[SOLVED] CGALPlugin install CMake

Blocked

Dear SOFA-forum,

I am trying to build the SkeletonPlugin. As I only have a pre-build version of SOFA, I tried my hand at installing SOFA through CMake. This works fine, both for the v19.12 and master version. However, ones I try to configure the CGALPlugin (which is required by the SkeletonPlugin), I get the following error:

Install prefix: /Users/mfit/sofa/build/master_experiment/install
SofaDenseSolver not found, disabling HexahedronCompositeFEMForceFieldAndMass compilation.
Adding collection SofaComponentAll
SofaTest: optional dependency SofaPython NOT found, Python_test won't be built
Adding module SofaExporter
SofaPython disabled, will not compile python bindings.
Adding module SofaSparseSolver
-- metis was not found, SparseLDLSolver won't be built
-- csparse was found, SparseLUSolver and SparseCholeskySolver will be built
Adding module SofaPreconditioner
Adding module SofaHaptics
Adding module SofaDenseSolver
Adding module SofaOpenglVisual
Adding plugin CImgPlugin
CImgPlugin: TIFF Image Format enabled
CImgPlugin: JPEG Image Format enabled
CImgPlugin: PNG Image Format enabled
Adding plugin SofaMiscCollision
SofaMiscModule: build all maintained sofa components.
SofaMiscCollision: optional dependency SofaSphFluid not found de-activing: <SpatialGridPointModel>
Adding plugin CGALPlugin
CGAL VERSION = 4.7.1000
CGALPlugin: could not find image, won't build MeshGenerationFromImage_test
-- PSL is an experimental feature, use it at your own risk.
Adding application runSofa
Write Plugin list at /Users/mfit/sofa/build/master_experiment/lib/plugin_list.conf.default
CMake Deprecation Warning at CMakeLists.txt:311 (message):
Deprecated components are activated (SOFA_WITH_DEPRECATED_COMPONENTS
variable is ON)

Configuring done

For some reason the CGALPlugin doesn’t seem to recognize the CGAL install, which I have set in the CGAL_DIR parameter in CMake. Do you have any tips on how to go further? As seen in the error message, I installed the CGAL 4.7 version. I am running MacOS, and have an UpToDate XCode install and GClang .

Thanks in advance,
MFit

22 April 2020 at 15:35 #15907

Guillaume

Keymaster

Hi,

There is no error in your output.

“CGALPlugin: could not find image, won’t build MeshGenerationFromImage_test”
This means that CGALPlugin tried to find another plugin called “image”. The plugin “image” is present in SOFA and can be activated in CMake-GUI. It is a soft dependency though, used only by the component MeshGenerationFromImage, so it shouldn’t prevent you from building and using CGALPlugin (you just won’t have MeshGenerationFromImage).

To understand how this soft dependency works, see this portion of CGALPlugin CMakeLists.

Guillaume.

22 April 2020 at 15:36 #15908

Keymaster

Hey @matfit

The SkeletonPlugin seems to have been build directly upon the CGAL library itself and not the SofaCGAL plugin. So you should only need to install CGAL.


sudo apt-get install libcgal-dev

FYI details on the compilation of SofaCGAL (for later if you want to use it) are in this post.

Hugo

22 April 2020 at 17:00 #15912

Blocked

Hi @Guillaume and @Hugo,

Thanks for the feedback. I installed cgal4.7 with homebrew, seems to work fine.

I tried installing the skeleton plugin without the CGALPlugin earlier and just now, and there were no errors in configuration and generation. However, when I make the build (on top of a clean build) in the terminal I get the following error:

/Users/mfit/sofa/PlugIn/SofaSkeletonPlugin/SkeletonPlugin/initSkeletonPlugin.cpp:22:10: fatal error: 
      'SkeletonPlugin/config.h' file not found
#include <SkeletonPlugin/config.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [external_directories/SofaSkeletonPlugin/SkeletonPlugin/CMakeFiles/SkeletonPlugin.dir/initSkeletonPlugin.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/Users/mfit/sofa/PlugIn/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.cpp:30:10: fatal error: 
      'SkeletonPlugin/config.h' file not found
#include <SkeletonPlugin/config.h>

The external location of the plugin folder of Skeleton plugin is recognized (I think) and the CMakeLists.txt is opened. The config.h file is not found, giving me the impression that I am missing a crucial step in the configuration fase in CMake.

Any idea’s on continuing? The Skeleton plugin looks very promising.

Thanks again,
MFit

22 April 2020 at 21:55 #15916

Keymaster

The file config.h.in is strange.
Try renaming it in config.h

Let us know if it helps

Hugo

23 April 2020 at 08:57 #15923

Blocked

I fixed it, with your help!

So indeed the config.h.in file needed to be renamed to config.h. That was problem 1 solved. Then I got the following error:

/usr/local/include/mpfr.h:326:42: note: expanded from macro 'MPFR_DEPRECATED'
# define MPFR_DEPRECATED __attribute__ ((deprecated))
                                         ^
In file included from /Users/mfit/SOFA_PlugIn/SkeletonPlugin/MeshSkeletonization.cpp:31:
In file included from /Users/mfit/SOFA_PlugIn/SkeletonPlugin/MeshSkeletonization.inl:31:
In file included from /Users/mfit/SOFA_PlugIn/SkeletonPlugin/MeshSkeletonization.h:52:
In file included from /Users/mfit/Downloads/CGAL-4.7/include/CGAL/extract_mean_curvature_flow_skeleton.h:30:
In file included from /Users/mfit/Downloads/CGAL-4.7/include/CGAL/Mean_curvature_flow_skeletonization.h:54:
In file included from /Users/mfit/Downloads/CGAL-4.7/include/CGAL/Delaunay_triangulation_3.h:37:
In file included from /Users/mfit/Downloads/CGAL-4.7/include/CGAL/Triangulation_3.h:47:
In file included from /Users/mfit/Downloads/CGAL-4.7/include/CGAL/spatial_sort.h:25:
/Users/mfit/Downloads/CGAL-4.7/include/CGAL/hilbert_sort.h:54:9: error: 
      no member named 'random_shuffle' in namespace 'std'; did you mean simply
      'random_shuffle'?
        std::random_shuffle(begin,end, rng);
        ^~~~~~~~~~~~~~~~~~~

Indicating to me that there was something wrong with the CGAL install. Instead of using the CGAL4.7 installed at /usr/locaal/Cellar/cgal4.7, it used the one in my download file. CGAL_DIR is specified in the cmake file. I removed all previous installations or and files of CGAL, and brew installed CGAL 5.0.2. This did the trick.

Should I inform the author of the Skeleton plugin about this?

Thanks again!

23 April 2020 at 09:14 #15924

Keymaster

This is a purely CGAL error, linked to the C++ version.
Please see github issue here. This has been solved but only in newer versions of CGAL.

You did well to upgrade your CGAL.
Yes please, do not hesitate to notice him so that he can update the README or make a PR on the README 😉

Hugo

23 April 2020 at 09:16 #15925

Keymaster

By the way, does it mean that it is now working @matfit?

23 April 2020 at 09:41 #15926

Blocked

Yes its working correctly!

23 April 2020 at 11:17 #15929

Blocked

Hi,

I have built the SkeletonPlugin successfully with Win10 and VS2017, and put them into the plugin file. I also add the plugin name and version in plugin_list.conf.default. But it failed to load this plugin in the runsofa frame. Did I miss some crucial steps?

Thank you!

23 April 2020 at 11:41 #15930

Keymaster

hey @enxing,

do you have any associated error message?

23 April 2020 at 12:44 #15931

Blocked

In the console of runsofa, I got
[PluginManager] Plugin loading failed (E:/Tools/sofa19.06-exe/plugins/SkeletonPlugin/bin/SkeletonPlugin.dll): ~

28 April 2020 at 11:45 #15968

Blocked

Hi, @Hugo @MatFit

I tried this plugin in Macos. And I get some errors when run “make” command.
here is the output:

make:

Scanning dependencies of target SkeletonPlugin
[ 33%] Building CXX object CMakeFiles/SkeletonPlugin.dir/initSkeletonPlugin.cpp.o
[ 66%] Building CXX object CMakeFiles/SkeletonPlugin.dir/MeshSkeletonization.cpp.o
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.cpp:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.inl:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.h:32:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/Vec.h:27:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/DataTypeInfo.h:27:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/vector.h:37:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/Messaging.h:81:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/MessageDispatcher.h:30:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/Message.h:38:
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:57:17: error: function
      definition does not declare parameters
    const char *filename {nullptr};
                ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:58:9: error: function
      definition does not declare parameters
    int line             {0};
        ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:59:37: error: member
      initializer 'filename' does not name a non-static data member or base class
    FileInfo(const char *f, int l): filename(f), line(l) {}
                                    ^~~~~~~~~~~
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:59:50: error: member
      initializer 'line' does not name a non-static data member or base class
    FileInfo(const char *f, int l): filename(f), line(l) {}
                                                 ^~~~~~~
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:62:17: error: member
      initializer 'filename' does not name a non-static data member or base class
    FileInfo(): filename(s_unknownFile), line(0) {}
                ^~~~~~~~~~~~~~~~~~~~~~~
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:62:42: error: member
      initializer 'line' does not name a non-static data member or base class
    FileInfo(): filename(s_unknownFile), line(0) {}
                                         ^~~~~~~
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:71:9: error: use of
      undeclared identifier 'filename'
        filename = tmp ;
        ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:72:9: error: use of
      undeclared identifier 'line'
        line = l ;
        ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:78:9: error: use of
      undeclared identifier 'filename'
        filename = tmp ;
        ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:79:9: error: use of
      undeclared identifier 'line'
        line = l ;
        ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:83:12: error: use of
      undeclared identifier 'filename'
        if(filename)
           ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/FileInfo.h:84:20: error: use of
      undeclared identifier 'filename'
            delete filename ;
                   ^
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.cpp:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.inl:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.h:32:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/Vec.h:27:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/DataTypeInfo.h:27:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/vector.h:37:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/Messaging.h:81:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/logging/MessageDispatcher.h:32:
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/system/SofaOStream.h:136:29: error: function
      definition does not declare parameters
    logging::FileInfo::SPtr m_fileInfo {helper::logging::EmptyFileInfo};
                            ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/system/SofaOStream.h:117:62: error: use of
      undeclared identifier 'm_fileInfo'; did you mean 'fileInfo'?
    const logging::FileInfo::SPtr& fileInfo() const { return m_fileInfo; }
                                                             ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/system/SofaOStream.h:117:36: note: 'fileInfo'
      declared here
    const logging::FileInfo::SPtr& fileInfo() const { return m_fileInfo; }
                                   ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/system/SofaOStream.h:125:9: error: use of
      undeclared identifier 'm_fileInfo'
        m_fileInfo = helper::logging::EmptyFileInfo;
        ^
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.cpp:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.inl:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.h:32:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/Vec.h:27:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/DataTypeInfo.h:27:
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/helper/vector.h:100:23: error: no template named
      'initializer_list' in namespace 'std'
    vector(const std::initializer_list<T>& t) : std::vector<T,Alloc>(t) {}
                 ~~~~~^
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.cpp:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.inl:31:
In file included from /Users/steven/Code/sofa/sofa/v19.06/SofaSkeletonPlugin/SkeletonPlugin/MeshSkeletonization.h:32:
In file included from /Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/Vec.h:27:
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/DataTypeInfo.h:1295:1: error: expected
      expression
{
^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/DataTypeInfo.h:1297:2: error: expected a
      type
};
 ^
/Applications/runSofa.app/Contents/MacOS/include/SofaFramework/sofa/defaulttype/DataTypeInfo.h:1297:2: error: expected
      '{' after base class list
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [CMakeFiles/SkeletonPlugin.dir/MeshSkeletonization.cpp.o] Error 1
make[1]: *** [CMakeFiles/SkeletonPlugin.dir/all] Error 2
make: *** [all] Error 2

I succeed in running ‘cmake’, but I get a lot of errors when running ‘make’ to generate the Library. I use the latest version of Sofa 19.12 and also try to use the old version of Sofa 19.06, but when I build it by “make install or make”, I get the same errors above.

I hope to receive the instruction according to these logs. Thank you!

28 April 2020 at 14:33 #15971