[SOLVED] Error with CImg: plugin with dependency to skeleton.h does not compile

[Rosalie]

Hi !

I tried to compile a private plugin which requires the Image plugin of Sofa and I get the following error :

p0086679@chum44232 ~/bezierskelet/build $ make -j7
Scanning dependencies of target SofaBezierSkeletonization
[ 28%] Building CXX object CMakeFiles/SofaBezierSkeletonization.dir/src/BezierHelper.cpp.o
[ 28%] Building CXX object CMakeFiles/SofaBezierSkeletonization.dir/src/BezierCubic.cpp.o
[ 42%] Building CXX object CMakeFiles/SofaBezierSkeletonization.dir/src/BezierSegment.cpp.o
[ 57%] Building CXX object CMakeFiles/SofaBezierSkeletonization.dir/src/initBezierSkelet.cpp.o
[ 71%] Building CXX object CMakeFiles/SofaBezierSkeletonization.dir/src/VesselMapToSkeleton.cpp.o
[ 85%] Building CXX object CMakeFiles/SofaBezierSkeletonization.dir/src/BezierSegmentTree.cpp.o
In file included from /home/p0086679/sofa/v16.08/build/install/include/CImg/SOFACImg.h:33:0,
                 from /home/p0086679/sofa/v16.08/build/install/include/image/ImageTypes.h:34,
                 from /home/p0086679/bezierskelet/src/VesselMapToSkeleton.h:52,
                 from /home/p0086679/bezierskelet/src/VesselMapToSkeleton.inl:8,
                 from /home/p0086679/bezierskelet/src/VesselMapToSkeleton.cpp:27:
/home/p0086679/sofa/v16.08/build/install/include/CImg/CImg.h:9341:21: fatal error: plugins/skeleton.h: No such file or directory
compilation terminated.
CMakeFiles/SofaBezierSkeletonization.dir/build.make:182: recipe for target 'CMakeFiles/SofaBezierSkeletonization.dir/src/VesselMapToSkeleton.cpp.o' failed
make[2]: *** [CMakeFiles/SofaBezierSkeletonization.dir/src/VesselMapToSkeleton.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/SofaBezierSkeletonization.dir/all' failed
make[1]: *** [CMakeFiles/SofaBezierSkeletonization.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

My compiler is GCC (gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609)

I looked at the directory /home/p0086679/sofa/v16.08/build/install/include/CImg and I found that the file skeleton.h was not inside /home/p0086679/sofa/v16.08/build/install/include/CImg/plugin but directly in /home/p0086679/sofa/v16.08/build/install/include/CImg

So I tried to fix the problem by modifying the file /home/p0086679/sofa/v16.08/build/install/include/CImg/SOFACImg.h:

I remplaced
#define cimg_plugin "plugin/skeleton.h"
by
#define cimg_plugin "skeleton.h"

This solved the compilation problem of the SofaBezierSkeletonization plugin.

However, changing a file in the install directory seemed weird to me and so I tried to change the file /home/p0086679/sofa/v16.08/src/extlibs/CImg/SOFACImg.h in the same way.

But then, of course, the Image plugin does not compile:

[ 90%] Building CXX object applications/plugins/image/CMakeFiles/image.dir/CollisionToCarvingEngine.cpp.o
In file included from /home/p0086679/sofa/v16.08/src/extlibs/CImg/../CImg/SOFACImg.h:33:0,
                 from /home/p0086679/sofa/v16.08/src/applications/plugins/image/ImageTypes.h:34,
                 from /home/p0086679/sofa/v16.08/src/applications/plugins/image/CollisionToCarvingEngine.h:26,
                 from /home/p0086679/sofa/v16.08/src/applications/plugins/image/CollisionToCarvingEngine.cpp:24:
/home/p0086679/sofa/v16.08/src/extlibs/CImg/../CImg/CImg.h:9341:21: fatal error: skeleton.h: No such file or directory
compilation terminated.
applications/plugins/image/CMakeFiles/image.dir/build.make:62: recipe for target 'applications/plugins/image/CMakeFiles/image.dir/CollisionToCarvingEngine.cpp.o' failed
make[2]: *** [applications/plugins/image/CMakeFiles/image.dir/CollisionToCarvingEngine.cpp.o] Error 1
CMakeFiles/Makefile2:9550: recipe for target 'applications/plugins/image/CMakeFiles/image.dir/all' failed
make[1]: *** [applications/plugins/image/CMakeFiles/image.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

I know that the plugin owner does not have this problem (neither on ubuntu nor on mac OS), so I guess I am missing something here.

P.S.: I also had a problem with this plugin dependencies (and again the plugin owner does not have this problem). I had to add SofaPhyton as a required dependency because if I did not do so I get the following error:

CMake Error at CMakeLists.txt:11 (find_package):
Found package configuration file:

/home/p0086679/sofa/master/newbuild/install/lib/cmake/image/imageConfig.cmake

but it set image_FOUND to FALSE so package "image" is considered to be NOT
FOUND. Reason given by package:

The following imported targets are referenced, but are missing: SofaPython

and I know that the image plugin does not require sofaPython (find_package(SofaPython QUIET))

Here is the CMakeList.txt of the plugin without my modification:

cmake_minimum_required(VERSION 3.1.0 FATAL_ERROR)
project(SofaBezierSkeletonization)

set(BEZIERSKELET_MAJOR_VERSION 0)
set(BEZIERSKELET_MINOR_VERSION 1)
set(BEZIERSKELET_VERSION ${BEZIERSKELET_MAJOR_VERSION}.${BEZIERSKELET_MINOR_VERSION})

find_package(SofaFramework REQUIRED)
find_package(SofaBase REQUIRED)
find_package(SofaGeneral REQUIRED)
find_package(image REQUIRED)

set(GENERAL_DEPENDENCIES SofaComponentBase SofaComponentGeneral SofaCore SofaLoader )
set(GENERAL_COMP_FLAGS "-DSOFA_BUILD_BEZIERSKELET" )

set(HEADER_FILES
    src/initBezierSkelet.h
    src/BezierHelper.h 
    src/BezierCubic.h 
    src/BezierSegment.h 
    src/BezierSegmentTree.h 
    src/BezierSegmentTree.inl 
    src/BezierSkeletonization.h

)
    
set(SOURCE_FILES
   src/initBezierSkelet.cpp
   src/BezierHelper.cpp 
   src/BezierCubic.cpp 
   src/BezierSegment.cpp 
   src/BezierSegmentTree.cpp 
)

set(README_FILE
	readme.txt
)

set (DIJKSTRA_CENTERLINES "0" CACHE BOOL "Set to activate compilation of the centerlines extraction using the minimum spanning Dijkstra tree")

if (DIJKSTRA_CENTERLINES)
	message(STATUS "Activating Dijkstra centerline extraction, requires image plugin")
	find_package(image REQUIRED)
	set(CENTERLINE_DEPENDENCIES image)

	list(APPEND HEADER_FILES
    		src/VesselMapToSkeleton.h 
    		src/VesselMapToSkeleton.inl
	)
	list(APPEND SOURCE_FILES
   		src/VesselMapToSkeleton.cpp 
	)
endif()

add_library(${PROJECT_NAME} SHARED ${HEADER_FILES} ${SOURCE_FILES} ${README_FILES} )

set_target_properties(${PROJECT_NAME} PROPERTIES VERSION "${BEZIERSKELET_VERSION}")
set_target_properties(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "${GENERAL_COMP_FLAGS}")
set_target_properties(${PROJECT_NAME} PROPERTIES PUBLIC_HEADER "${HEADER_FILES}")
target_link_libraries(${PROJECT_NAME} ${GENERAL_DEPENDENCIES} ${CENTERLINE_DEPENDENCIES})

include_directories("${CMAKE_CURRENT_SOURCE_DIR}/src")
target_compile_features(${PROJECT_NAME} PRIVATE cxx_range_for)
target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")
target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>")
target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>")

install(TARGETS SofaBezierSkeletonization 
        EXPORT SofaBezierSkeletonization
        RUNTIME DESTINATION bin
        LIBRARY DESTINATION lib
        ARCHIVE DESTINATION lib
        PUBLIC_HEADER DESTINATION include/SVSTK)

[jnbrunet]

Hi Rosalie!

My guess would be at the difference between your CMake version and the plugin’s owner.

It seems that in your case, the install command of the image/extlibs/CImg/CMakeLists.txt does not preserve the file’s directory hierarchy.

Can you try changing image/extlibs/CImg/CMakeLists.txt :

install(FILES 
    CImg.h
    SOFACImg.h
    plugins/add_fileformat.h
    plugins/chlpca.h
    plugins/draw_gradient.h
    plugins/ipl_alt.h
    plugins/jpeg_buffer.h
    plugins/matlab.h
    plugins/patchmatch.h
    plugins/tiff_stream.h
    plugins/vrml.h
    plugins/bayer.h
    plugins/cvMat.h
    plugins/inpaint.h
    plugins/ipl.h
    plugins/loop_macros.h
    plugins/nlmeans.h
    plugins/skeleton.h
    plugins/tinymatwriter.h
    plugins/vtk.h
        DESTINATION include/CImg
        COMPONENT CImg_headers)

To:

install(FILES 
    CImg.h
    SOFACImg.h
        DESTINATION include/CImg
        COMPONENT CImg_headers)
install(DIRECTORY 
    plugins
        DESTINATION include/CImg
        COMPONENT CImg_headers)

And try again the compilation and the install?

Edit: Actually, you could only run the install command in your sofa’s build directory after the modification, no need to relauch the compilation.

[Rosalie]

Hi Jean Nicolas !

Thanks for your help ! It works perfectly fine now.

Do you think the difference in the CMake version could also be responsible for the second problem (set image_FOUND to FALSE because SofaPython is not found)?

Rosalie

[jnbrunet]

Hi Rosalie!

For the Python problem:
Issue: https://github.com/sofa-framework/sofa/issues/135
PR : https://github.com/sofa-framework/sofa/pull/137

For the image’s headers installation path
Issue: https://github.com/sofa-framework/sofa/issues/136
PR : https://github.com/sofa-framework/sofa/pull/138

Jean-Nico

[Author]

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