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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
440 stars 194 forks source link

Linking CXX executable ../../bin/relion_maingui error #428

Closed GiantFurosemide closed 5 years ago

GiantFurosemide commented 5 years ago

Hi,

I got this error message when trying to install relion3.0. ubuntu18.04 gcc 7.3.0 cmake version 3.10.2

[ 90%] Built target autopick_mpi [ 91%] Built target ctf_toolbox [ 92%] Built target particle_symmetry_expand [ 93%] Built target particle_polish_mpi [ 94%] Built target particle_sort_mpi [ 95%] Built target pipeliner [ 96%] Built target postprocess_mpi [ 97%] Built target prepare_subtomo [ 98%] Built target run_motioncorr [ 98%] Linking CXX executable ../../bin/relion_maingui [ 99%] Built target project [100%] Built target display ../../lib/librelion_gui_lib.a(gui_mainwindow.cpp.o):(.data.rel.ro._ZTV13StdOutDisplay[_ZTV13StdOutDisplay]+0x60): undefined reference to `Fl_Text_Display::recalc_display()' collect2: error: ld returned 1 exit status src/apps/CMakeFiles/maingui.dir/build.make:109: recipe for target 'bin/relion_maingui' failed make[2]: [bin/relion_maingui] Error 1 CMakeFiles/Makefile2:1885: recipe for target 'src/apps/CMakeFiles/maingui.dir/all' failed make[1]: [src/apps/CMakeFiles/maingui.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2

Anyone got the similar error?

GiantFurosemide commented 5 years ago

This is my cmake output:

root@parric-ThinkPad-T470p:/usr/local/src/relion-3.0_beta/build# cmake .. -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- 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 -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- CUDA enabled - Building CUDA-accelerated version of RELION -- Setting cpu precision to double -- Setting accelerated code precision to single CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) -- Using non-cuda compilation.... -- CMAKE_C_COMPILER : /usr/bin/cc -- CMAKE_CXX_COMPILER : /usr/bin/c++ -- MPI_C_COMPILER : -- MPI_CXX_COMPILER : -- CMAKE_CXX_COMPILER_ID : GNU -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-- MPI_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include -- MPI_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include -- MPI_CXX_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.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 -- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so -- Found FLTK: fltk_images;fltk_forms;fltk
-- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so;/usr/lib/x86_64-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3f.so;/usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for sincos -- Looking for sincos - not found -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.0.9") BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/usr/local/src/relion-3.0_beta/build TIFF FOUND -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
OPENMP FOUND -- Configuring done -- Generating done -- Build files have been written to: /usr/local/src/relion-3.0_beta/build

GiantFurosemide commented 5 years ago

then I try to make:

root@parric-ThinkPad-T470p:/usr/local/src/relion-3.0_beta/build# make -j10 Scanning dependencies of target copy_scripts Scanning dependencies of target relion_lib [ 0%] Built target copy_scripts [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//args.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//CPlot2D.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//backprojector.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//complex.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//ctf.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//autopicker_mpi.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//ctffind_runner.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//error.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//euler.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//exp_model.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//fftw.cpp.o [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//filename.cpp.o [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//flex_analyser.cpp.o /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp: In member function ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double, double, double*, int, std::cxx11::string)’: /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp:716:6: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] void CPlot2D::ComputeLabelTickSpacing(double dataMin, double dataMax, double plotMin, double plotMax, double tickSpacing, int numTicks, std::string axis) ^~~ /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp:716:6: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:862:0, from /usr/include/c++/7/cstdio:42, from /usr/include/c++/7/ext/string_conversions.h:43, from /usr/include/c++/7/bits/basic_string.h:6352, from /usr/include/c++/7/string:52, from /usr/include/c++/7/bits/locale_classes.h:40, from /usr/include/c++/7/bits/ios_base.h:41, from /usr/include/c++/7/ios:42, from /usr/include/c++/7/ostream:38, from /usr/include/c++/7/iostream:39, from /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘builtin___sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 bos (s), fmt, __va_arg_pack ()); ^ /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp:716:6: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] void CPlot2D::ComputeLabelTickSpacing(double dataMin, double dataMax, double plotMin, double plotMax, double tickSpacing, int numTicks, std::string axis) ^~~ /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp:716:6: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:862:0, from /usr/include/c++/7/cstdio:42, from /usr/include/c++/7/ext/string_conversions.h:43, from /usr/include/c++/7/bits/basic_string.h:6352, from /usr/include/c++/7/string:52, from /usr/include/c++/7/bits/locale_classes.h:40, from /usr/include/c++/7/bits/ios_base.h:41, from /usr/include/c++/7/ios:42, from /usr/include/c++/7/ostream:38, from /usr/include/c++/7/iostream:39, from /usr/local/src/relion-3.0_beta/src/CPlot2D.cpp:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘builtin___sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 bos (s), fmt, va_arg_pack ()); ^ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//healpix_sampling.cpp.o [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//helix.cpp.o [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//helix_inimodel2d.cpp.o [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//image.cpp.o [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//local_symmetry.cpp.o [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//local_symmetry_mpi.cpp.o [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//matrix1d.cpp.o [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//matrix2d.cpp.o [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//metadata_container.cpp.o [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//metadata_label.cpp.o [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//metadata_table.cpp.o [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//micrograph_model.cpp.o [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//ml_model.cpp.o [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//ml_optimiser.cpp.o [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//ml_optimiser_mpi.cpp.o [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//motioncorr_runner.cpp.o [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//motioncorr_runner_mpi.cpp.o [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//mpi.cpp.o [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//multidim_array.cpp.o [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//numerical_recipes.cpp.o [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//particle_polisher.cpp.o [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//particle_polisher_mpi.cpp.o [ 19%] Building 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src/apps/CMakeFiles/relion_lib.dir//jaz/optimization/lbfgs.cpp.o [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/optimization/nelder_mead.cpp.o [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/optimization/optimization.cpp.o [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/ctf/ctf_refiner.cpp.o [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/ctf/ctf_refiner_mpi.cpp.o [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/ctf/defocus_estimator.cpp.o [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/ctf/defocus_helper.cpp.o [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/ctf/magnification_estimator.cpp.o [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/ctf/magnification_helper.cpp.o [ 48%] Building CXX object 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src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/slvsec3.c.o [ 57%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/lbfgs/lbfgs.c.o [ 57%] Linking CXX static library ../../lib/librelion_lib.a [ 57%] Built target relion_lib Scanning dependencies of target refine Scanning dependencies of target star_handler Scanning dependencies of target reconstruct Scanning dependencies of target run_motioncorr_mpi Scanning dependencies of target run_ctffind_mpi Scanning dependencies of target ref_aberration_plot Scanning dependencies of target refine_mpi Scanning dependencies of target reconstruct_mpi Scanning dependencies of target tiltpair_plot Scanning dependencies of target flex_analyse_mpi [ 57%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o [ 57%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o [ 58%] Building CXX object src/apps/CMakeFiles/ref_aberration_plot.dir/ref_aberration_plot.cpp.o [ 59%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o [ 59%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o [ 59%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o [ 60%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o [ 61%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o [ 62%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o [ 62%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o [ 63%] Linking CXX executable ../../bin/relion_reconstruct [ 63%] Built target reconstruct Scanning dependencies of target helix_toolbox [ 64%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o [ 64%] Linking CXX executable ../../bin/relion_reconstruct_mpi [ 64%] Linking CXX executable ../../bin/relion_run_ctffind_mpi [ 64%] Built target reconstruct_mpi Scanning dependencies of target run_ctffind 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src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o /usr/local/src/relion-3.0_beta/src/apps/stack_create.cpp: In member function ‘void stack_create_parameters::run()’: /usr/local/src/relion-3.0_beta/src/apps/stack_create.cpp:153:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command.c_str());


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../../lib/librelion_gui_lib.a(gui_mainwindow.cpp.o):(.data.rel.ro._ZTV13StdOutDisplay[_ZTV13StdOutDisplay]+0x60): undefined reference to `Fl_Text_Display::recalc_display()'
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biochem-fan commented 5 years ago

Please make a new build directory and run cmake with -DFORCE_OWN_FLTK=ON.

GiantFurosemide commented 5 years ago

It works well, thank you very much. I think I installed a wrong fltk before.

nrakurniawan commented 3 years ago

Please make a new build directory and run cmake with -DFORCE_OWN_FLTK=ON.

I'm sorry, can you tell me how to run cmake with -DFORCE_OWN_FLTK=ON?