NAME} ${CMAKE_EXE_LINKER_FLAGS})
QT5_USE_MODULES(${PROCESSOR_EXEC_NAME} Widgets Gui OpenGL Xml)
set_target_properties(${PROJECT_NAME}
PROPERTIES
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
)